# claims

claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:95bf71760161836bb337
claim_id: claim:95bf71760161836bb337
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
In addition, DCN and COL6A1 are expressed in both fibroblast and myofibroblast populations, whereas SPARC , BGN , and COL6A2 are expressed in all three stromal cell types.

summary:
In Homo sapiens, SPARC, BGN, and COL6A2 are expressed in pericytes as one of the three stromal cell types in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:e4499d8bca124e12a338
claim_id: claim:e4499d8bca124e12a338
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
The proximal tubule in particular expressed proinflammatory cytokine genes, such as CXCL14 , which induces monocyte chemotaxis, and IL32 , which induces expression of TNF α by macrophages

summary:
In Homo sapiens, proximal tubule cells express the proinflammatory cytokine genes CXCL14 and IL32 in the rejecting kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:2f9f20449d831bec39e1
claim_id: claim:2f9f20449d831bec39e1
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
ITGB6 , a gene previously shown to be expressed in distal tubule of the diseased kidney transplant, 31 was specifically induced in the loop of Henle in our biopsy dataset.

summary:
In Homo sapiens, ITGB6 was specifically induced in the loop of Henle cells in the kidney allograft biopsy.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:626838d7fede38564cf3
claim_id: claim:626838d7fede38564cf3
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
summary: In Homo sapiens, pancreatic beta cells are characterized by expression of insulin (INS).
span_literal:
Pancreatic endocrine cells are characterized by their most abundant hormone, namely insulin (INS; β-cells), glucagon (GCG; α-cells), somatostatin (SST; δ-cells), pancreatic polypeptide (PPY; PP cells), and ghrelin (GHRL; ε-cells).


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:7e2a69b7fe13e2069fd3
claim_id: claim:7e2a69b7fe13e2069fd3
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
summary:
In Homo sapiens, pancreatic PP cells are characterized by expression of pancreatic polypeptide (PPY).


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:fed77c760678bfc0a30d
claim_id: claim:fed77c760678bfc0a30d
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
These markers include the major hormone genes ( GCG , INS , SST , GHRL , and PPY ), genes that encode acinar cell–specific digestive enzymes ( PRSS1 and PNLIP ), and genes associated with ductal cells (i.e., KRT19 , SPP1 , and HNF1B ).

summary:
In Homo sapiens, acinar cells are marked by expression of the digestive enzyme genes PRSS1 and PNLIP.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:9fd70f74cb4125a33f89
claim_id: claim:9fd70f74cb4125a33f89
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
For example, β-cells had high levels of PDX1 , IAPP , PCSK1 , MAFA , and IGF2 , whereas α-cells had high expression of IRX2 and ARX .

summary:
In Homo sapiens, beta cells had high levels of PDX1, IAPP, PCSK1, MAFA, and IGF2, whereas alpha cells had high expression of IRX2 and ARX.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:0561647064508fd12ba4
claim_id: claim:0561647064508fd12ba4
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
For example, β-cells had high levels of PDX1 , IAPP , PCSK1 , MAFA , and IGF2 , whereas α-cells had high expression of IRX2 and ARX .

summary:
In Homo sapiens, alpha cells had high expression of IRX2 and ARX, whereas beta cells had high levels of other markers.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:8f1d6c96ca70a7fc1001
claim_id: claim:8f1d6c96ca70a7fc1001
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
Both cell types have comparable levels of FOXA2 , NKX2 - 2 , NEUROD1 , and MAFB , although cell-to-cell heterogeneity is also apparent.

summary:
In Homo sapiens, both alpha cells and beta cells have comparable levels of FOXA2, NKX2-2, NEUROD1, and MAFB.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:e33ee13aafb4e240d16b
claim_id: claim:e33ee13aafb4e240d16b
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
For example, ARX is expressed highly in both α- and PP cells, whereas ETV1 is highly enriched in PP and δ-cells

summary:
In Homo sapiens, ARX is expressed highly in both alpha cells and PP cells, whereas ETV1 is highly enriched in PP cells and delta cells.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:a9266cda6928467f7078
claim_id: claim:a9266cda6928467f7078
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
For example, β-cells expressed high levels of INS and low levels of acinar and ductal markers, whereas duct cells showed high transcript levels for KRT19 but only marginal signals for hormone genes

summary:
In Homo sapiens, beta cells expressed high levels of INS, whereas duct cells showed high transcript levels for KRT19.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:307c2bdd61f3670fe8d6
claim_id: claim:307c2bdd61f3670fe8d6
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
DYRK1A and GSK3B were both repressed in this proliferating cell, consistent with recent reports that inhibition of both molecules induces proliferation of human endocrine cells

summary:
In Homo sapiens, DYRK1A and GSK3B were both repressed in a proliferating alpha cell compared with quiescent alpha cells.


claim_key: hca:0335_10.2337_db16-0405_ae79f269d3:claim:f5d59a85bc99874ece0b
claim_id: claim:f5d59a85bc99874ece0b
paper_key: hca:0335_10.2337_db16-0405_ae79f269d3
span_literal:
One of the α-cells analyzed from an adult donor without diabetes was clearly proliferating, as indicated by a very high level of Ki67 mRNA expression.

summary:
In Homo sapiens, a proliferating alpha cell was identified by a very high level of Ki67 mRNA expression.


claim_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0:claim:98c81280b429844231eb
claim_id: claim:98c81280b429844231eb
paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
summary: In Homo sapiens, microglia cluster 0 is uniquely enriched in AXL, CLEC7A, and CYBB.
span_literal:
Microglia in cluster 0 were uniquely enriched in the genes AXL, CLEC7A, CYBB ( Figure 3D , Supplementary Tables S6 , S7 ).


claim_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0:claim:dd8deaf55c7b3201bc49
claim_id: claim:dd8deaf55c7b3201bc49
paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
span_literal:
In addition, microglia in cluster 0 were uniquely enriched in cytoskeleton-related genes ( FGD2, ACTB, SRGAP2 ; Figure 3D , Supplementary Tables S6 , S7 ).

summary:
In Homo sapiens, microglia cluster 0 is uniquely enriched in cytoskeleton-related genes FGD2, ACTB, and SRGAP2.


claim_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0:claim:840392eada4861a5ec06
claim_id: claim:840392eada4861a5ec06
paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
span_literal:
Microglia in cluster 1 uniquely expressed genes involved in transcriptional activity ( ZNF302, NEAT1 , and ANKRD11 ; Figure 3D , Supplementary Tables S6 , S7 )

summary:
In Homo sapiens, microglia cluster 1 uniquely expressed ZNF302, NEAT1, and ANKRD11, which are involved in transcriptional activity.


claim_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0:claim:4d0ba2f07070cf09d1bb
claim_id: claim:4d0ba2f07070cf09d1bb
paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
span_literal:
Microglia in cluster 2 were uniquely enriched in genes associated with neurodegenerative diseases ( TREM2 , GLUL , S100A ; Keren-Shaul et al., 2017 ; Krasemann et al., 2017 ; Cristóvaõ and Gomes, 2019 ) and immune activated microglia ( CD63 , HLA genes, CD14 , TSPO ; Beschorner et al., 2002 ; Kamphuis et al., 2016 ; Beckers et al., 2018 ) and in ribosomal genes ( RPL genes; Figure 3D , Supplementary Tables S6 , S7 ).

summary:
In Homo sapiens, microglia cluster 2 is uniquely enriched in TREM2, GLUL, S100A, CD63, CD14, and TSPO.


claim_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0:claim:ee12374a04467b7a9d13
claim_id: claim:ee12374a04467b7a9d13
paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
summary: In Homo sapiens, microglia cluster 3 showed unique enrichment for SMIM11A and SMIM11B.
span_literal:
The small clusters showed a unique enrichment for SMIM11A and - B (cluster 3); MEF2C , GPR89A , and - B (cluster 4); SERF1A and - B (cluster 5); and FRG1 and FRG1CP (cluster 6; Figure 3D , Supplementary Tables S6 , S7 ).


claim_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0:claim:aa93253eac1441024834
claim_id: claim:aa93253eac1441024834
paper_key: hca:0338_10.3389_fnmol.2020.00134_d9eafa03d0
span_literal:
Multiple genes associated with increased susceptibility for sporadic AD are preferentially expressed in microglia, including APOE , CR1 , CD33 , INPP5D , PLCG2 , MS4A6A , and TREM2 (Ulrich et al., 2014 ; Sarlus and Heneka, 2017 ).

summary:
In Homo sapiens, microglia preferentially express APOE, CR1, CD33, INPP5D, PLCG2, MS4A6A, and TREM2, which are associated with increased susceptibility for sporadic Alzheimer's disease.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:be01e12ff4b25dc7f540
claim_id: claim:be01e12ff4b25dc7f540
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
Periodontal ligament fibroblasts (PLF, sC 1) occupied the most fibroblasts annotated by the expression of ASPN , an extracellular connective tissue marker intensely expressed within the PDL (Figure 2 B and Figure S2 B)

summary:
In Homo sapiens, periodontal ligament fibroblasts are marked by the expression of ASPN, an extracellular connective tissue marker expressed within the periodontal ligament.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:33180372ae3960196464
claim_id: claim:33180372ae3960196464
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
The enrichment of TNFRSF21 + fibroblasts with high expression of CXCL1, CXCL2, CXCL5, CXCL6, CXCL13 , and IL24 was detected in patients with periodontitis compared to healthy individuals.

summary:
In Homo sapiens, TNFRSF21-positive fibroblasts show high expression of CXCL1, CXCL2, CXCL5, CXCL6, CXCL13, and IL24 in patients with periodontitis.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:7edf0a1445df145f7f23
claim_id: claim:7edf0a1445df145f7f23
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
The fractions of CD55 + mesenchymal stem cells (MSCs), APOE + pre-osteoblasts (pre-OBs), and IBSP + osteoblasts decreased significantly in response to initial periodontal therapy.

summary:
In Homo sapiens, CD55 is a positive marker of mesenchymal stem cells, APOE is a positive marker of pre-osteoblasts, and IBSP is a positive marker of osteoblasts in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:72e0da02bc5ef1017e26
claim_id: claim:72e0da02bc5ef1017e26
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
In addition, CXCL12 + MSC-like pericytes could convert their identity into a pre-OB state during inflammatory responses even after initial periodontal therapy confirmed by single-cell trajectory.

summary:
In Homo sapiens, CXCL12 is a positive marker of mesenchymal stem cell-like pericytes in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:91f739659e91aeb903c0
claim_id: claim:91f739659e91aeb903c0
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
three subclusters of osteoblastic lineage cells, including CD55 + MSCs (sC 2), APOE + pre-OBs (sC 3), and IBSP + OBs (sC 4)

summary:
In Homo sapiens, CD55 marks mesenchymal stem cells, APOE marks pre-osteoblasts, and IBSP marks osteoblasts among osteoblastic lineage cells in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:7b8a4543649704a0d695
claim_id: claim:7b8a4543649704a0d695
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
three subclusters of osteoblastic lineage cells, including CD55 + MSCs (sC 2), APOE + pre-OBs (sC 3), and IBSP + OBs (sC 4)

summary:
In Homo sapiens, APOE marks pre-osteoblasts among osteoblastic lineage cells in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:95f2dec7fbb4963e1f92
claim_id: claim:95f2dec7fbb4963e1f92
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
Subcluster 2, which was annotated as CD55 + MSCs, also expressed other classical MSC markers, NT5E 31 - 33 and LepR 34 , 35

summary:
In Homo sapiens, mesenchymal stem cells express CD55, NT5E, and LepR as classical markers in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:3b4c0d1806e7d8ff70bd
claim_id: claim:3b4c0d1806e7d8ff70bd
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
summary: In Homo sapiens, pericytes and myofibroblasts uniformly express RGS5 in periodontal tissues.
span_literal:
We noted that merged pericytes and myofibroblasts uniformly expressed RGS5 , but the expression patterns and levels varied for individual canonical cell lineage markers (Figure 3 A)


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:646684b2fa58cfa5e083
claim_id: claim:646684b2fa58cfa5e083
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
We detected two subpopulations of high MYH11- and ACTA2- expression myofibroblasts (subclusters 3 and 4).

summary:
In Homo sapiens, myofibroblasts are characterized by high expression of MYH11 and ACTA2 in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:1b34e9cf1daa0b2b1c1d
claim_id: claim:1b34e9cf1daa0b2b1c1d
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
summary: In Homo sapiens, SPON2 is a positive marker of a pericyte subcluster in periodontal tissues.
span_literal:
Interestingly, the SPON2 + pericytes were clearly upregulated in the PD group compared with the HC group (Figure 3 B and Table S3 ).


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:6925b7f7ee1506c4fd81
claim_id: claim:6925b7f7ee1506c4fd81
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
The abundance of SPON2 + pericytes with significantly high levels of cell proliferation-related genes ( MCM3 , MCM4 , MCM6 , PCNA ) alluded that they were in a stimulated state (Figure 3 A and Table S2 ).

summary:
In Homo sapiens, SPON2-positive pericytes express high levels of MCM3, MCM4, MCM6, and PCNA, indicating a stimulated proliferative state.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:506d2a129277618942da
claim_id: claim:506d2a129277618942da
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
Besides, cluster 5 with high expression of osteoclast-related genes ( ACP5, CD14, FCGR3A, and ITGAV) was proposed as osteoclast precursor cells (OCPs) (Figure 4 A-B, Figure S5 D, and Table S2 ).

summary:
In Homo sapiens, osteoclast precursor cells are characterized by high expression of ACP5, CD14, FCGR3A, and ITGAV in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:de05a845f1e7323f14af
claim_id: claim:de05a845f1e7323f14af
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
OC marker genes, including ACP5, NFATC1, and TNFRSF11A , were also slightly increased in the PD group compared with the HC group and were partly rescued after initial periodontal therapy

summary:
In Homo sapiens, osteoclast marker genes include ACP5, NFATC1, and TNFRSF11A in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:7d2b84ed6a751b010c54
claim_id: claim:7d2b84ed6a751b010c54
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
Furthermore, the expressions of IL1B and CCL20 were highly expressed in monocytes/macrophages while decreased with osteoclastogenesis (Figure 4 H).

summary:
In Homo sapiens, IL1B and CCL20 are highly expressed in monocytes and macrophages in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:b304399437398ae69ea5
claim_id: claim:b304399437398ae69ea5
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
EGFR ligand genes AREG and EREG were overrepresented in monocytes/macrophages but decreased during osteoclastogenesis (Figure 4 H), hinting that monocytes and macrophages may regulate the proliferation of epithelial cells, especially in an inflammatory status 50 .

summary:
In Homo sapiens, AREG and EREG are overrepresented in monocytes and macrophages in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:77ee1acf162ce96559bc
claim_id: claim:77ee1acf162ce96559bc
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
Importantly, the expression of proinflammatory cytokines ( IL18 and CCL18 ) was highly expressed in OCPs, indicating that OCPs might also possess immune cell functions (Figure 4 H and Table S4 ).

summary:
In Homo sapiens, osteoclast precursor cells highly express the proinflammatory cytokines IL18 and CCL18 in periodontal tissues.


claim_key: hca:0339_10.7150_thno.65694_e762e5f2bb:claim:c9fa6d6840f09c9d2c13
claim_id: claim:c9fa6d6840f09c9d2c13
paper_key: hca:0339_10.7150_thno.65694_e762e5f2bb
span_literal:
these TNFRSF21 + subclusters also displayed high expression of genes involved in neutrophil trafficking factors ( CXCL1, CXCL2, CXCL5, CXCL6), B cell and T FH positioning ( CXCL13 ), and upregulation of the immune system (IL24)

summary:
In Homo sapiens, TNFRSF21-positive fibroblast subclusters display high expression of CXCL1, CXCL2, CXCL5, CXCL6, CXCL13, and IL24 in periodontal tissues.


claim_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00:claim:8dbdef9c6512a6c40397
claim_id: claim:8dbdef9c6512a6c40397
paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
span_literal:
Two macrophage types are known to populate the normal adult lung, including the alveolar (AM) type highly expressing the MARCO , FABP4 , and MCEMP1 genes, and the interstitial type derived from circulating monocytes

summary:
In Homo sapiens, alveolar macrophages highly express MARCO, FABP4, and MCEMP1 in the normal adult lung.


claim_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00:claim:b7d7959d31471cab31e3
claim_id: claim:b7d7959d31471cab31e3
paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
span_literal:
We mainly detected the AM type in normal lung tissues, including anti-inflammatory AM (M − C1 and 6; APOE +, CD163 +, and C1QB +)

summary:
In Homo sapiens, anti-inflammatory alveolar macrophages (M-C1 and 6) express APOE, CD163, and C1QB in normal lung tissues.


claim_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00:claim:1627c8201c67239b900f
claim_id: claim:1627c8201c67239b900f
paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
span_literal:
Sub-clustering of fibroblasts revealed 12 distinct clusters, assigned to seven known cell types, including COL13A1 + and COL14A1 + matrix fibroblasts, myofibroblasts, smooth muscle cells, mesothelial cells, fibroblast-like cells in mBrain, and pericytes

summary:
In Homo sapiens, COL13A1-positive matrix fibroblasts and COL14A1-positive matrix fibroblasts were identified among fibroblast subtypes in lung adenocarcinoma tissues.


claim_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00:claim:ea2c11aae1856cff0e70
claim_id: claim:ea2c11aae1856cff0e70
paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
summary: In Homo sapiens, fibroblast-like cells in metastatic brain (FB-C7) express CYP1B1 and APOD.
span_literal:
The fibroblast-like cells in mBrain (Fig. 3f, g ; Supplementary Fig. 5d, e ; FB-C7; CYP1B1 + and APOD +)


claim_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00:claim:1cf9bb1a3d162765bf8c
claim_id: claim:1cf9bb1a3d162765bf8c
paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
span_literal:
The infiltration of myofibroblasts in LUAD was confirmed by the expression of the marker protein alpha smooth muscle actin (α-SMA) ( ACTA2 gene product) in the tumor stroma

summary:
In Homo sapiens, myofibroblasts in lung adenocarcinoma express the marker gene ACTA2 (alpha smooth muscle actin).


claim_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00:claim:f15a11707b29c3f7ad61
claim_id: claim:f15a11707b29c3f7ad61
paper_key: hca:0340_10.1038_s41467-020-16164-1_15fae00c00
span_literal:
The pDCs demonstrated an immunosuppressive phenotype 45 represented by the upregulation of leukocyte immunoglobulin-like receptor (LILR) family genes 46 , granzyme B ( GZMB ) production 47 , and loss of CD86 , CD83 , CD80 , and LAMP3 activation marker expression

summary:
In Homo sapiens, plasmacytoid dendritic cells demonstrate an immunosuppressive phenotype with upregulation of GZMB and loss of CD86, CD83, CD80, and LAMP3 expression.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:b481ce18719ff4d45a75
claim_id: claim:b481ce18719ff4d45a75
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal: clusters C01, C02, C04, C11 were CD11b + CD66b + granulocytes
summary:
In Homo sapiens femoral head tissue, granulocytes are marked by positive expression of CD11b and CD66b.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:041009797e9b8b43b056
claim_id: claim:041009797e9b8b43b056
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal: clusters C06, C08, C12 were CD19 + CD79A + CD20 + B cells
summary:
In Homo sapiens femoral head tissue, B cells are marked by positive expression of CD19, CD79A, and CD20.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:47d5f4fba0b52e0853cd
claim_id: claim:47d5f4fba0b52e0853cd
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal: cluster C14 was CD31 + VWF + endothelial cells (ECs)
summary:
In Homo sapiens femoral head tissue, endothelial cells are marked by positive expression of CD31 and VWF.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:93a96d00a4d6f3302b68
claim_id: claim:93a96d00a4d6f3302b68
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal: cluster C15 was CD117 + CD133 + endothelial progenitor cells (EPCs)
summary:
In Homo sapiens femoral head tissue, endothelial progenitor cells are marked by positive expression of CD117 and CD133.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:cf98a4577d6439cb0265
claim_id: claim:cf98a4577d6439cb0265
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal: cluster C16 was GZMB + IL3RA + plasmacytoid dendritic cells (PDCs)
summary:
In Homo sapiens femoral head tissue, plasmacytoid dendritic cells are marked by positive expression of GZMB and IL3RA.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:b1ff70344931cd003acf
claim_id: claim:b1ff70344931cd003acf
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified three putative subtypes: IL1B + monocytes (M1), C1QA + monocytes (M2), and MS4A3 + granulocyte-monocyte progenitors (M3).

summary:
In Homo sapiens femoral head tissue, IL1B-positive monocytes (M1) are marked by positive expression of IL1B.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:79f96ee59d13f511e0c8
claim_id: claim:79f96ee59d13f511e0c8
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified three putative subtypes: IL1B + monocytes (M1), C1QA + monocytes (M2), and MS4A3 + granulocyte-monocyte progenitors (M3).

summary:
In Homo sapiens femoral head tissue, C1QA-positive monocytes (M2) are marked by positive expression of C1QA.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:685c47cbf19bef11a155
claim_id: claim:685c47cbf19bef11a155
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified three putative subtypes: IL1B + monocytes (M1), C1QA + monocytes (M2), and MS4A3 + granulocyte-monocyte progenitors (M3).

summary:
In Homo sapiens femoral head tissue, granulocyte-monocyte progenitors (M3) are marked by positive expression of MS4A3.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:7d87041f9d40f071ebc7
claim_id: claim:7d87041f9d40f071ebc7
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
summary: In Homo sapiens femoral head tissue, CD4 T cells (T1) are marked by positive expression of CD4.
span_literal:
we identified one CD4 cluster (T1), and six CD8 clusters: GZMK + CCL4L2 + T cells (T2), CCR7 + T cells (T3), GZMK + CCR6 + T cells (T4), GZMB + GNLY + T cells (T5), GZMK + CXCL8 + T cells (T6), and GZMK + HSPA1A + T cells (T7).


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:33a9cd875f1c3228ec75
claim_id: claim:33a9cd875f1c3228ec75
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified one CD4 cluster (T1), and six CD8 clusters: GZMK + CCL4L2 + T cells (T2), CCR7 + T cells (T3), GZMK + CCR6 + T cells (T4), GZMB + GNLY + T cells (T5), GZMK + CXCL8 + T cells (T6), and GZMK + HSPA1A + T cells (T7).

summary:
In Homo sapiens femoral head tissue, GZMK-positive CCL4L2-positive CD8 T cells (T2) are marked by positive expression of GZMK and CCL4L2.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:a9593e53edd85fbfc8f5
claim_id: claim:a9593e53edd85fbfc8f5
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified one CD4 cluster (T1), and six CD8 clusters: GZMK + CCL4L2 + T cells (T2), CCR7 + T cells (T3), GZMK + CCR6 + T cells (T4), GZMB + GNLY + T cells (T5), GZMK + CXCL8 + T cells (T6), and GZMK + HSPA1A + T cells (T7).

summary:
In Homo sapiens femoral head tissue, CCR7-positive CD8 T cells (T3) are marked by positive expression of CCR7.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:22bf69f9656db4b111ad
claim_id: claim:22bf69f9656db4b111ad
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
summary:
In Homo sapiens femoral head tissue, GZMK-positive CCR6-positive CD8 T cells (T4) are marked by positive expression of GZMK and CCR6.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:5db34205ed8440426f3f
claim_id: claim:5db34205ed8440426f3f
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
summary:
In Homo sapiens femoral head tissue, GZMB-positive GNLY-positive CD8 T cells (T5) are marked by positive expression of GZMB and GNLY.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:9029d5328859893ec147
claim_id: claim:9029d5328859893ec147
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
summary:
In Homo sapiens femoral head tissue, GZMK-positive CXCL8-positive CD8 T cells (T6) are marked by positive expression of GZMK and CXCL8.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:86c83fa6a309f4901c9f
claim_id: claim:86c83fa6a309f4901c9f
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
summary:
In Homo sapiens femoral head tissue, GZMK-positive HSPA1A-positive CD8 T cells (T7) are marked by positive expression of GZMK and HSPA1A.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:edfc4e52b101d97f3f08
claim_id: claim:edfc4e52b101d97f3f08
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified DNTT + / MME + pre-B cell (B2 and B5), MSHA1 + mature/activated B cell (B4), CD27 + memory B cell (B3), and a plasmablast cluster (B1) with high expression of immunoglobulin genes and XBP1 (a transcription factor for plasma cell differentiation)

summary:
In Homo sapiens femoral head tissue, pre-B cells (B2 and B5) are marked by positive expression of DNTT and MME.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:3ac012bffad3a55996a7
claim_id: claim:3ac012bffad3a55996a7
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
we identified DNTT + / MME + pre-B cell (B2 and B5), MSHA1 + mature/activated B cell (B4), CD27 + memory B cell (B3), and a plasmablast cluster (B1) with high expression of immunoglobulin genes and XBP1 (a transcription factor for plasma cell differentiation)

summary:
In Homo sapiens femoral head tissue, mature/activated B cells (B4) are marked by positive expression of MSHA1.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:8f69bb92f309f8b80ab2
claim_id: claim:8f69bb92f309f8b80ab2
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
summary:
In Homo sapiens femoral head tissue, plasmablasts (B1) are marked by high positive expression of XBP1.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:beb5fa2173b148007e14
claim_id: claim:beb5fa2173b148007e14
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal: CCL20 was highly expressed in GZMK + CCR6 + CD8 T cells (T4)
summary:
In Homo sapiens femoral head tissue, GZMK-positive CCR6-positive CD8 T cells (T4) are marked by high positive expression of CCL20.


claim_key: hca:0342_10.18632_aging.203124_280d72e18e:claim:6a6d0643ec71a5f2024a
claim_id: claim:6a6d0643ec71a5f2024a
paper_key: hca:0342_10.18632_aging.203124_280d72e18e
span_literal:
another subpopulation of CD8 T cells, GZMK + CXCL8 + T cells (T6), specifically express high levels of LTF

summary:
In Homo sapiens femoral head tissue, GZMK-positive CXCL8-positive CD8 T cells (T6) specifically express high levels of LTF (lactotransferrin).


claim_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1:claim:571a4de7d3673b4cc5fe
claim_id: claim:571a4de7d3673b4cc5fe
paper_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1
summary: In Homo sapiens kidney, AQP2 is a marker of collecting duct principal cells.
span_literal:
Violin plot showing the expression of the collecting duct principal cell marker AQP2 and the collecting duct intercalated cell markers ATP6V1B1, ATP6V0D2 and ATP6V1G3 .


claim_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1:claim:c7503ea602078b71c20b
claim_id: claim:c7503ea602078b71c20b
paper_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1
span_literal:
Violin plot showing the expression of the collecting duct principal cell marker AQP2 and the collecting duct intercalated cell markers ATP6V1B1, ATP6V0D2 and ATP6V1G3 .

summary:
In Homo sapiens kidney, ATP6V1B1, ATP6V0D2, and ATP6V1G3 are markers of collecting duct intercalated cells.


claim_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1:claim:39b604132b0899e11518
claim_id: claim:39b604132b0899e11518
paper_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1
span_literal:
By modifying the parameters to 20 PCs and 0.8 resolution, we could accurately distinguish NKT cells ( CD3D + CD3E + GNLY + NKG7 + ) and T cells ( CD3D + CD3E + IL7R + )

summary:
In Homo sapiens kidney, natural killer T cells are positive for CD3D, CD3E, GNLY, and NKG7, distinguishing them from T cells.


claim_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1:claim:1a43443f2c8a16c4f51c
claim_id: claim:1a43443f2c8a16c4f51c
paper_key: hca:0343_10.1038_s41597-019-0351-8_0cf4fb36a1
span_literal:
By modifying the parameters to 20 PCs and 0.8 resolution, we could accurately distinguish NKT cells ( CD3D + CD3E + GNLY + NKG7 + ) and T cells ( CD3D + CD3E + IL7R + )

summary:
In Homo sapiens kidney, T cells are positive for CD3D, CD3E, and IL7R, distinguishing them from natural killer T cells.


claim_key: hca:0344_10.1172_jci148517_dbd0d2bd7b:claim:91cf60686bc0c7288938
claim_id: claim:91cf60686bc0c7288938
paper_key: hca:0344_10.1172_jci148517_dbd0d2bd7b
span_literal:
Five epithelial cell clusters — basal, suprabasal, club, goblet, and ciliated cells — were identified ( Figure 1M ) by annotation of clusters based on expression of data-driven genes and epithelial cell type–specific marker genes such as KRT15 , KRT5 , SERPINB4 , KRT7 , SCGB1A1 , MUC5AC , and FOXJ1

summary:
In Homo sapiens nasal epithelium, basal cells are identified by expression of the marker gene KRT15. In Homo sapiens nasal epithelium, basal cells are identified by expression of the marker gene KRT5.


claim_key: hca:0344_10.1172_jci148517_dbd0d2bd7b:claim:09b3733148b58bee2766
claim_id: claim:09b3733148b58bee2766
paper_key: hca:0344_10.1172_jci148517_dbd0d2bd7b
span_literal:
Five epithelial cell clusters — basal, suprabasal, club, goblet, and ciliated cells — were identified ( Figure 1M ) by annotation of clusters based on expression of data-driven genes and epithelial cell type–specific marker genes such as KRT15 , KRT5 , SERPINB4 , KRT7 , SCGB1A1 , MUC5AC , and FOXJ1

summary:
In Homo sapiens nasal epithelium, suprabasal cells are identified by expression of the marker gene SERPINB4. In Homo sapiens nasal epithelium, suprabasal cells are identified by expression of the marker gene KRT7.


claim_key: hca:0344_10.1172_jci148517_dbd0d2bd7b:claim:80ff83fa2f43c4594d87
claim_id: claim:80ff83fa2f43c4594d87
paper_key: hca:0344_10.1172_jci148517_dbd0d2bd7b
span_literal:
Five epithelial cell clusters — basal, suprabasal, club, goblet, and ciliated cells — were identified ( Figure 1M ) by annotation of clusters based on expression of data-driven genes and epithelial cell type–specific marker genes such as KRT15 , KRT5 , SERPINB4 , KRT7 , SCGB1A1 , MUC5AC , and FOXJ1

summary:
In Homo sapiens nasal epithelium, club cells are identified by expression of the marker gene SCGB1A1.


claim_key: hca:0344_10.1172_jci148517_dbd0d2bd7b:claim:e6bccad19abc73f7209e
claim_id: claim:e6bccad19abc73f7209e
paper_key: hca:0344_10.1172_jci148517_dbd0d2bd7b
summary:
In Homo sapiens nasal epithelium, goblet cells are identified by expression of the marker gene MUC5AC.


claim_key: hca:0344_10.1172_jci148517_dbd0d2bd7b:claim:9f93b250d6e5ec9ce92b
claim_id: claim:9f93b250d6e5ec9ce92b
paper_key: hca:0344_10.1172_jci148517_dbd0d2bd7b
summary:
In Homo sapiens nasal epithelium, ciliated cells are identified by expression of the marker gene FOXJ1.


claim_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb:claim:0820427462dc763d46bf
claim_id: claim:0820427462dc763d46bf
paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
span_literal:
Five major immune cells types were identified, including CD4+ T cells (clusters 1, 2, 3, 4, 5, 6, 7, and 8) with canonical marker genes CD3D , CD3E , CD3G , and CD4 ; CD8+ T cells (clusters 9, 10, 11, 12, and 13) with marker genes CD3D , CD3E , CD3G , CD8A , and CD8B ; B cells (clusters 14, 15, and 16) with marker genes CD19 , CD79A , and CD79B ; natural killer (NK) cells (clusters 17, 18, and 19) with marker genes NKG7 , GZMB , GNLY , and NCR1 ; and monocyte–macrophage cells (cluster 20) with marker genes CD14 and CD68

summary:
In Homo sapiens peripheral blood mononuclear cells, CD4-positive T cells are identified by the marker genes CD3D, CD3E, CD3G, and CD4.


claim_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb:claim:43191f585f298b318159
claim_id: claim:43191f585f298b318159
paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
span_literal:
Five major immune cells types were identified, including CD4+ T cells (clusters 1, 2, 3, 4, 5, 6, 7, and 8) with canonical marker genes CD3D , CD3E , CD3G , and CD4 ; CD8+ T cells (clusters 9, 10, 11, 12, and 13) with marker genes CD3D , CD3E , CD3G , CD8A , and CD8B ; B cells (clusters 14, 15, and 16) with marker genes CD19 , CD79A , and CD79B ; natural killer (NK) cells (clusters 17, 18, and 19) with marker genes NKG7 , GZMB , GNLY , and NCR1 ; and monocyte–macrophage cells (cluster 20) with marker genes CD14 and CD68

summary:
In Homo sapiens peripheral blood mononuclear cells, CD8-positive T cells are identified by the marker genes CD3D, CD3E, CD3G, CD8A, and CD8B.


claim_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb:claim:d0579130412f050ea6bd
claim_id: claim:d0579130412f050ea6bd
paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
span_literal:
Five major immune cells types were identified, including CD4+ T cells (clusters 1, 2, 3, 4, 5, 6, 7, and 8) with canonical marker genes CD3D , CD3E , CD3G , and CD4 ; CD8+ T cells (clusters 9, 10, 11, 12, and 13) with marker genes CD3D , CD3E , CD3G , CD8A , and CD8B ; B cells (clusters 14, 15, and 16) with marker genes CD19 , CD79A , and CD79B ; natural killer (NK) cells (clusters 17, 18, and 19) with marker genes NKG7 , GZMB , GNLY , and NCR1 ; and monocyte–macrophage cells (cluster 20) with marker genes CD14 and CD68

summary:
In Homo sapiens peripheral blood mononuclear cells, B cells are identified by the marker genes CD19, CD79A, and CD79B.


claim_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb:claim:a9d9018710dcff96a5b4
claim_id: claim:a9d9018710dcff96a5b4
paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
summary:
In Homo sapiens peripheral blood mononuclear cells, natural killer cells are identified by the marker genes NKG7, GZMB, GNLY, and NCR1.


claim_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb:claim:32b63d89a0b5043c90b0
claim_id: claim:32b63d89a0b5043c90b0
paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
summary:
In Homo sapiens peripheral blood mononuclear cells, monocyte-macrophage cells are identified by the marker genes CD14 and CD68.


claim_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb:claim:1ddb34cfa76d8d13ff5d
claim_id: claim:1ddb34cfa76d8d13ff5d
paper_key: hca:0345_10.3389_fimmu.2021.645666_15198bd9bb
span_literal: In addition, cluster 21 highly expressed HBB , HBA2 , PF4 , and PPBP genes.
summary:
In Homo sapiens peripheral blood mononuclear cells, cluster 21 (a hemoglobin and platelet-containing cluster) highly expressed HBB, HBA2, PF4, and PPBP genes.


claim_key: hca:0346_10.34067_kid.0005522021_6c9059bd87:claim:090f73d7125668c13859
claim_id: claim:090f73d7125668c13859
paper_key: hca:0346_10.34067_kid.0005522021_6c9059bd87
summary: In Homo sapiens, ACE2 is expressed on proximal tubule cells throughout the urinary system.
span_literal:
The primary SARS-CoV-2 receptor ACE2 is expressed on epithelial cells throughout the urinary system, including proximal tubule cells and urothelial cells


claim_key: hca:0346_10.34067_kid.0005522021_6c9059bd87:claim:de73eb7b5a1522ad6a3f
claim_id: claim:de73eb7b5a1522ad6a3f
paper_key: hca:0346_10.34067_kid.0005522021_6c9059bd87
span_literal:
ACE2 and TMPRSS2 transcripts were detected on various epithelial cells from the kidney and were particularly abundant in urothelial cells

summary:
In Homo sapiens, ACE2 and TMPRSS2 transcripts were particularly abundant in urothelial cells among kidney epithelial cells.


claim_key: hca:0346_10.34067_kid.0005522021_6c9059bd87:claim:f363f7d03d1d8f9d7608
claim_id: claim:f363f7d03d1d8f9d7608
paper_key: hca:0346_10.34067_kid.0005522021_6c9059bd87
span_literal: ACE2 and TMPRSS2 expression was highest in urothelial cells among cell types recovered.
summary:
In Homo sapiens, ACE2 and TMPRSS2 expression was highest in urothelial cells among recovered urinary cell types.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:d34a95e9827deaea3350
claim_id: claim:d34a95e9827deaea3350
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
The largest cluster comprised CD3D+ T cells, consisting of mutually exclusive populations of CD8A+ GZMA+ cytotoxic (TC-5) and CD4+ T-helper cells (TC-2: CCR7 ; TC-3: CXCL13 ; TC-4: TNFRSF4 ; TC-6: CXCR4 ; TC-9: CCR7, MX1 ), including FOXP3+ CTLA4+ regulatory T cells (TC-1) and proliferating T cells (TC-7)

summary:
In Homo sapiens, cytotoxic T cells (TC-5) are marked by positive expression of CD8A and GZMA within the CD3D-positive T cell population.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:ff4e86ddb7683b934933
claim_id: claim:ff4e86ddb7683b934933
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
The largest cluster comprised CD3D+ T cells, consisting of mutually exclusive populations of CD8A+ GZMA+ cytotoxic (TC-5) and CD4+ T-helper cells (TC-2: CCR7 ; TC-3: CXCL13 ; TC-4: TNFRSF4 ; TC-6: CXCR4 ; TC-9: CCR7, MX1 ), including FOXP3+ CTLA4+ regulatory T cells (TC-1) and proliferating T cells (TC-7)

summary:
In Homo sapiens, T-helper cells are marked by positive expression of CD4 within the CD3D-positive T cell population.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:60121f394ad92b117a5b
claim_id: claim:60121f394ad92b117a5b
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal: DC-1: CD1A, CD1C , and partly CD207
summary:
In Homo sapiens, dendritic cell cluster DC-1 is marked by positive expression of CD1A, CD1C, and CD207.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:c40ce6d35d08adbd3a69
claim_id: claim:c40ce6d35d08adbd3a69
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
summary: In Homo sapiens, B cells are marked by positive expression of CD19.
span_literal:
Smaller leukocyte clusters included B cells ( CD19 ), plasmacytoid DCs (pDCs: LILRA4 ) and plasma cells (PC: IGKC ).


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:f61ba86e4eae66368a10
claim_id: claim:f61ba86e4eae66368a10
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
summary: In Homo sapiens, fibroblasts are marked by positive expression of COL1A2.
span_literal:
A larger population of COL1A2+ fibroblasts contained five clusters (FB-1: COL1A1, MFAP5, FBN1 -positive cells constituting the largest group [ 20 ]; FB-2: CCL19, CXCL9; FB-3: POSTN, CCL2, COL6A5, COL18A1 and CCL19 cells previously described as inflammatory fibroblasts in AD [ 21 ]; FB-4: APOD, CFD, APOE, CXCL12; and FB-5: COL1A1, SPARC ; Fig. 1 C, Fig. S 1 C-D, Table S 2 ).


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:27034a6b2a807fdbe58f
claim_id: claim:27034a6b2a807fdbe58f
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
A larger population of COL1A2+ fibroblasts contained five clusters (FB-1: COL1A1, MFAP5, FBN1 -positive cells constituting the largest group [ 20 ]; FB-2: CCL19, CXCL9; FB-3: POSTN, CCL2, COL6A5, COL18A1 and CCL19 cells previously described as inflammatory fibroblasts in AD [ 21 ]; FB-4: APOD, CFD, APOE, CXCL12; and FB-5: COL1A1, SPARC ; Fig. 1 C, Fig. S 1 C-D, Table S 2 ).

summary:
In Homo sapiens, fibroblast cluster FB-1 is marked by positive expression of COL1A1, MFAP5, and FBN1.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:9122d89ff17164587cd5
claim_id: claim:9122d89ff17164587cd5
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
summary:
In Homo sapiens, inflammatory fibroblast cluster FB-3 is marked by positive expression of POSTN, CCL2, COL6A5, COL18A1, and CCL19.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:9051c85ec6f37f00ea27
claim_id: claim:9051c85ec6f37f00ea27
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
summary:
In Homo sapiens, fibroblast cluster FB-4 is marked by positive expression of APOD, CFD, APOE, and CXCL12.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:f9eac4aa88e899d133e4
claim_id: claim:f9eac4aa88e899d133e4
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
summary: In Homo sapiens, keratinocytes are marked by positive expression of KRT5.
span_literal:
We also found KRT5+ keratinocytes (basal KC-1: KRT15, KRT14; suprabasal KC-2: KRT1, KRT10 , Fig. S 1 D), myofibroblasts (MFB: ACTA2 ), blood endothelial cells EC-1 and EC-2 ( VWF ) and lymphoendothelial cells (LEC: LYVE1, PDPN )


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:9e6b4ff4aa1d6e9d5dc6
claim_id: claim:9e6b4ff4aa1d6e9d5dc6
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
We also found KRT5+ keratinocytes (basal KC-1: KRT15, KRT14; suprabasal KC-2: KRT1, KRT10 , Fig. S 1 D), myofibroblasts (MFB: ACTA2 ), blood endothelial cells EC-1 and EC-2 ( VWF ) and lymphoendothelial cells (LEC: LYVE1, PDPN )

summary:
In Homo sapiens, basal keratinocyte cluster KC-1 is marked by positive expression of KRT15 and KRT14.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:afc897a27ae65488fd3c
claim_id: claim:afc897a27ae65488fd3c
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
We also found KRT5+ keratinocytes (basal KC-1: KRT15, KRT14; suprabasal KC-2: KRT1, KRT10 , Fig. S 1 D), myofibroblasts (MFB: ACTA2 ), blood endothelial cells EC-1 and EC-2 ( VWF ) and lymphoendothelial cells (LEC: LYVE1, PDPN )

summary:
In Homo sapiens, suprabasal keratinocyte cluster KC-2 is marked by positive expression of KRT1 and KRT10.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:8263a67da7b5ecc2cdcb
claim_id: claim:8263a67da7b5ecc2cdcb
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
One of the few markers generally downregulated in malignant cells included CD7 (Fig. 2 F, S 2 J-L), in line with a malignant phenotype, and as seen in histopathology (Fig. 1 A) [ 24 ].

summary:
In Homo sapiens, malignant T cells in mycosis fungoides show negative (downregulated) expression of CD7.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:f76f8048fd0804a80308
claim_id: claim:f76f8048fd0804a80308
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
Only a few genes were consistently upregulated in clonally expanded T cells, including CD70 , a marker of highly activated lymphocytes, and GTSF1 (gametocyte specific factor 1) (Fig. 2 E, M, N), as previously reported in CTCL [ 12 , 26 , 27 ].

summary:
In Homo sapiens, clonally expanded malignant T cells in cutaneous T-cell lymphoma show positive (upregulated) expression of CD70 and GTSF1 (gametocyte specific factor 1).


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:d98f9b1b5fab36903ab8
claim_id: claim:d98f9b1b5fab36903ab8
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
we discovered six genes to be downregulated in all patients in plaque/tumor vs. patch lesions, namely the chemokine receptor CXCR4 , the skin residency marker CD69 , the heat shock protein HSPA1A , the anti-inflammatory mediator tristetraprolin (i.e. zinc finger protein 36 homolog ZFP36 ), the interleukin-7 receptor IL7R , and the thioredoxin-interacting protein TXNIP (Fig. 3 H, Table S 3 ).

summary:
In Homo sapiens, the malignant T cell clone in advancing mycosis fungoides lesions shows negative (downregulated) expression of CXCR4, CD69, HSPA1A, ZFP36, IL7R, and TXNIP compared to patch lesions.


claim_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890:claim:70970c7dc0362d81866f
claim_id: claim:70970c7dc0362d81866f
paper_key: hca:0347_10.1186_s12943-021-01419-2_236ba26890
span_literal:
we found a population of IGFL2 + KIR3DL2 + tumor cells that was largely absent in nonlesional MF or healthy control skin, which might be crucially involved in the formation of actively inflamed, clinically visible MF lesions.

summary:
In Homo sapiens, a population of malignant T cells in lesional mycosis fungoides is marked by positive expression of IGFL2 and KIR3DL2.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:cfc29b5ea446abe207c9
claim_id: claim:cfc29b5ea446abe207c9
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
we identified a unique HAS1 hi ECM-producing population, which is markedly enriched in lungs from patients with IPF and localizes to peripheral and subpleural regions

summary:
In Homo sapiens, HAS1 high fibroblast is a unique extracellular matrix-producing population enriched in idiopathic pulmonary fibrosis lungs, marked by high expression of HAS1.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:a93b7e7d46c7ae2ed088
claim_id: claim:a93b7e7d46c7ae2ed088
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
summary: In Homo sapiens, immune cells are marked by positive expression of PTPRC.
span_literal:
PTPRC + (immune cells), EPCAM + (epithelial cells), PECAM1 + /PTPRC − (endothelial cells), and PTPRC − /EPCAM − /PECAM1 − (mesenchymal cells) were used to split Seurat clusters into four subgroups


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:c3ff56aafdc74ea4cb8a
claim_id: claim:c3ff56aafdc74ea4cb8a
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
PTPRC + (immune cells), EPCAM + (epithelial cells), PECAM1 + /PTPRC − (endothelial cells), and PTPRC − /EPCAM − /PECAM1 − (mesenchymal cells) were used to split Seurat clusters into four subgroups

summary:
In Homo sapiens, endothelial cells are marked by positive expression of PECAM1 and negative expression of PTPRC.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:35b2c46cdb03d09a2e69
claim_id: claim:35b2c46cdb03d09a2e69
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
Among these four secretory cell types, two expressed classical secretory lineage marker SCGB1A1 and airways mucins ( MUC5AC and/or MUC5B ), while the other two were defined by the expression of SCGB1A1 and SCGB3A2 or SCGB3A2 only

summary:
In Homo sapiens, secretory cells include subtypes defined by expression of the classical secretory lineage marker SCGB1A1 and airway mucins MUC5AC and/or MUC5B, or by expression of SCGB1A1 and SCGB3A2, or SCGB3A2 only.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:40fe89f87f3ec15b3487
claim_id: claim:40fe89f87f3ec15b3487
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
the SCGB3A2 + cells expressed a subset of alveolar programs including NKX2-1 , HOPX , CAV1 , surfactant genes, and major histocompatibility complex–II

summary:
In Homo sapiens, SCGB3A2-positive secretory cells express alveolar programs including NKX2-1, HOPX, and CAV1.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:3a5d366ef52570344b23
claim_id: claim:3a5d366ef52570344b23
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
we identified a transitional AT2 cell state characterized by simultaneous expression of lower levels of canonical AT2 programs compared to AT2 cells in addition to a subset of AT1 markers, including CAV1 and AGER

summary:
In Homo sapiens, transitional alveolar type 2 cell is characterized by expression of a subset of alveolar type 1 markers including CAV1 and AGER.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:493a521fcb85e2fdf64c
claim_id: claim:493a521fcb85e2fdf64c
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
summary: In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell expresses COL1A1 and FN1.
span_literal:
this analysis also identified a previously undescribed population of KRT5 − /KRT17 + epithelial cells that expressed COL1A1 , FN1 , and other pathologic ECM components


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:4f0a9f43b65f45162066
claim_id: claim:4f0a9f43b65f45162066
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
summary: In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell expresses CDH2.
span_literal:
These KRT5 − /KRT17 + cells expressed multiple collagens, other ECM components, and CDH2 (encoding for N-cadherin)


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:d125b2afa083626e0e68
claim_id: claim:d125b2afa083626e0e68
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal: but lacked ACTA2 , PDGFRA , S100A4 , or other canonical fibroblast markers
summary:
In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell lacks expression of ACTA2, PDGFRA, and S100A4.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:ace5721b100d62405c62
claim_id: claim:ace5721b100d62405c62
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
Unexpectedly, these cells expressed genes typical of a distal epithelial program including SOX9 , NAPSA , and ITGB6

summary:
In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell expresses distal epithelial program genes including SOX9, NAPSA, and ITGB6.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:4023a965a4ed9c085628
claim_id: claim:4023a965a4ed9c085628
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
summary: In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell highly expresses CDKN2A.
span_literal:
and highly expressed CDKN2A (encoding for p16), suggesting cell cycle arrest and/or a senescent phenotype


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:370c48a82c9182176b91
claim_id: claim:370c48a82c9182176b91
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
KRT5 − /KRT17 + cells expressed canonical basal cell transcription factor TP63 , but these cells lacked expression of the basal cell marker KRT5

summary:
In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell expresses TP63 but lacks expression of the basal cell marker KRT5.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:0e4f7f719660f5e06e13
claim_id: claim:0e4f7f719660f5e06e13
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
there was also a specific enrichment in fibrotic lungs of ACTA2 + myofibroblasts, a PLIN2 + lipofibroblast-like group, and a previously undescribed HAS1 hi fibroblast population

summary:
In Homo sapiens, myofibroblasts are marked by ACTA2, lipofibroblast-like cells are marked by PLIN2, and a fibroblast population is marked by high HAS1 expression.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:a2236e23fb3071c5ba90
claim_id: claim:a2236e23fb3071c5ba90
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
Analysis of genes that were up-regulated in HAS1 hi cells indicated enrichment for pathways associated with cellular stress, interleukin-4 (IL4)/IL13 signaling (fig. S19), and programs previously implicated in epithelial-mesenchymal transition in other systems ( TWIST and SNAI1 )

summary:
In Homo sapiens, HAS1 high fibroblast shows up-regulation of TWIST and SNAI1, genes previously implicated in epithelial-mesenchymal transition.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:b86a9bad250038ef68ac
claim_id: claim:b86a9bad250038ef68ac
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
summary: In Homo sapiens, fibroblast is marked by LUM as a pan-fibroblast marker.
span_literal:
there was notable expansion of LUM + cells (a pan-fibroblast marker) in PF lungs compared to control


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:a3f703fb9812f12fe0b4
claim_id: claim:a3f703fb9812f12fe0b4
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
KRT5 − /KRT17 + cells retain canonical epithelial lineage-defining genes ( EPCAM , NKX2-1 , and cytokeratins) while coexpressing a small subset of “typical” mesenchymal genes, including COL1A1 , FN1 , and CDH2 (N-cadherin), while lacking generally recognized stromal surface markers and transcription factors

summary:
In Homo sapiens, KRT5-negative/KRT17-positive epithelial cell retains canonical epithelial lineage-defining genes EPCAM and NKX2-1 while coexpressing COL1A1, FN1, and CDH2.


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:767f3bf101a59b1e66a9
claim_id: claim:767f3bf101a59b1e66a9
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
summary: In Homo sapiens, transitional alveolar type 2 cell shows increased SOX4 expression.
span_literal:
we observed an increase in SOX4 expression in transitional AT2 cells, high expression of SOX4 in SCGB3A2 + cells, and high expression of SOX9 in KRT5 − /KRT17 + cells


claim_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c:claim:6e088c93d5bb4a5f94c7
claim_id: claim:6e088c93d5bb4a5f94c7
paper_key: hca:0348_10.1126_sciadv.aba1972_746bae0b3c
span_literal:
the expression of the airway mucin MUC5B is not restricted to a SPDEF hi , “Goblet”-like cell ( MUC5AC + cells), but rather is predominantly expressed in a distinct SCGB1A1 + secretory population

summary:
In Homo sapiens, the airway mucin MUC5B is predominantly expressed in a distinct SCGB1A1-positive secretory cell population rather than being restricted to a SPDEF high goblet-like cell.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:47f332a600c1b81a3bf0
claim_id: claim:47f332a600c1b81a3bf0
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Full dataset (Fig. 1C ): T/NK ( CD3E ), epithelial ( KRT19 ), endothelial ( VWF, PECAM1 ), myeloid ( CD68 ), proliferating epithelial ( KRT19, MKI67 ), proliferating lymphoid ( CD3E, MKI67 ), B/plasma ( CD79A ), proliferating myeloid ( CD68, MKI67 ), mesenchyme ( DCN ), mast ( KIT ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, T/natural killer cells are identified by the marker CD3E.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:b0102b58f55592a593bc
claim_id: claim:b0102b58f55592a593bc
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Full dataset (Fig. 1C ): T/NK ( CD3E ), epithelial ( KRT19 ), endothelial ( VWF, PECAM1 ), myeloid ( CD68 ), proliferating epithelial ( KRT19, MKI67 ), proliferating lymphoid ( CD3E, MKI67 ), B/plasma ( CD79A ), proliferating myeloid ( CD68, MKI67 ), mesenchyme ( DCN ), mast ( KIT ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, epithelial cells are identified by the marker KRT19.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:efcc264a19bb53ca9267
claim_id: claim:efcc264a19bb53ca9267
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Full dataset (Fig. 1C ): T/NK ( CD3E ), epithelial ( KRT19 ), endothelial ( VWF, PECAM1 ), myeloid ( CD68 ), proliferating epithelial ( KRT19, MKI67 ), proliferating lymphoid ( CD3E, MKI67 ), B/plasma ( CD79A ), proliferating myeloid ( CD68, MKI67 ), mesenchyme ( DCN ), mast ( KIT ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, endothelial cells are identified by the markers VWF and PECAM1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:11373b08e6de5641af71
claim_id: claim:11373b08e6de5641af71
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, proliferating epithelial cells are identified by the markers KRT19 and MKI67.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:4379a9e61c152cd11443
claim_id: claim:4379a9e61c152cd11443
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, proliferating lymphoid cells are identified by the markers CD3E and MKI67.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:0a59a84da8a2ec5a8225
claim_id: claim:0a59a84da8a2ec5a8225
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, B/plasma cells are identified by the marker CD79A.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:6089509daeb7d3c80b2b
claim_id: claim:6089509daeb7d3c80b2b
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, proliferating myeloid cells are identified by the markers CD68 and MKI67.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:b7f9ca1db5db8240d1a2
claim_id: claim:b7f9ca1db5db8240d1a2
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, mesenchymal cells are identified by the marker DCN.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:b6c6fc8ab487a3da0717
claim_id: claim:b6c6fc8ab487a3da0717
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Mesenchyme (Fig. 3A ): myCAF ( ACTA2, MMP11, COL10A1 − ), iCAF ( C3, C7, CFD, PTGDS ), pericyte ( ACTA2 + , RGS5 + , CSPG4, NOTCH3 ), proliferating ( MKI67 ), peri-islet Schwann cells ( SOX10, S100B, PLP1 ), epithelial-like ( KRT19, EPCAM ), chondrocyte-like (SPP 1, IBSP, MMP13 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, myofibroblastic cancer-associated fibroblasts are identified by positive expression of ACTA2 and MMP11 and negative expression of COL10A1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:6f7caaf4534b18f97fd5
claim_id: claim:6f7caaf4534b18f97fd5
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Mesenchyme (Fig. 3A ): myCAF ( ACTA2, MMP11, COL10A1 − ), iCAF ( C3, C7, CFD, PTGDS ), pericyte ( ACTA2 + , RGS5 + , CSPG4, NOTCH3 ), proliferating ( MKI67 ), peri-islet Schwann cells ( SOX10, S100B, PLP1 ), epithelial-like ( KRT19, EPCAM ), chondrocyte-like (SPP 1, IBSP, MMP13 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, inflammatory cancer-associated fibroblasts are identified by the markers C3, C7, CFD, and PTGDS.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:2154d4ca63d782226d94
claim_id: claim:2154d4ca63d782226d94
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Mesenchyme (Fig. 3A ): myCAF ( ACTA2, MMP11, COL10A1 − ), iCAF ( C3, C7, CFD, PTGDS ), pericyte ( ACTA2 + , RGS5 + , CSPG4, NOTCH3 ), proliferating ( MKI67 ), peri-islet Schwann cells ( SOX10, S100B, PLP1 ), epithelial-like ( KRT19, EPCAM ), chondrocyte-like (SPP 1, IBSP, MMP13 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, pericytes are identified by positive expression of ACTA2, RGS5, CSPG4, and NOTCH3.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:430e489a33b80b0c03b0
claim_id: claim:430e489a33b80b0c03b0
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, peri-islet Schwann cells are identified by the markers SOX10, S100B, and PLP1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:886354f3badf1980b68a
claim_id: claim:886354f3badf1980b68a
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
T/NK (Fig. 4A ): CCR7 + CD4 + T cells ( CCR7 ), IL7R + CD4 + T cells ( IL7R ), FOXP3 + CD4 + T cells ( FOXP3 ), CXCL13 + CD4 + T cells ( CXCL13 ), GZMH + CD8 + T cells ( GZMH ), GZMK + CD8 + T cells ( GZMK ), ITGA1 + CD8 + T cells ( ITGA1 ), ISG15 + T cells ( ISG15 ), GNLY + NK cells ( GNLY, NCAM1 ), XCL1 + NK cells ( XCL1, NCAM1 ), KIT + mast ( KIT ), CD79 + B/Plasma ( CD79A ), MKI67 + proliferating ( MKI67 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CCR7+ CD4+ T cells are identified by the marker CCR7.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:41023c5c57c4a407b821
claim_id: claim:41023c5c57c4a407b821
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
T/NK (Fig. 4A ): CCR7 + CD4 + T cells ( CCR7 ), IL7R + CD4 + T cells ( IL7R ), FOXP3 + CD4 + T cells ( FOXP3 ), CXCL13 + CD4 + T cells ( CXCL13 ), GZMH + CD8 + T cells ( GZMH ), GZMK + CD8 + T cells ( GZMK ), ITGA1 + CD8 + T cells ( ITGA1 ), ISG15 + T cells ( ISG15 ), GNLY + NK cells ( GNLY, NCAM1 ), XCL1 + NK cells ( XCL1, NCAM1 ), KIT + mast ( KIT ), CD79 + B/Plasma ( CD79A ), MKI67 + proliferating ( MKI67 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, IL7R+ CD4+ T cells are identified by the marker IL7R.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:8b424245204a8e860c3d
claim_id: claim:8b424245204a8e860c3d
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
T/NK (Fig. 4A ): CCR7 + CD4 + T cells ( CCR7 ), IL7R + CD4 + T cells ( IL7R ), FOXP3 + CD4 + T cells ( FOXP3 ), CXCL13 + CD4 + T cells ( CXCL13 ), GZMH + CD8 + T cells ( GZMH ), GZMK + CD8 + T cells ( GZMK ), ITGA1 + CD8 + T cells ( ITGA1 ), ISG15 + T cells ( ISG15 ), GNLY + NK cells ( GNLY, NCAM1 ), XCL1 + NK cells ( XCL1, NCAM1 ), KIT + mast ( KIT ), CD79 + B/Plasma ( CD79A ), MKI67 + proliferating ( MKI67 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, FOXP3+ CD4+ T cells (regulatory T cells) are identified by the marker FOXP3.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:a0aadb0167a3be8bda2f
claim_id: claim:a0aadb0167a3be8bda2f
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CXCL13+ CD4+ T cells are identified by the marker CXCL13.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:d6834e51ed9f9c051ba0
claim_id: claim:d6834e51ed9f9c051ba0
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, GZMH+ CD8+ T cells are identified by the marker GZMH.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:171684e66c42bdb09b93
claim_id: claim:171684e66c42bdb09b93
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, GZMK+ CD8+ T cells are identified by the marker GZMK.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:12efb60a78424c55e855
claim_id: claim:12efb60a78424c55e855
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, ITGA1+ CD8+ T cells are identified by the marker ITGA1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:6d85c7c270289100be6b
claim_id: claim:6d85c7c270289100be6b
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, ISG15+ T cells are identified by the marker ISG15.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:d6523898c84f6027d1c8
claim_id: claim:d6523898c84f6027d1c8
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, GNLY+ natural killer cells are identified by the markers GNLY and NCAM1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:abae6df1202d2c4e78ce
claim_id: claim:abae6df1202d2c4e78ce
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, XCL1+ natural killer cells are identified by the markers XCL1 and NCAM1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:e931c209e9fc8fedf8e5
claim_id: claim:e931c209e9fc8fedf8e5
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
CD8 + T cells (Fig. 4C ): GZMK + CD8 + T cells (GZMK), GZMH + CD8 + T cell ( GZMH ), ITGA1 + CD8 + T cells ( ITGA1 ), SELL + CD8 + T cells ( SELL ), ISG15 + CD8 + T cells ( ISG15 ), CTLA4 + CD8 + T cells ( CTLA4 ), HSPA6 + CD8 + T cells ( HSPA6 ), epithelial-like ( KRT19 ), erythrocytes ( HBB ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, SELL+ CD8+ T cells are identified by the marker SELL.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:d585f716d6342e179ec7
claim_id: claim:d585f716d6342e179ec7
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
CD8 + T cells (Fig. 4C ): GZMK + CD8 + T cells (GZMK), GZMH + CD8 + T cell ( GZMH ), ITGA1 + CD8 + T cells ( ITGA1 ), SELL + CD8 + T cells ( SELL ), ISG15 + CD8 + T cells ( ISG15 ), CTLA4 + CD8 + T cells ( CTLA4 ), HSPA6 + CD8 + T cells ( HSPA6 ), epithelial-like ( KRT19 ), erythrocytes ( HBB ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CTLA4+ CD8+ T cells are identified by the marker CTLA4.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:3a36e5d5db78081b0694
claim_id: claim:3a36e5d5db78081b0694
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
CD8 + T cells (Fig. 4C ): GZMK + CD8 + T cells (GZMK), GZMH + CD8 + T cell ( GZMH ), ITGA1 + CD8 + T cells ( ITGA1 ), SELL + CD8 + T cells ( SELL ), ISG15 + CD8 + T cells ( ISG15 ), CTLA4 + CD8 + T cells ( CTLA4 ), HSPA6 + CD8 + T cells ( HSPA6 ), epithelial-like ( KRT19 ), erythrocytes ( HBB ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, HSPA6+ CD8+ T cells are identified by the marker HSPA6.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:45954ca97d3d4a4f0d87
claim_id: claim:45954ca97d3d4a4f0d87
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Myeloid (Fig. 5 ): SPP 1 + macrophage (SPP 1, MARCO ), C1QC + macrophage ( C1QA, C1QB, C1QC ), MDSC ( S100A8, S100A9, S100A12 ), monocyte ( FCGR3A, CDKN1C ), cDC1 ( CLEC9A, XCR1 ), cDC2 ( CD1C, FCER1A ), cDC3 ( CCL19, CCL22, CCR7 ), pDC ( LILRA4, PLD4 ), proliferating ( MKI67 ), mast ( KIT ), T ( CD3E ), epithelial-like ( KRT18, KRT19 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, SPP1+ tumor-associated macrophages are identified by the markers SPP1 and MARCO.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:d4d82b411b4655689158
claim_id: claim:d4d82b411b4655689158
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Myeloid (Fig. 5 ): SPP 1 + macrophage (SPP 1, MARCO ), C1QC + macrophage ( C1QA, C1QB, C1QC ), MDSC ( S100A8, S100A9, S100A12 ), monocyte ( FCGR3A, CDKN1C ), cDC1 ( CLEC9A, XCR1 ), cDC2 ( CD1C, FCER1A ), cDC3 ( CCL19, CCL22, CCR7 ), pDC ( LILRA4, PLD4 ), proliferating ( MKI67 ), mast ( KIT ), T ( CD3E ), epithelial-like ( KRT18, KRT19 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, C1QC+ tumor-associated macrophages are identified by the markers C1QA, C1QB, and C1QC.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:c74c39e99bd052b6b3fa
claim_id: claim:c74c39e99bd052b6b3fa
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
Myeloid (Fig. 5 ): SPP 1 + macrophage (SPP 1, MARCO ), C1QC + macrophage ( C1QA, C1QB, C1QC ), MDSC ( S100A8, S100A9, S100A12 ), monocyte ( FCGR3A, CDKN1C ), cDC1 ( CLEC9A, XCR1 ), cDC2 ( CD1C, FCER1A ), cDC3 ( CCL19, CCL22, CCR7 ), pDC ( LILRA4, PLD4 ), proliferating ( MKI67 ), mast ( KIT ), T ( CD3E ), epithelial-like ( KRT18, KRT19 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, myeloid-derived suppressor cells are identified by the markers S100A8, S100A9, and S100A12.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:d95ffcd3811fe60770fa
claim_id: claim:d95ffcd3811fe60770fa
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, monocytes are identified by the markers FCGR3A and CDKN1C.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:042cd9812c39eeaf853f
claim_id: claim:042cd9812c39eeaf853f
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, conventional dendritic cell type 1 is identified by the markers CLEC9A and XCR1.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:9cbf8f2067de78bab1df
claim_id: claim:9cbf8f2067de78bab1df
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, conventional dendritic cell type 2 is identified by the markers CD1C and FCER1A.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:70a56fc4943d654be7d0
claim_id: claim:70a56fc4943d654be7d0
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, conventional dendritic cell type 3 is identified by the markers CCL19, CCL22, and CCR7.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:8c05f097f74bbf6514ca
claim_id: claim:8c05f097f74bbf6514ca
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, plasmacytoid dendritic cells are identified by the markers LILRA4 and PLD4.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:acdedd03f9bb3804d4c3
claim_id: claim:acdedd03f9bb3804d4c3
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
At this finer granularity, we discerned a small CTLA4 + CD8 + T cell cluster with high levels of exhaustion markers ( CTLA4, HAVCR2, LAG3, TIGIT ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CTLA4+ CD8+ T cells express high levels of the exhaustion markers CTLA4, HAVCR2, LAG3, and TIGIT.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:bc3ea10c25f4c45271a3
claim_id: claim:bc3ea10c25f4c45271a3
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
We found TIGIT to be the highest and most broadly expressed inhibitory checkpoint molecule, while PDCD1 was expressed at low levels and in a minority of CD8 + T cells (Fig. 7D ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, TIGIT is the highest and most broadly expressed inhibitory checkpoint molecule on CD8+ T cells, while PDCD1 is expressed at low levels.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:c02023e61992ee7c3dda
claim_id: claim:c02023e61992ee7c3dda
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
SPP 1 + TAMs showed increased expression of S100A8 and S100A9 , genes previously linked to immunosuppressive macrophages 36 , while C1QC + TAMs had increased expression of HLA-DRB5 and CXCL9 , which is involved in the anticancer immune response 37 (Supplimentary Fig. 5C , Supplimentary Data 4 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, SPP1+ tumor-associated macrophages show increased expression of S100A8 and S100A9, while C1QC+ tumor-associated macrophages show increased expression of HLA-DRB5 and CXCL9.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:1c808749870fca0e522d
claim_id: claim:1c808749870fca0e522d
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
SPP 1 + TAMs showed increased expression of S100A8 and S100A9 , genes previously linked to immunosuppressive macrophages 36 , while C1QC + TAMs had increased expression of HLA-DRB5 and CXCL9 , which is involved in the anticancer immune response 37 (Supplimentary Fig. 5C , Supplimentary Data 4 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, C1QC+ tumor-associated macrophages show increased expression of HLA-DRB5 and CXCL9.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:9bbd2e24aa9777e90453
claim_id: claim:9bbd2e24aa9777e90453
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
In myCAFs, SDC1 31 , a gene linked to CAF-mediated regulation of breast cancer cell migration, was upregulated, while in iCAFs, CCL19 32 , a gene linked to cytotoxic T cell recruitment by CAFs in lung cancer, was highly expressed (Supplimentary Fig. 3D , Supplimentary Data 4 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, SDC1 is upregulated in myofibroblastic cancer-associated fibroblasts.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:8a87812e52f532aa9113
claim_id: claim:8a87812e52f532aa9113
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
In myCAFs, SDC1 31 , a gene linked to CAF-mediated regulation of breast cancer cell migration, was upregulated, while in iCAFs, CCL19 32 , a gene linked to cytotoxic T cell recruitment by CAFs in lung cancer, was highly expressed (Supplimentary Fig. 3D , Supplimentary Data 4 ).

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CCL19 is highly expressed in inflammatory cancer-associated fibroblasts.


claim_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19:claim:e649fbba3d3ab1ba478e
claim_id: claim:e649fbba3d3ab1ba478e
paper_key: hca:0349_10.1038_s41467-023-36296-4_67ae3c1e19
span_literal:
TIGIT was the most expressed inhibitory checkpoint molecule on CD8 + T cells and its expression, as with other checkpoint molecules, decreased with treatment.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, TIGIT is the most expressed inhibitory checkpoint molecule on CD8+ T cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:f0fffde6793bd642473f
claim_id: claim:f0fffde6793bd642473f
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
summary: In Homo sapiens, T cells are identified by the marker gene CD3D.
span_literal:
each identified by their unique signature genes CD3D (T cell marker), KLRF1 (NKp80, NK marker), CD19 (B cell marker), SDC1 (CD138, PC marker), CD14 (monocyte marker) and FCGR3A (CD16), respectively


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:79bb792a2ea3e72c307f
claim_id: claim:79bb792a2ea3e72c307f
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
unique genes in MAIT cells included MAIT-specific genes ( SLC4A10 and KLRB1 ), chemokine receptors ( CXCR6 , CCR5 , and CCR6 ), transcriptional factors ( IKZF2 and ZBTB16 )

summary:
In Homo sapiens, mucosal-associated invariant T cells express unique genes including SLC4A10, KLRB1, CXCR6, CCR5, CCR6, IKZF2, and ZBTB16.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:af927fbe04b163533316
claim_id: claim:af927fbe04b163533316
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
In total, 63 genes were highly expressed in Trm cells including chemokines ( XCL2 , CCL3 , and CCL4 ), cell adhesion molecules ( ICAM1 , VCAM1 , and ITGAD ), transcriptional factors ( EOMES and IKZF2 ) and others.

summary:
In Homo sapiens, tissue-resident memory T cells highly express XCL2, CCL3, CCL4, ICAM1, VCAM1, ITGAD, EOMES, and IKZF2.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:2f94a7af8e6b220c5861
claim_id: claim:2f94a7af8e6b220c5861
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
This comparative analysis revealed the core genes of TrNK and Trm cells, including KLRB1 , GZMK , CD160 , CXCR6 , EMOES , etc.

summary:
In Homo sapiens, tissue-resident natural killer cells and tissue-resident memory T cells share core genes including KLRB1, GZMK, CD160, CXCR6, and EOMES.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:081309ffc6c6846ad8b4
claim_id: claim:081309ffc6c6846ad8b4
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
This comparative analysis revealed the core genes of TrNK and Trm cells, including KLRB1 , GZMK , CD160 , CXCR6 , EMOES , etc.

summary:
In Homo sapiens, tissue-resident memory T cells share core genes including KLRB1, GZMK, CD160, CXCR6, and EOMES.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:6a2a175eb8836b77143a
claim_id: claim:6a2a175eb8836b77143a
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
C15 was identified as cycling T and NK cells that expressed replicating markers such as MKI67 in comparison with non-cycling T and NK cells

summary:
In Homo sapiens, cycling T and natural killer cells express the replicating marker MKI67 in comparison with non-cycling T and natural killer cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:e40aa892fbf722b44854
claim_id: claim:e40aa892fbf722b44854
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
Cells in C7 belong to a lymphoid subset with NK cell markers, such as NCAM1 , KLRF1 , and early differentiation markers, including CCR7 , SELL , IL7R , IL18RAP , and TNFRSF18

summary:
In Homo sapiens, the C7-cycling lymphoid subset expresses natural killer cell markers NCAM1 and KLRF1, and early differentiation markers CCR7, SELL, IL7R, IL18RAP, and TNFRSF18.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:bf680120b4a878f71afe
claim_id: claim:bf680120b4a878f71afe
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal: CCR7 is uniquely expressed by naïve/CM CD4 + (C1) and CD8 + T cells (C5).
summary:
In Homo sapiens, CCR7 is uniquely expressed by naive/central memory CD4-positive and CD8-positive T cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:aba4b6c05b9ce9d97bb6
claim_id: claim:aba4b6c05b9ce9d97bb6
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal: CX3CR1 is uniquely expressed by GZMB + CD8 + Tc (C11) and cNK cells (C13).
summary:
In Homo sapiens, CX3CR1 is uniquely expressed by GZMB-positive CD8-positive cytotoxic T cells and conventional natural killer cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:1ab7b81fea787485fcc5
claim_id: claim:1ab7b81fea787485fcc5
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
CCR7 defines the naive/CM state identified by MYC , LEF1 , TSHZ2 , MAL , NOSIP , and TCF7 expression.

summary:
In Homo sapiens, the naive/central memory state of T cells is defined by CCR7 and identified by MYC, LEF1, TSHZ2, MAL, NOSIP, and TCF7 expression.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:00b95fc77dadb70f2622
claim_id: claim:00b95fc77dadb70f2622
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
CXCR6 defines the tissue resident lineages identified by the aforementioned resident core signature molecules, including EOMES , GZMK , etc., while the CX3CR1 defined the terminal differentiation state with co-expression of many cytotoxic molecules, including FGFBP2 , GZMB , GNLY , SPON2 , PRF1 , etc.

summary:
In Homo sapiens, CXCR6 defines tissue-resident T and natural killer cell lineages identified by EOMES and GZMK, while CX3CR1 defines the terminally differentiated cytotoxic state with co-expression of FGFBP2, GZMB, GNLY, SPON2, and PRF1.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:93e3bbfabb501b2949c7
claim_id: claim:93e3bbfabb501b2949c7
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
CXCR6 defines the tissue resident lineages identified by the aforementioned resident core signature molecules, including EOMES , GZMK , etc., while the CX3CR1 defined the terminal differentiation state with co-expression of many cytotoxic molecules, including FGFBP2 , GZMB , GNLY , SPON2 , PRF1 , etc.

summary:
In Homo sapiens, CX3CR1 defines the terminally differentiated cytotoxic T and natural killer cell state with co-expression of FGFBP2, GZMB, GNLY, SPON2, and PRF1.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:b8c78cdca6603e62d0f4
claim_id: claim:b8c78cdca6603e62d0f4
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
The list shows specific markers such as MHC class II molecules, MS4A1 , CD79B for B cells, and TNFRSF17 , CD38 , XBP1 , etc. for ASCs.

summary:
In Homo sapiens, B cells are marked by MS4A1 and CD79B, while antibody-secreting cells are marked by TNFRSF17, CD38, and XBP1.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:d0ede3cfe445005533c4
claim_id: claim:d0ede3cfe445005533c4
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal: BCL11A and PAX5 are expressed by B cells but lacking in ASCs.
summary:
In Homo sapiens, B cells express BCL11A and PAX5, while antibody-secreting cells lack BCL11A and PAX5.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:5012b1b965f12243f134
claim_id: claim:5012b1b965f12243f134
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal: By contrast, PRDM1 and IRF4 are preferentially expressed by ASCs compared to B cells
summary:
In Homo sapiens, antibody-secreting cells preferentially express PRDM1 and IRF4 compared to B cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:95b3790725ecfbd2b774
claim_id: claim:95b3790725ecfbd2b774
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
For CD8 + T cells, CCR7 defines Tnaive and Tcm cells, CXCR3 does for circulating Tem cells, CXCR6 does for MAIT, Trm, and γδ T cells and CX3CR1 does for GZMB + Tc cells.

summary:
In Homo sapiens, CCR7 defines naive and central memory CD8-positive T cells, CXCR3 defines circulating effector memory T cells, CXCR6 defines mucosal-associated invariant T cells, tissue-resident memory T cells, and gamma delta T cells, and CX3CR1 defines GZMB-positive cytotoxic T cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:7239da929272c38f8fef
claim_id: claim:7239da929272c38f8fef
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
For CD8 + T cells, CCR7 defines Tnaive and Tcm cells, CXCR3 does for circulating Tem cells, CXCR6 does for MAIT, Trm, and γδ T cells and CX3CR1 does for GZMB + Tc cells.

summary:
In Homo sapiens, CXCR6 defines mucosal-associated invariant T cells, tissue-resident memory T cells, and gamma delta T cells among CD8-positive T cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:4422854097f478bf4523
claim_id: claim:4422854097f478bf4523
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
CXCR6 and CX3CR1 define LrNK and cNK cells in similar manner, which is consistent with distinct expression of TFs such as EMOES , PLZF , and TBX21 , and granules such as GZMK and GZMB , respectively, in agreement with early reports characterizing LrNK cells 6 .

summary:
In Homo sapiens, CXCR6 defines liver-resident natural killer cells, which express EOMES, PLZF, and GZMK, while CX3CR1 defines conventional natural killer cells, which express TBX21 and GZMB.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:84b767db1c76133e71ee
claim_id: claim:84b767db1c76133e71ee
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
CXCR6 and CX3CR1 define LrNK and cNK cells in similar manner, which is consistent with distinct expression of TFs such as EMOES , PLZF , and TBX21 , and granules such as GZMK and GZMB , respectively, in agreement with early reports characterizing LrNK cells 6 .

summary:
In Homo sapiens, CX3CR1 defines conventional natural killer cells, which express TBX21 and GZMB, as distinguished from liver-resident natural killer cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:d4e6640b125b1cae1f7e
claim_id: claim:d4e6640b125b1cae1f7e
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
liver-resident T & NK cells, including adhesion and integrin markers, chemokine and their receptors, co-inhibitory markers, killer lectin-like receptors, and transcriptional factors EOMES , ZBTB16 , IKZF2 , and RORC

summary:
In Homo sapiens, liver-resident T and natural killer cells express core hallmark transcriptional factors EOMES, ZBTB16, IKZF2, and RORC.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:7fa4010c24525abb7781
claim_id: claim:7fa4010c24525abb7781
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
Trm preferentially expresses EMOES, PLZF, and Helios, while CX3CR1 + Tc cells preferentially expresses T-bet.

summary:
In Homo sapiens, tissue-resident memory T cells preferentially express EOMES, PLZF, and Helios, while CX3CR1-positive cytotoxic T cells preferentially express T-bet.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:564e48db88a4ac45fddc
claim_id: claim:564e48db88a4ac45fddc
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
Trm preferentially expresses EMOES, PLZF, and Helios, while CX3CR1 + Tc cells preferentially expresses T-bet.

summary:
In Homo sapiens, CX3CR1-positive cytotoxic T cells preferentially express T-bet compared to tissue-resident memory T cells.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:c205111b89422ad453ee
claim_id: claim:c205111b89422ad453ee
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
Similarly, CXCR6 + NK cells which mainly reside in the liver (Fig. 4d ) express high levels of EOMES and PLZF, while CX3CR1 + NK cells only express T-bet

summary:
In Homo sapiens, CXCR6-positive natural killer cells express high levels of EOMES and PLZF, while CX3CR1-positive natural killer cells only express T-bet.


claim_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26:claim:af622e85706475428d89
claim_id: claim:af622e85706475428d89
paper_key: hca:0350_10.1038_s41421-020-0157-z_3083f6da26
span_literal:
Similarly, CXCR6 + NK cells which mainly reside in the liver (Fig. 4d ) express high levels of EOMES and PLZF, while CX3CR1 + NK cells only express T-bet

summary:
In Homo sapiens, CX3CR1-positive natural killer cells express T-bet, as distinguished from CXCR6-positive natural killer cells.


claim_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666:claim:bfd2e91b34a233387502
claim_id: claim:bfd2e91b34a233387502
paper_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666
span_literal:
Furthermore, HepLPCs not only retained the expression of hepatocyte-lineage marker genes including HNF1A, HNF4A, ALB (weakly expressed) and CK18 but also displayed expression of liver progenitor cell markers such as SOX9, CK19, CD24 and EpCAM

summary:
In Homo sapiens, hepatocyte-derived liver progenitor-like cells retain expression of hepatocyte-lineage markers HNF1A, HNF4A, ALB, and CK18, and display expression of liver progenitor cell markers SOX9, CK19, CD24, and EpCAM.


claim_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666:claim:dbbb6480f49a4eeb7316
claim_id: claim:dbbb6480f49a4eeb7316
paper_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666
span_literal:
The expression of hepatic lineage markers such as HNF1A, HNF4A, ALB and CK18 were scattered or widely distributed in HepLPCs whereas the progenitor markers (EpCAM, CD24, CK19 and SOX9) were generally expressed at varying levels, suggesting that proliferative HepLPCs acquired liver progenitor features at the transcriptional level

summary:
In Homo sapiens, hepatocyte-derived liver progenitor-like cells express hepatic lineage markers HNF1A, HNF4A, ALB, and CK18, and progenitor markers EpCAM, CD24, CK19, and SOX9 at varying levels.


claim_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666:claim:c9e39adc1c48f7f2f53b
claim_id: claim:c9e39adc1c48f7f2f53b
paper_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666
span_literal:
Specifically, HepLPCs from 3 donors showed consistent expression of the hepatic marker ALB (14.9% ± 4.0%) and the progenitor marker CK19 (99.6% ± 0.2%) in HepLPCs at both early and late passages

summary:
In Homo sapiens, hepatocyte-derived liver progenitor-like cells consistently express the hepatic marker ALB and the progenitor marker CK19.


claim_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666:claim:dad7d3bdf1591a4bf0f7
claim_id: claim:dad7d3bdf1591a4bf0f7
paper_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666
span_literal:
we first isolated human primary hepatocytes from normal liver tissues using FACS-based sorting to exclude CD24 + or EpCAM + progenitor cells

summary:
In Homo sapiens, liver progenitor cells are positive for CD24 and EpCAM, and are excluded from hepatocyte isolations by sorting against these markers.


claim_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666:claim:d90677069a645aba2143
claim_id: claim:d90677069a645aba2143
paper_key: hca:0351_10.1038_s41422-018-0103-x_169d6c1666
span_literal:
Re-differentiated hepatocytes also displayed homogenous expression of hepatic markers, including E-cadherin, CYP3A4, HNF1A, and ALB

summary:
In Homo sapiens, re-differentiated hepatocytes display homogenous expression of hepatic markers E-cadherin, CYP3A4, HNF1A, and ALB.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:91dab9932b4957b3cbeb
claim_id: claim:91dab9932b4957b3cbeb
paper_key: hca:0352_10.1038_nature25980_27cde67bed
summary: In Homo sapiens developing prefrontal cortex, SFRP1 is a marker of neural progenitor cells.
span_literal:
we identified SFRP1 and RBFOX1 as markers of NPCs and excitatory neurons and verified this by immunofluorescence


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:e07cb2a806e5f1f19c81
claim_id: claim:e07cb2a806e5f1f19c81
paper_key: hca:0352_10.1038_nature25980_27cde67bed
summary: In Homo sapiens brain, PAX6 is used as a marker of neural progenitor cells.
span_literal:
PAX6 , NEUROD2 , GAD1 , PDGFRA , AQP4 and PTPRC were used as markers to identify the major cell types in the brain: neural progenitor cells (NPCs), excitatory neurons, interneurons, oligodendrocyte progenitor cells (OPCs), astrocytes and microglia, respectively.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:9a8fe94013ab89da57a1
claim_id: claim:9a8fe94013ab89da57a1
paper_key: hca:0352_10.1038_nature25980_27cde67bed
span_literal:
EOMES was expressed in clusters 3, 4 and 5, which suggests that the NPCs in these clusters were intermediate progenitor cells (IPCs)

summary:
In Homo sapiens, EOMES expression identifies intermediate progenitor cells among neural progenitor cells in the developing prefrontal cortex.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:0924e377f10df5ec99d8
claim_id: claim:0924e377f10df5ec99d8
paper_key: hca:0352_10.1038_nature25980_27cde67bed
span_literal:
To identify markers for IPCs, we selected genes that were highly expressed in clusters 3, 4 and 5, including NHLH1 , NHLH2 , TP53I11 , SLA1C3 and PPP1R17

summary:
In Homo sapiens, NHLH1, NHLH2, TP53I11, SLC1A3, and PPP1R17 were identified as markers for intermediate progenitor cells in the developing prefrontal cortex.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:cabf50afbc4334c59344
claim_id: claim:cabf50afbc4334c59344
paper_key: hca:0352_10.1038_nature25980_27cde67bed
span_literal:
Groups of cells expressing interneuron progenitor markers, such as TTF1 , LHX6 and DLX1 , were detected at an early timepoint in a pseudo-time alignment by Monocle analysis, and persisted throughout development

summary:
In Homo sapiens developing prefrontal cortex, TTF1, LHX6, and DLX1 are markers of interneuron progenitor cells.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:696c3be7de0083c1a8a4
claim_id: claim:696c3be7de0083c1a8a4
paper_key: hca:0352_10.1038_nature25980_27cde67bed
span_literal:
CALB2 + and SST + interneurons appeared early in pseudo-time, and were followed by CALB1 + , CCK + and VIP + interneurons

summary:
In Homo sapiens developing prefrontal cortex, CALB2 and SST are markers of early-appearing interneurons, while CALB1, CCK, and VIP are markers of later-appearing interneurons.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:5db8a2dcab634ee2eb85
claim_id: claim:5db8a2dcab634ee2eb85
paper_key: hca:0352_10.1038_nature25980_27cde67bed
span_literal:
In the upper layer neurons (SATB2 + FOXP2 − ), action potentials were only barely initiated, with a low level of outward potassium and inward sodium channel currents

summary:
In Homo sapiens prefrontal cortex, upper layer neurons are positive for SATB2 and negative for FOXP2.


claim_key: hca:0352_10.1038_nature25980_27cde67bed:claim:549058eba893c0e95e22
claim_id: claim:549058eba893c0e95e22
paper_key: hca:0352_10.1038_nature25980_27cde67bed
span_literal: microglia-specific genes ( PTPRC , CSF1R , AIF1
summary:
In Homo sapiens, PTPRC, CSF1R, and AIF1 are microglia-specific genes in the developing prefrontal cortex.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:40469628c3b93fd03cbf
claim_id: claim:40469628c3b93fd03cbf
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
MGE-derived cortical interneurons differentiate into either Parvalbumin (PVALB) or Somatostatin (SST)-expressing cells

summary:
In Homo sapiens, medial ganglionic eminence-derived cortical interneurons differentiate into either parvalbumin (PVALB) or somatostatin (SST)-expressing cells.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:96740986203ec5dc94c6
claim_id: claim:96740986203ec5dc94c6
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
Populations expressing high levels of SOX2 were composed of neuronal and glial precursors, including a mixture of radial glia and intermediate precursors (P4: EOMES , PAX6 , HOPX , VIM ), astrocyte precursors (P11: AQP4 ), and oligodendrocyte precursors (P10: OLIG1, PDGFRα )

summary:
In Homo sapiens fetal cortex, radial glia and intermediate precursors express EOMES, PAX6, HOPX, and VIM; astrocyte precursors express AQP4; and oligodendrocyte precursors express OLIG1 and PDGFRα.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:26744e030db902d46f54
claim_id: claim:26744e030db902d46f54
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
The P9 population expressed the highest levels of GAD1 , and was the only population to show substantial expression of SST or LHX6 , indicating this population is enriched for cortical interneurons.

summary:
In Homo sapiens fetal cortex, the cortical interneuron-enriched population (P9) expresses the highest levels of GAD1, SST, and LHX6.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:84e6f7559f07b306a372
claim_id: claim:84e6f7559f07b306a372
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal: The P8 population likely consists of LGE-derived interneurons, express expressed PAX6 and SP8 .
summary:
In Homo sapiens fetal cortex, lateral ganglionic eminence-derived interneurons express PAX6 and SP8.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:19d5796c23a082e2c5b2
claim_id: claim:19d5796c23a082e2c5b2
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
Cit − clusters had higher VIM and SOX2 expression, whereas Cit + clusters expressed more DCX and GAD1 (Padj < 0.001, FDR for Cit + vs. Cit − ).

summary:
In Homo sapiens in vitro-derived cells, progenitor clusters have higher VIM and SOX2 expression compared to neuron clusters.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:0d30933196e80d059d8b
claim_id: claim:0d30933196e80d059d8b
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
Cit − clusters had higher VIM and SOX2 expression, whereas Cit + clusters expressed more DCX and GAD1 (Padj < 0.001, FDR for Cit + vs. Cit − ).

summary:
In Homo sapiens in vitro-derived cells, neuron clusters express more DCX and GAD1 compared to progenitor clusters.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:c9f30619d2e8dd74033f
claim_id: claim:c9f30619d2e8dd74033f
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal: GAD1 + ,PAX6 + , SP8 + clusters were deemed LGE neurons (nLGE)
summary:
In Homo sapiens in vitro-derived cells, lateral ganglionic eminence neurons are positive for GAD1, PAX6, and SP8.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:e7844716065577170333
claim_id: claim:e7844716065577170333
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
summary: In Homo sapiens in vitro-derived cells, oligodendrocyte precursors express OLIG1 and PDGFRα.
span_literal:
while clusters that expressed OLIG1 and PDGFRα were classified as oligodendrocyte precursors (oMGE).


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:bb57e88b9af37546de4b
claim_id: claim:bb57e88b9af37546de4b
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
Cortistatin (CORT), a neuropeptide expressed by a subset of cortical interneurons, was previously implicated in regulation of slow-wave sleep

summary:
In Homo sapiens, cortistatin (CORT) is a neuropeptide expressed by a subset of cortical interneurons.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:5d7e0afbe9e8c83b7d49
claim_id: claim:5d7e0afbe9e8c83b7d49
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
from D100 through D125, Cit − clusters expressed HOPX , AQP4 and S100B (Padj < 0.001 for Cit − cells at D100 and D125).

summary:
In Homo sapiens in vitro-derived cells, late-stage progenitor clusters express HOPX, AQP4, and S100B.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:cb94aaf1732863ee760d
claim_id: claim:cb94aaf1732863ee760d
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
Clusters that co-expressed OLIG1 , OLIG2 and PCDH15 emerged after D100, indicating that oligodendrocyte precursors were present at late timepoints.

summary:
In Homo sapiens in vitro-derived cells, oligodendrocyte precursors co-express OLIG1, OLIG2, and PCDH15.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:b75607f0461f473196fb
claim_id: claim:b75607f0461f473196fb
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
After D54, pMGE clusters also express higher levels of HOPX , in addition to AQP4, S100B, ANXA1 , and S100A10 compared to earlier clusters.

summary:
In Homo sapiens in vitro-derived cells, late medial ganglionic eminence progenitor clusters express higher levels of HOPX, AQP4, S100B, ANXA1, and S100A10 compared to earlier clusters.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:1b53474441f961aa1b1c
claim_id: claim:1b53474441f961aa1b1c
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
LHX8 is expressed early during MGE-derived interneuron production, and its expression is reduced in cortical interneurons

summary:
In Homo sapiens, LHX8 is expressed early during medial ganglionic eminence-derived interneuron production and its expression is reduced in cortical interneurons.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:7326543945c282207b5d
claim_id: claim:7326543945c282207b5d
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
LHX8 is expressed early during MGE-derived interneuron production, and its expression is reduced in cortical interneurons

summary:
In Homo sapiens, LHX8 expression is reduced in cortical interneurons compared to early medial ganglionic eminence-derived interneurons.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:fe46a20881d4fd6ebbd7
claim_id: claim:fe46a20881d4fd6ebbd7
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal: CORT − cells expressed more CXCR4 and NKX2-1 , which are repressed as cortical interneurons mature.
summary:
In Homo sapiens, immature cortical interneurons (CORT-negative) express more CXCR4 and NKX2-1, which are repressed as cortical interneurons mature.


claim_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467:claim:3be2a5d405dde56f812e
claim_id: claim:3be2a5d405dde56f812e
paper_key: hca:0353_10.1016_j.neuron.2017.02.014_ebc3a9c467
span_literal:
The CORT + cells expressed higher levels of SST , GRIA4 , and RBFOX3 (see Figure 4A , Padj <0.001 for all genes described, CORT − vs. CORT + clusters).

summary:
In Homo sapiens, more mature cortical interneurons (CORT-positive) express higher levels of SST, GRIA4, and RBFOX3 compared to CORT-negative clusters.


claim_key: hca:0354_10.1172_jci128475_002a5124c6:claim:a92b6b79330b02a28f88
claim_id: claim:a92b6b79330b02a28f88
paper_key: hca:0354_10.1172_jci128475_002a5124c6
span_literal:
In addition, CD69 (second panel), which has been postulated as a marker of T RM as well as being an early activation marker

summary:
In Homo sapiens, CD69 has been postulated as a marker of tissue-resident memory T cells as well as being an early activation marker.


claim_key: hca:0354_10.1172_jci128475_002a5124c6:claim:67b29dbd881c8357e3db
claim_id: claim:67b29dbd881c8357e3db
paper_key: hca:0354_10.1172_jci128475_002a5124c6
span_literal:
Further, this expression profile is consistent with upregulation of the key regulator of the universal T RM transcriptional program ZNF683 (Hobit), which causes downregulation of KLF2 (fourth panel)

summary:
In Homo sapiens, tissue-resident memory T cells show upregulation of ZNF683 (Hobit), a key regulator of the tissue-resident memory T cell transcriptional program, and downregulation of KLF2.


claim_key: hca:0354_10.1172_jci128475_002a5124c6:claim:506f3b5df6952ccd45fd
claim_id: claim:506f3b5df6952ccd45fd
paper_key: hca:0354_10.1172_jci128475_002a5124c6
span_literal:
The top panel of this heatmap shows expression of homing receptors and molecules involved in T cell egress, including CCR7, SELL (CD62L), TCF7 (TCF-1), and S1PR1. These markers are gradually downregulated from NIC, via nonexpanded cells from SCNI and MS subjects, to expanded clones from SCNI and MS subjects. In the latter case, all markers are downregulated, indicating a fully established T RM phenotype

summary:
In Homo sapiens, tissue-resident memory T cells show downregulation of CCR7, SELL, TCF7, and S1PR1, indicating a fully established tissue-resident memory T cell phenotype.


claim_key: hca:0354_10.1172_jci128475_002a5124c6:claim:789884c8c681b2595b6c
claim_id: claim:789884c8c681b2595b6c
paper_key: hca:0354_10.1172_jci128475_002a5124c6
span_literal:
The homing marker S1PR1 is expressed on all T cells but is downregulated when a cell adopts a T RM phenotype.

summary:
In Homo sapiens, S1PR1 is expressed on T cells but is downregulated when a cell adopts a tissue-resident memory T cell phenotype.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:0315d04b6c6b2e0c744c
claim_id: claim:0315d04b6c6b2e0c744c
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 7 were MS4A1, TCL1A, LINC00926, FCER2, CD19, FCRL1, FCRLA, BLK, LINC01857, and LINC02397

summary:
In Homo sapiens, B cells are marked by MS4A1, TCL1A, LINC00926, FCER2, CD19, FCRL1, FCRLA, BLK, LINC01857, and LINC02397 as top marker genes in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:a23085dfecb611055b57
claim_id: claim:a23085dfecb611055b57
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 14 were DERL3, SDC1, IGHG4, JSRP1, IGLL5, FCRL5, TNFRSF17, SPAG4, TXNDC5, and TNFRSF13B

summary:
In Homo sapiens, plasma cells are marked by DERL3, SDC1, IGHG4, JSRP1, IGLL5, FCRL5, TNFRSF17, SPAG4, TXNDC5, and TNFRSF13B as top marker genes in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:dea6740e5bb9fe21e4b1
claim_id: claim:dea6740e5bb9fe21e4b1
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Clusters 2 and 15 were LGALS2, TMEM176A, SLC7A7, RBP7, CD300E, LRP1, CD163, TREM1, NRG1, and HK3

summary:
In Homo sapiens, monocytes are marked by LGALS2, TMEM176A, SLC7A7, RBP7, CD300E, LRP1, CD163, TREM1, NRG1, and HK3 as top marker genes in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:9a2c14800581927b95ae
claim_id: claim:9a2c14800581927b95ae
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 11 were LCN2, CMTM2, S100P, PROK2, ANXA3, CD177, MCEMP1, RETN, PGLYRP1, and FOLR3

summary:
In Homo sapiens, neutrophil granulocytes are marked by LCN2, CMTM2, S100P, PROK2, ANXA3, CD177, MCEMP1, RETN, PGLYRP1, and FOLR3 as top marker genes in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:5ea4478d0cb5d81ef9ce
claim_id: claim:5ea4478d0cb5d81ef9ce
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
There were common genes in Clusters 1, 5, 8, 10, and 13, including SPINK2, SOX4, FAM30A, CDK6, AC084033.3 , STMN1, SMIM24, PRSS57, MEF2C, and IGLL1.

summary:
In Homo sapiens, hematopoietic stem and progenitor cells share common marker genes SPINK2, SOX4, FAM30A, CDK6, AC084033.3, STMN1, SMIM24, PRSS57, MEF2C, and IGLL1 in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:c724e5d4e2c3a2095e28
claim_id: claim:c724e5d4e2c3a2095e28
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
There were common genes in Clusters 6, 9, and 12, including SELENBP1, GMPR, IFI27, DMTN, KRT1, PHOSPHO1, AC130456.3, and LINC00570.

summary:
In Homo sapiens, erythroblasts share common marker genes SELENBP1, GMPR, IFI27, DMTN, KRT1, PHOSPHO1, AC130456.3, and LINC00570 in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:0b8611eff2090c8e00dc
claim_id: claim:0b8611eff2090c8e00dc
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 6 were SELENBP, IFIT1B, GMPR, IFI27, DMTN, KRT1, PHOSPHO1, AC130456.3, PDZK1IP1, TMCC2, and LINC00570.

summary:
In Homo sapiens, erythroblast cluster 6 is marked by SELENBP, IFIT1B, GMPR, IFI27, DMTN, KRT1, PHOSPHO1, AC130456.3, PDZK1IP1, TMCC2, and LINC00570 in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:dcc42cf4d72accb99f63
claim_id: claim:dcc42cf4d72accb99f63
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 9 were SPTA1, SOX6, YPEL4, TSPO2, ANKRD9, FHDC1, FRMD4A, HEPACAM2, AC100835.2 , and SLFN14.

summary:
In Homo sapiens, erythroblast cluster 9 is marked by SPTA1, SOX6, YPEL4, TSPO2, ANKRD9, FHDC1, FRMD4A, HEPACAM2, AC100835.2, and SLFN14 in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:6fdab12137e696a98b6e
claim_id: claim:6fdab12137e696a98b6e
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 12 were AQP1, HJURP, A4GALT, TMEM233, PBK, SKA1, CA3, CCDC68, SLC25A21, and KREMEN1.

summary:
In Homo sapiens, erythroblast cluster 12 is marked by AQP1, HJURP, A4GALT, TMEM233, PBK, SKA1, CA3, CCDC68, SLC25A21, and KREMEN1 in bone marrow.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:6dc79e31dbef2aa9c1bb
claim_id: claim:6dc79e31dbef2aa9c1bb
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
Meanwhile, erythrocyte-specific transcription factors, including GATA-1, GATA-2, and KLF1, were expressed in Clusters 6, 9, and 12.

summary:
In Homo sapiens, erythroblasts express erythrocyte-specific transcription factors GATA-1, GATA-2, and KLF1.


claim_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7:claim:ee4dad760a290db296fa
claim_id: claim:ee4dad760a290db296fa
paper_key: hca:0355_10.3389_fgene.2021.745483_5f4326fce7
span_literal:
The top 10 marker genes of Cluster 16 were PF4V1, AC147651.1 , AP001189.1 , ENKUR, AP001189.3 , BEND2, LY6G6F, AC090409.1 , C15orf54, and TRAPPC3L.

summary:
In Homo sapiens, megakaryocytes are marked by PF4V1, AC147651.1, AP001189.1, ENKUR, AP001189.3, BEND2, LY6G6F, AC090409.1, C15orf54, and TRAPPC3L as top marker genes in bone marrow.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:5e1615dd8a63690e299b
claim_id: claim:5e1615dd8a63690e299b
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
UnstimC1, the largest cluster, represented more than half of total unstimulated NKT cells (64%). Few specific gene markers were identified except for the marginal upregulation of GZMK and FOSB

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 1 (UnstimC1) is marked by marginal upregulation of GZMK and FOSB.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:586282943067637134f8
claim_id: claim:586282943067637134f8
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
Within UnstimC2 (26% of total), multiple CDC42 related genes (CDC42SE1, CDC42SE2, CDC42) were upregulated, which were reported to control T cell cytoskeleton organization, trans-endothelial migration and polarization

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 2 (UnstimC2) shows upregulation of CDC42SE1, CDC42SE2, and CDC42.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:373fee51eeae0394c326
claim_id: claim:373fee51eeae0394c326
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
In addition, B4GALT1, a member of β-1,4-GalT family, is involved in T cell activation and intercellular contact formation ( Sun et al., 2014 ), while PRDM1 (Blimp1) is associated with tissue resident memory T cell differentiation ( Zundler et al., 2019 )

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 2 (UnstimC2) shows upregulation of B4GALT1 and PRDM1.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:efa4437c65966ebdd62f
claim_id: claim:efa4437c65966ebdd62f
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
UnstimC3 distinctively over expressed multiple cytotoxic-related genes, including GZMH, GZMB, FGFBP2, KLRD1, GNLY, KLRC1, and NKG7

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 3 (UnstimC3) distinctively overexpresses cytotoxic-related genes GZMH, GZMB, FGFBP2, KLRD1, GNLY, KLRC1, and NKG7.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:16a8728439e310f489ab
claim_id: claim:16a8728439e310f489ab
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
In addition, upregulated CCL4 and CCL5 may work as chemoattractant for the recruitment of natural killer (NK) cells, monocytes and T cells for a synergistic effector function and local inflammation.

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 3 (UnstimC3) shows upregulated CCL4 and CCL5.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:c9ea30cce3179d5e8afd
claim_id: claim:c9ea30cce3179d5e8afd
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
it represented a subpopulation of NKT cells with the upregulated central memory T cell marker CD62L, LEF1 and immature maker CD79A

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 4 (UnstimC4) shows upregulation of the central memory T cell marker SELL (CD62L), LEF1, and the immature marker CD79A.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:648794fdd5ca1294dd44
claim_id: claim:648794fdd5ca1294dd44
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
Intriguingly, cells from this cluster showed upregulation of multiple cellular metabolism related genes, including the lactate dehydrogenase subunit B (LDHB) ( Chen et al., 2016 ) and nitric oxide synthase interacting protein (NOSIP)

summary:
In Homo sapiens, unstimulated natural killer T cell cluster 4 (UnstimC4) shows upregulation of lactate dehydrogenase subunit B (LDHB) and nitric oxide synthase interacting protein (NOSIP).


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:0a604ea8d5f0c9994221
claim_id: claim:0a604ea8d5f0c9994221
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
In StimC1, the major post-stimulation NKT cluster, multiple chemokines including CCL3, CCL3L1, CCL4L2, CCL4, were upregulated

summary:
In Homo sapiens, stimulated natural killer T cell cluster 1 (StimC1) shows upregulation of CCL3, CCL3L1, CCL4L2, and CCL4.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:91424ba0c8f65b25a754
claim_id: claim:91424ba0c8f65b25a754
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal: Interestingly, IL23R and RORC, the NKT17-signature genes, were upregulated sparsely within StimC1
summary:
In Homo sapiens, stimulated natural killer T cell cluster 1 (StimC1) shows sparse upregulation of IL23R and RORC, the natural killer T 17 (NKT17) signature genes.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:57e2dba4f83dd8ecf17e
claim_id: claim:57e2dba4f83dd8ecf17e
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
StimC2 represented the NKT cells highly expressing multiple cytokines, including IL4, IFNγ, IL13, IL2, and IL10, as well as the C class chemokines XCL1 and XCL2

summary:
In Homo sapiens, stimulated natural killer T cell cluster 2 (StimC2) highly expresses IL4, IFNG, IL13, IL2, IL10, XCL1, and XCL2.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:d1d33e45af1455b62aca
claim_id: claim:d1d33e45af1455b62aca
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
In addition to the cytotoxic related signature genes in UnstimC3, StimC3 showed upregulated PRF1 (perforin) and multiple chemokines including XCL1, XCL2, CCL4L1

summary:
In Homo sapiens, stimulated natural killer T cell cluster 3 (StimC3) shows upregulation of PRF1, XCL1, XCL2, and CCL4L1.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:3d84bc21b6724125fbac
claim_id: claim:3d84bc21b6724125fbac
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
In addition to SELL and CD55, StimC4 showed an extra cluster of upregulated genes compared to UnstimC4

summary:
In Homo sapiens, stimulated natural killer T cell cluster 4 (StimC4) shows upregulation of SELL and CD55.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:c77ad6bf508fecd81064
claim_id: claim:c77ad6bf508fecd81064
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
CD200, the top upregulated gene in the cluster, may deliver an inhibitory signal for macrophage lineage, while MT2A, a free radical scavenger, plays a crucial pathophysiological role in anti-oxidation, anti-apoptosis and anti-inflammation

summary:
In Homo sapiens, stimulated natural killer T cell cluster 4 (StimC4) shows CD200 as the top upregulated gene and MT2A as an upregulated gene.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:2965989c9296da8ebe23
claim_id: claim:2965989c9296da8ebe23
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
StimC5, a unique post-stimulation NKT cluster, showed the upregulation of multiple immediate early genes (IEGs) ( Figures 3B–D ). including FOS, JUN, FOSB, DNAJB1, DUSP1, EGR1, and HSPs.

summary:
In Homo sapiens, stimulated natural killer T cell cluster 5 (StimC5) shows upregulation of the immediate early genes FOS, JUN, FOSB, DNAJB1, DUSP1, and EGR1.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:4ceb96399aba8af99ed5
claim_id: claim:4ceb96399aba8af99ed5
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
Other than IEGs, the top two in the upregulated gene list, Thioredoxin-interacting protein (TXNIP) and Glucocorticoid-induced leucine zipper (TLC22D3), repress cellular glucose uptake and regulate T-cell receptor activation, respectively

summary:
In Homo sapiens, stimulated natural killer T cell cluster 5 (StimC5) shows upregulation of thioredoxin-interacting protein (TXNIP) and glucocorticoid-induced leucine zipper (TSC22D3).


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:1e1ce3aec10e6e93656e
claim_id: claim:1e1ce3aec10e6e93656e
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
sub-cluster1 (StimC2-A) was represented by NKT cells highly expressing XCL1, XCL2, IFNγ, IL4, and IL13, whereas sub-cluster2 (StimC2-B) exhibits high expression of IL2, IL10, TNFRSF4 (OX40) and ICOS

summary:
In Homo sapiens, stimulated natural killer T cell cluster 2 sub-cluster A (StimC2-A) highly expresses XCL1, XCL2, IFNG, IL4, and IL13, whereas stimulated natural killer T cell cluster 2 sub-cluster B (StimC2-B) highly expresses IL2, IL10, TNFRSF4, and ICOS.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:62756aa488f3e73d5769
claim_id: claim:62756aa488f3e73d5769
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
sub-cluster1 (StimC2-A) was represented by NKT cells highly expressing XCL1, XCL2, IFNγ, IL4, and IL13, whereas sub-cluster2 (StimC2-B) exhibits high expression of IL2, IL10, TNFRSF4 (OX40) and ICOS

summary:
In Homo sapiens, stimulated natural killer T cell cluster 2 sub-cluster B (StimC2-B) highly expresses IL2, IL10, TNFRSF4 (OX40), and ICOS.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:c0e440805ddd0660cec8
claim_id: claim:c0e440805ddd0660cec8
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
The StimC2-B (IL2 + IL10 + OX40 + ICOS + IL4 – IFNγ – XCL – ) may represent the NKTreg subset with the transcriptome featuring the IL10 producing regulatory NKT cells identified in mouse

summary:
In Homo sapiens, stimulated natural killer T cell cluster 2 sub-cluster B (StimC2-B), a potential regulatory natural killer T cell subset, is positive for IL2, IL10, TNFRSF4 (OX40), and ICOS, and negative for IL4, IFNG, and XCL1.


claim_key: hca:0356_10.3389_fcell.2020.00384_845548ef53:claim:5b506a030f176993150d
claim_id: claim:5b506a030f176993150d
paper_key: hca:0356_10.3389_fcell.2020.00384_845548ef53
span_literal:
multiple upregulated genes in StimC2-B cluster are among the gene list specifically expressed in human PBMC Treg and/or mouse spleen Tregs, such as TNFRSF4 (OX40), ICOS, S100A4, ITGB1, IL2RA

summary:
In Homo sapiens, stimulated natural killer T cell cluster 2 sub-cluster B (StimC2-B) upregulates TNFRSF4 (OX40), ICOS, S100A4, ITGB1, and IL2RA, genes specifically expressed in regulatory T cells.


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:ef6068577370c74cf65e
claim_id: claim:ef6068577370c74cf65e
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
span_literal:
The NK compartment consisted of NK Bright cells expressing high levels of GNLY and moderate levels of NKG7 and NK Dim cells expressing high levels of NKG7 and CD16 ( FCGR3A )

summary:
In Homo sapiens, NK Bright cells express high levels of GNLY and moderate levels of NKG7, while NK Dim cells express high levels of NKG7 and FCGR3A (CD16).


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:b1a6bff2cd7168b3ed76
claim_id: claim:b1a6bff2cd7168b3ed76
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
summary: In Homo sapiens, naïve B cells express TCL1A.
span_literal:
The B cell compartment consisted of naïve cells expressing TCL1A (B Naïve ), memory cells expressing BANK1 (B Mem ), plasma cells expressing MZB1 (B Plasma ), and an atypical memory subpopulation expressing FCRL5, CD11c , and TBX21 and lacking expression of CD21 (B Atypical ; Fig. 2B ).


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:369a30d833e595b51bbc
claim_id: claim:369a30d833e595b51bbc
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
summary: In Homo sapiens, naïve CD4+ T cells express CCR7.
span_literal:
In the CD4 + T cell compartment, we identified canonical subpopulations of naïve cells expressing CCR7 (CD4 Naïve ), effector memory cells lacking CCR7 expression while expressing OX40 receptor ( TNFRSF4 ) and IL7R (CD4 EM ), and regulatory cells expressing the canonical transcription factor FOXP3 and its direct target RTKN2 ( 20 ) (CD4 Reg ; Fig. 2 , A and B ).


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:20d7d0ff8f9473407085
claim_id: claim:20d7d0ff8f9473407085
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
span_literal:
In the CD4 + T cell compartment, we identified canonical subpopulations of naïve cells expressing CCR7 (CD4 Naïve ), effector memory cells lacking CCR7 expression while expressing OX40 receptor ( TNFRSF4 ) and IL7R (CD4 EM ), and regulatory cells expressing the canonical transcription factor FOXP3 and its direct target RTKN2 ( 20 ) (CD4 Reg ; Fig. 2 , A and B ).

summary:
In Homo sapiens, effector memory CD4+ T cells lack CCR7 expression while expressing TNFRSF4 and IL7R.


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:6ab114714bb5632a2fc8
claim_id: claim:6ab114714bb5632a2fc8
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
span_literal:
In the CD4 + T cell compartment, we identified canonical subpopulations of naïve cells expressing CCR7 (CD4 Naïve ), effector memory cells lacking CCR7 expression while expressing OX40 receptor ( TNFRSF4 ) and IL7R (CD4 EM ), and regulatory cells expressing the canonical transcription factor FOXP3 and its direct target RTKN2 ( 20 ) (CD4 Reg ; Fig. 2 , A and B ).

summary:
In Homo sapiens, regulatory CD4+ T cells express the transcription factor FOXP3 and its direct target RTKN2.


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:8c3382e6c81b0717db1b
claim_id: claim:8c3382e6c81b0717db1b
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
summary: In Homo sapiens, naïve CD8+ T cells express CCR7.
span_literal:
Within the CD8 + T cell compartment, we identified naïve cells expressing CCR7 (CD8 Naïve ) and three effector memory subpopulations, including mucosal-associated invariant T cells expressing KLRB1 and GZMK (CD8 MAIT ) and two clusters lacking expression of KLRB1 and expressing the chemokine CCL5 , effector molecule PRF1 , and exhaustion marker LAG3 ( Fig. 2 , A and B ).


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:2bf9b5ea3b9c12faf07b
claim_id: claim:2bf9b5ea3b9c12faf07b
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
summary: In Homo sapiens, GZMH+ cytotoxic CD8+ T cells express GZMH and GZMB.
span_literal:
The two non-MAIT clusters could be distinguished by the expression of granzymes (CD8 GZMH , GZMH and GZMB ; CD8 GZMK GZMK ) and mirrored the NK subpopulations (NK Dim , GZMH and GZMB ; NK Bright , GZMK ) ( Fig. 2B and fig. S3C ).


claim_key: hca:0357_10.1126_science.abf1970_a409ac73f2:claim:45aba8c6a67fcb3b5d36
claim_id: claim:45aba8c6a67fcb3b5d36
paper_key: hca:0357_10.1126_science.abf1970_a409ac73f2
summary: In Homo sapiens, classical monocytes are CD14+.
span_literal:
we reclustered myeloid cells into six clusters differentiating the monocyte lineage (cM, CD14 + classical; ncM, FCGR3A + nonclassical; ncM comp , C1QA + / FCGR3A + complement-expressing nonclassical) and the dendritic cell lineage (cDC1, CLEC10A + conventional type 1; cDC2, CLEC9A + conventional type 2; pDC, IRF7 + plasmacytoid; Fig. 3 , C and D , and fig. S4 , C and D ).


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:9e21bee1878ba997bae2
claim_id: claim:9e21bee1878ba997bae2
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
these cells express the basal cell markers TP63, KRT17, LAMB3, and LAMC2 but do not express other established basal markers such as KRT5 and KRT15

summary:
In Homo sapiens, aberrant basaloid cells express the basal cell markers TP63, KRT17, LAMB3, and LAMC2 but do not express KRT5 and KRT15.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:c5f96bc53f3777dc33f6
claim_id: claim:c5f96bc53f3777dc33f6
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
These cells express markers of epithelial-mesenchymal transition (EMT) such as VIM, CDH2, FN1, COL1A1, TNC, and HMGA2

summary:
In Homo sapiens, aberrant basaloid cells express epithelial-mesenchymal transition markers VIM, CDH2, FN1, COL1A1, TNC, and HMGA2.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:961c31bf002085b16c75
claim_id: claim:961c31bf002085b16c75
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal: senescence-related genes including CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and GDF15
summary:
In Homo sapiens, aberrant basaloid cells express senescence-related genes CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and GDF15.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:d3f36ed068d42d3342b8
claim_id: claim:d3f36ed068d42d3342b8
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
the highest normalized expression levels across all profiled cell types of established IPF-related molecules, such as matrix metallopeptidase 7 (MMP7)

summary:
In Homo sapiens, aberrant basaloid cells have the highest expression of matrix metallopeptidase 7 (MMP7) across all profiled cell types.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:cb1cdf5b17a3161aa0a8
claim_id: claim:cb1cdf5b17a3161aa0a8
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal: the cells exhibit high levels of expression and evidence of downstream activation of SOX9
summary:
In Homo sapiens, aberrant basaloid cells exhibit high levels of expression and downstream activation of SOX9.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:318c2d7e89a65bd6c676
claim_id: claim:318c2d7e89a65bd6c676
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal: A fifth VE population is best distinguished by its expression of COL15A1.
summary:
In Homo sapiens, peribronchial vascular endothelial cells are best distinguished by expression of COL15A1.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:81933d1d63d5d91fcfa9
claim_id: claim:81933d1d63d5d91fcfa9
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
then removed cells characterized as smooth muscle cells (DES, ACTG2, and PLN) or pericytes (RGS5 and COX4I2)

summary:
In Homo sapiens, smooth muscle cells are characterized by DES, ACTG2, and PLN, while pericytes are characterized by RGS5 and COX4I2.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:f5dde5dc9cbe342ca67b
claim_id: claim:f5dde5dc9cbe342ca67b
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
fibroblasts, characterized by expression of CD34, FBN1, FBLN2, and VIT and myofibroblasts that consistently express MYLK, NEBL, MYO10, MYO1D, RYR2, and ITGA8

summary:
In Homo sapiens, fibroblasts are characterized by expression of CD34, FBN1, FBLN2, and VIT, while myofibroblasts consistently express MYLK, NEBL, MYO10, MYO1D, RYR2, and ITGA8.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:aa755445b40ebeef02fd
claim_id: claim:aa755445b40ebeef02fd
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
a fibroblast phenotype that exhibits increased expression of HAS1, HAS2, FBN1, and the SHH-induced chemokine, CXCL14

summary:
In Homo sapiens, the idiopathic pulmonary fibrosis fibroblast phenotype exhibits increased expression of HAS1, HAS2, FBN1, and CXCL14.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:a5ffbab7cb0e3b1de85b
claim_id: claim:a5ffbab7cb0e3b1de85b
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
SPP1 and cholesterol esterases lipoprotein lipase and LIPA expression steadily increasing in expression relatively early along the trajectory, ECM remodeling genes SPARC, GPC4, PALLD, CTSK, and MMP9 ramping up in expression further along the manifold

summary:
In Homo sapiens, the profibrotic idiopathic pulmonary fibrosis macrophage archetype shows increasing expression of SPP1, lipoprotein lipase, LIPA, SPARC, GPC4, PALLD, CTSK, and MMP9 along the trajectory.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:c33659b970c06455412e
claim_id: claim:c33659b970c06455412e
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
At the terminus of the IPF archetype, macrophage start expressing CSF1, suggesting the possibility of an autocrine feedback loop for recruitment and activation.

summary:
In Homo sapiens, at the terminus of the idiopathic pulmonary fibrosis archetype, profibrotic macrophages start expressing CSF1.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:b8685796c6adbb693b4e
claim_id: claim:b8685796c6adbb693b4e
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
they express some of the most typical airway basal cell markers (TP63, KRT17, and LAMB3 LAMC2), they seem to have lost others (KRT5 and KRT15)

summary:
In Homo sapiens, aberrant basaloid cells express the airway basal cell markers TP63, KRT17, LAMB3, and LAMC2 but have lost KRT5 and KRT15.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:6ccb56057ff115430cf8
claim_id: claim:6ccb56057ff115430cf8
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal: express SOX9, a transcription factor critical to distal airway development and repair
summary:
In Homo sapiens, aberrant basaloid cells express SOX9, a transcription factor critical to distal airway development and repair.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:c60fa433b8954cac0ff8
claim_id: claim:c60fa433b8954cac0ff8
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
they express mesenchymal markers (COL1A1, CDH2, and HMGA2) and have lost the expression MIR205HG, a gene containing mir-205 and a gatekeeper against EMT

summary:
In Homo sapiens, aberrant basaloid cells express mesenchymal markers COL1A1, CDH2, and HMGA2 and have lost expression of MIR205HG.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:d5b170fba22ca393cd10
claim_id: claim:d5b170fba22ca393cd10
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal: they express multiple markers of senescence (CDKN1A, CDKN2A, MDM2, and GDF15)
summary:
In Homo sapiens, aberrant basaloid cells express multiple markers of senescence including CDKN1A, CDKN2A, MDM2, and GDF15.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:364efbc1935cfa35faa8
claim_id: claim:364efbc1935cfa35faa8
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal:
these cells are the highest expressers of genes implicated in the pathogenesis of IPF such as AVB6 ( 14 ), MMP7 ( 13 ), GDF15 ( 12 ), and EPHB2

summary:
In Homo sapiens, aberrant basaloid cells are the highest expressers of AVB6, MMP7, GDF15, and EPHB2.


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:422bf0aada23c01a9570
claim_id: claim:422bf0aada23c01a9570
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
summary: In Homo sapiens, myofibroblasts consistently express MYLK, NEBL, MYO10, and MYO1D.
span_literal:
This population consistently expresses other genes associated with muscle like MYLK, NEBL, MYO10, and MYO1D, suggesting that the pathological phenotype observed in IPF is an extended, disease-related feature of this population


claim_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb:claim:d184edc9e8951863dad8
claim_id: claim:d184edc9e8951863dad8
paper_key: hca:0358_10.1126_sciadv.aba1983_17b603cdcb
span_literal: cell populations characterized by PDGFRB expression
summary:
In Homo sapiens, fibroblast and myofibroblast cell populations are characterized by PDGFRB expression.


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:348f4ff7d8e7b1b348e3
claim_id: claim:348f4ff7d8e7b1b348e3
paper_key: hca:0359_10.1101_759902_400af2c5fc
span_literal:
In addition to epithelial markers, these cells express the basal cell markers TP63, KRT17, LAMB3 and LAMC2, but do not express other established basal markers such as KRT5 and KRT15.

summary:
In Homo sapiens, aberrant basaloid cells express the basal cell markers TP63, KRT17, LAMB3, and LAMC2, but do not express other established basal markers such as KRT5 and KRT15.


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:e5e17d70c6d63aaebe2c
claim_id: claim:e5e17d70c6d63aaebe2c
paper_key: hca:0359_10.1101_759902_400af2c5fc
span_literal:
These cells express markers of epithelial mesenchymal transition (EMT) such as VIM, CDH2, FN1, COL1A1, TNC, and HMGA2 (9, 10, 11, 12), senescence related genes including CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and GDF15 (13-15) ([Figure 2C](759902v3_fig2.tif), right) and the highest levels of established IPF-related molecules, such as MMP7 (16), αVβ6 subunits (17) and EPHB2 (18).

summary:
In Homo sapiens, aberrant basaloid cells express epithelial mesenchymal transition markers VIM, CDH2, FN1, COL1A1, TNC, and HMGA2, senescence related genes CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and GDF15, and IPF-related molecules MMP7 and EPHB2.


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:168941390c0cb3d98d57
claim_id: claim:168941390c0cb3d98d57
paper_key: hca:0359_10.1101_759902_400af2c5fc
span_literal:
The cells exhibit high levels of expression and evidence of downstream activation of SOX9 ([Figure 2C](759902v3_fig2.tif) upper panel), a transcription factor critical to distal airway development, repair, also indicated in oncogenesis (19, 20).

summary:
In Homo sapiens, aberrant basaloid cells exhibit high levels of expression and downstream activation of SOX9.


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:87c48fa2e9d10614e026
claim_id: claim:87c48fa2e9d10614e026
paper_key: hca:0359_10.1101_759902_400af2c5fc
span_literal: A fifth VE population is best distinguished by its expression of COL15A1.
summary:
In Homo sapiens, peribronchial vascular endothelial cells are distinguished by expression of COL15A1.


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:badc42f0915d03c3775b
claim_id: claim:badc42f0915d03c3775b
paper_key: hca:0359_10.1101_759902_400af2c5fc
summary: In Homo sapiens, smooth muscle cells are characterized by DES, ACTG2, and PLN.
span_literal:
we then removed cells characterized as smooth muscle cells (DES, ACTG2 and PLN) or pericytes (RGS5, COX4I2).


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:25cf714457c54919d180
claim_id: claim:25cf714457c54919d180
paper_key: hca:0359_10.1101_759902_400af2c5fc
summary: In Homo sapiens, fibroblasts are characterized by expression of CD34, FBN1, FBLN2, and VIT.
span_literal:
This strategy allowed us to identify two distinct stromal populations: fibroblasts, characterized by expression of CD34, FBN1, FBLN2 and VIT; myofibroblasts consistently express MYLK, NEBL, MYO10, MYO1D, RYR2 and ITGA8, as described in the murine lung (24) ([Fig. 4A](759902v3_fig4.tif)).


claim_key: hca:0359_10.1101_759902_400af2c5fc:claim:ca1e988d0a15664041a9
claim_id: claim:ca1e988d0a15664041a9
paper_key: hca:0359_10.1101_759902_400af2c5fc
span_literal: we first focused on cell populations characterized by PDGFRB expression
summary:
In Homo sapiens, stromal cell populations including fibroblasts and myofibroblasts are characterized by PDGFRB expression.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:ec3bc3b02dd6a317de19
claim_id: claim:ec3bc3b02dd6a317de19
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
Breton et al. identify CD172a as a lineage marker that distinguishes human cDC precursor (pre-cDC) subpopulations committed to the CD1c + lineage (CD172a + pre-cDCs) or CD141 + lineage (CD172a − pre-cDCs).

summary:
In Homo sapiens, CD172a is a positive marker of conventional dendritic cell precursor committed to the CD1c+ lineage (CD172a+ pre-conventional dendritic cell) and a negative marker of conventional dendritic cell precursor committed to the CD141+ lineage (CD172a− pre-conventional dendritic cell).


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:cbe000a363d18190d310
claim_id: claim:cbe000a363d18190d310
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
Breton et al. identify CD172a as a lineage marker that distinguishes human cDC precursor (pre-cDC) subpopulations committed to the CD1c + lineage (CD172a + pre-cDCs) or CD141 + lineage (CD172a − pre-cDCs).

summary:
In Homo sapiens, CD172a is a negative marker of conventional dendritic cell precursor committed to the CD141+ lineage (CD172a− pre-conventional dendritic cell), distinguishing it from CD172a+ pre-conventional dendritic cell.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:aa3224def81858e8d704
claim_id: claim:aa3224def81858e8d704
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
summary: In Homo sapiens, plasmacytoid dendritic cells can be identified by expression of BDCA-2/CD303.
span_literal:
Plasmacytoid DCs (pDCs) are specialized to produce type I IFN and can be identified by expression of BDCA-2/CD303


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:ca4c5e235b5827f6f435
claim_id: claim:ca4c5e235b5827f6f435
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
CD1c + cDCs selectively express Clec10A, CD1c, ZEB2, and ETS2, whereas the CD141 + cDCs selectively express Clec9A, IDO1, and IRF8

summary:
In Homo sapiens, CD1c+ conventional dendritic cells selectively express CLEC10A, CD1c, ZEB2, and ETS2.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:ab75684e8c0fdf1dcba3
claim_id: claim:ab75684e8c0fdf1dcba3
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
A small percentage of pre-cDCs expresses cell-surface markers and transcription factors associated with CD141 + cDCs (P < 1e-27; Fisher’s exact test), such as Clec9A, IDO1, IRF8, BATF3, HLA-DR, CD135/Flt3, and CD117/cKit (CD141 + lineage–primed pre-cDCs; Fig. 1 e ).

summary:
In Homo sapiens, CD141+ lineage-primed pre-conventional dendritic cells express CLEC9A, IDO1, IRF8, BATF3, HLA-DR, CD135/FLT3, and CD117/KIT.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:abb268ce85a12b4d2821
claim_id: claim:abb268ce85a12b4d2821
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
A second larger group of pre-cDCs expresses genes associated with the CD1c + cDC fate (P < 1e-28; Fisher’s exact test), such as Clec10A, CD1c, IRF4, HLA-DR, CD11c, and IRF8 (CD1c + lineage–primed pre-cDCs; Fig. 1 e ).

summary:
In Homo sapiens, CD1c+ lineage-primed pre-conventional dendritic cells express CLEC10A, CD1c, IRF4, HLA-DR, CD11c, and IRF8.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:2804aad2b9378ddfee8a
claim_id: claim:2804aad2b9378ddfee8a
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
The third group of cells does not express genes associated with cDC differentiation (P > 0.1; Fisher’s exact test) and instead is characterized by CSF-R, CD172a, CD11c, and IRF8 expression (non-DCs; Fig. 1 e ).

summary:
In Homo sapiens, the non-dendritic cell population among pre-conventional dendritic cells is characterized by CSF1R, CD172a, CD11c, and IRF8 expression.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:630df67c8530f08ca640
claim_id: claim:630df67c8530f08ca640
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
summary: In Homo sapiens, CD172a/SIRPA is selectively expressed by CD1c+ conventional dendritic cells.
span_literal:
Within cDCs, CD172a/SIRPα is selectively expressed by human CD1c + cDCs and by mouse CD4 + DCs, which represent their functional equivalent


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:86042a3016eb408d9ba2
claim_id: claim:86042a3016eb408d9ba2
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
This observation is consistent with the higher expression of IRF8, BATF3, and ID2 by the CD172a − pre-cDCs and ETS2, ZEB2, and IRF4 by CD172a + pre-cDCs.

summary:
In Homo sapiens, CD172a− pre-conventional dendritic cells show higher expression of IRF8, BATF3, and ID2 compared to CD172a+ pre-conventional dendritic cells.


claim_key: hca:0360_10.1084_jem.20161135_0465d3ea50:claim:ec97abfe5792c847b52a
claim_id: claim:ec97abfe5792c847b52a
paper_key: hca:0360_10.1084_jem.20161135_0465d3ea50
span_literal:
This observation is consistent with the higher expression of IRF8, BATF3, and ID2 by the CD172a − pre-cDCs and ETS2, ZEB2, and IRF4 by CD172a + pre-cDCs.

summary:
In Homo sapiens, CD172a+ pre-conventional dendritic cells show higher expression of ETS2, ZEB2, and IRF4 compared to CD172a− pre-conventional dendritic cells.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:90d5b21dd6ddee075357
claim_id: claim:90d5b21dd6ddee075357
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
The dNK4 subset is positive for expression of FCGR3A / CD16 , which was uniquely accumulated in the decidual tissues from RM patients.

summary:
In Homo sapiens, the decidual natural killer cell 4 subset is positive for expression of FCGR3A/CD16.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:5081588671942babe28a
claim_id: claim:5081588671942babe28a
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
dNKp cells highly expressed MCM5 , STMN1 , and PCNA , indicating their manifest proliferative capacity.

summary:
In Homo sapiens, decidual natural killer proliferative cells highly express MCM5, STMN1, and PCNA, indicating their proliferative capacity.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:511a6c0036a13103a772
claim_id: claim:511a6c0036a13103a772
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
summary: In Homo sapiens, decidual natural killer cell 1 strongly expresses ENTPD1/CD39, CSF1, and KIR2DL1.
span_literal:
dNK1 cells strongly expressed ENTPD1 / CD39 , CSF1 , and KIR2DL1 , and showed active oxidative phosphorylation and glycolysis activities.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:c4a4ff8b3c8c13312b44
claim_id: claim:c4a4ff8b3c8c13312b44
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal: The defining markers for dNK2 cells included XCL1 , XCL2 , and ZNF683 .
summary:
In Homo sapiens, the defining markers for decidual natural killer cell 2 include XCL1, XCL2, and ZNF683.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:e6c1cf73ed07ea58ed66
claim_id: claim:e6c1cf73ed07ea58ed66
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
summary: In Homo sapiens, decidual natural killer cell 3 is defined by ITGAE/CD103, CD160, and KLRB1.
span_literal:
dNK3 cells were defined by ITGAE/ CD103 , CD160 , and KLRB1 , and exhibited certain cytotoxic and immune-activated property.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:b289719c170da6473ae3
claim_id: claim:b289719c170da6473ae3
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
FCGR3A/CD16 , and PLAC8 were enriched in dNK4 cells, which indicates an active cytotoxicity status of these cells.

summary:
In Homo sapiens, FCGR3A/CD16 and PLAC8 are enriched in decidual natural killer cell 4, indicating an active cytotoxicity status.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:ba9a1af31be537e354a8
claim_id: claim:ba9a1af31be537e354a8
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
We found that dNK1 cells expressed high level of KIR2DL3 and KIR2DL1 , which encode inhibitory killer cell immunoglobulin like receptor (KIR) for HLA-C, and LILRB1 , which encodes the high-affinity receptor for HLA-G.

summary:
In Homo sapiens, decidual natural killer cell 1 expresses high levels of KIR2DL3, KIR2DL1, and LILRB1.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:3177ef99b48f8909550c
claim_id: claim:3177ef99b48f8909550c
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
Interestingly, high levels of LILRB1 , KLRC2 / NKG2C , and KLRC3 / NKG2E were observed in dNK4 cells

summary:
In Homo sapiens, high levels of LILRB1, KLRC2/NKG2C, and KLRC3/NKG2E are observed in decidual natural killer cell 4.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:37834a5b19e739f52947
claim_id: claim:37834a5b19e739f52947
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
dNK1 cells emerged at the early developmental stage with high expression of classical transcription factor gene EOMES that marks immature NK cells.

summary:
In Homo sapiens, decidual natural killer cell 1 has high expression of the transcription factor gene EOMES, which marks immature natural killer cells.


claim_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535:claim:2e214474bcaa3f060734
claim_id: claim:2e214474bcaa3f060734
paper_key: hca:0361_10.1016_j.gpb.2020.11.002_84c7c58535
span_literal:
apart from dNK4 cells, the other four dNK subsets co-expressed the tissue-resident markers ITGA1 / CD49A , indicating their uterine resident feature.

summary:
In Homo sapiens, decidual natural killer cell 4 does not express the tissue-resident marker ITGA1/CD49A, unlike the other four decidual natural killer cell subsets.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:5c8ac7668d35c0de9383
claim_id: claim:5c8ac7668d35c0de9383
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal:
MKI67 expression identified CCR10 hi CD4 + T cells as the major subset with a proliferative gene signature (Cluster 1, Fig. 4c , d ).

summary:
In Homo sapiens, CCR10-high CD4-positive T cells are marked by MKI67 expression, identifying them as the major subset with a proliferative gene signature.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:6ec2077c537df9477bad
claim_id: claim:6ec2077c537df9477bad
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal:
Unsupervised analysis revealed PBMC T cell subclusters with high nDEGs, which were characterized by high expression of CCR4 and CCR10, which function as skin-homing chemokine receptors 13 , 14 , and low expression of CCR7 , which enables migration of circulating T cells 15 , 16 ( Fig. 2c , Extended Data Fig. 2d ).

summary:
In Homo sapiens, peripheral blood mononuclear cell T cell subclusters with high numbers of differentially expressed genes were characterized by high expression of CCR4 and CCR10 and low expression of CCR7.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:4d98fe003d72c0c629b2
claim_id: claim:4d98fe003d72c0c629b2
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal:
We found enrichment of pathways regarding lymphocyte activation and cytokine signaling, which were in part driven by the upregulation IL2RG , JAK3 and STAT1 ( Fig. 1e , f ; Supplementary Table 1 ).

summary:
In Homo sapiens, skin-infiltrating lymphocytes in drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms showed upregulation of IL2RG, JAK3, and STAT1.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:b16dfd86a3a1d380ae68
claim_id: claim:b16dfd86a3a1d380ae68
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal:
Also upregulated were genes involved in cell proliferation, such as MIK67 , and migration, such as CCR10 ( Fig. 1e , f ), whereas transcripts for potentially targetable cytokines were undetected.

summary:
In Homo sapiens, skin-infiltrating lymphocytes in drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms showed upregulation of MKI67 and CCR10.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:b9e2dea38abb6e0d90da
claim_id: claim:b9e2dea38abb6e0d90da
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal:
Furthermore, this CD4 + T cell cluster exhibited increased STAT1 and other genes downstream of the JAK-STAT signaling pathway including CISH and SOCS3 29 , suggesting SMX/TMP-induced activation of the pathway in this cluster ( Extended Data Fig. 4b , c ).

summary:
In Homo sapiens, the CCR10-high CD4-positive T cell cluster exhibited increased expression of STAT1, CISH, and SOCS3 upon sulfamethoxazole/trimethoprim stimulation.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:2e64ce32b58569a90642
claim_id: claim:2e64ce32b58569a90642
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal: IL13 , a potentially targetable cytokine 30 – 32 , was also upregulated ( Extended Data Fig. 4c ).
summary:
In Homo sapiens, IL13 was upregulated in the CCR10-high CD4-positive T cell cluster upon sulfamethoxazole/trimethoprim stimulation.


claim_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b:claim:8f926fa9854df4b55f21
claim_id: claim:8f926fa9854df4b55f21
paper_key: hca:0362_10.1038_s41591-019-0733-7_d499f1b21b
span_literal:
SMX/TMP triggered the upregulation of CCL17 and CCL22 , ligands for CCR4, as well as genes encoding MHC class II (MHC II) in monocytes, suggesting that T cell recruitment and subsequent antigen presentation is mediated by monocytes upon exposure to the culprit drug ( Extended Data Fig. 4d , e ).

summary:
In Homo sapiens, monocytes showed upregulation of CCL17 and CCL22 upon sulfamethoxazole/trimethoprim stimulation.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:65dc82b6e359e21c7732
claim_id: claim:65dc82b6e359e21c7732
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
Cells in cluster 0, 1, 3, and 8 cells expressed high levels of EPCAM, CDH1, and CDKN2A and were classified as epithelial/cancer cells.

summary:
In Homo sapiens cervical cancer, epithelial/cancer cells express high levels of EPCAM, CDH1, and CDKN2A.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:b171164c4b95cd693308
claim_id: claim:b171164c4b95cd693308
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal: Cluster 4 had a high level of EGFL7, EMCN, and PECAM1 and was identified as an EC cluster
summary:
In Homo sapiens cervical cancer, endothelial cells are identified by high expression of EGFL7, EMCN, and PECAM1.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:38cb9b042517daf367db
claim_id: claim:38cb9b042517daf367db
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
Clusters 2 and 6 were assigned as smooth muscle cells, as distinguished by selective expression of ACTG2.

summary:
In Homo sapiens cervical cancer, smooth muscle cells are distinguished by selective expression of ACTG2.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:b53edfa065e3f25ac7a4
claim_id: claim:b53edfa065e3f25ac7a4
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
In view of the high expression level of SUSD2, cells in clusters 5, 9, and 12 were assigned as endometrial stromal cells.

summary:
In Homo sapiens cervical cancer, endometrial stromal cells are assigned based on high expression of SUSD2.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:3b768952567c67321f62
claim_id: claim:3b768952567c67321f62
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
We next explored epithelial/cancer cells and mutual expression patterns of their marker genes (EPCAM, TP63, CDH1, and CDKN2A).

summary:
In Homo sapiens cervical cancer, epithelial/cancer cells are marked by EPCAM, TP63, CDH1, and CDKN2A.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:9f42cb201e74f7e29c68
claim_id: claim:9f42cb201e74f7e29c68
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
We found that proliferation-related genes, such as MKI67 (KI67 gene), CCNB1, and TOP2A, were enriched in cluster 3

summary:
In Homo sapiens cervical cancer, tumor cell cluster 3 is enriched for the proliferation-related genes MKI67, CCNB1, and TOP2A.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:0252a6f3995bd8e84b78
claim_id: claim:0252a6f3995bd8e84b78
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal: Cluster 1 showed a high level of CEACAM6, CD55, and GJB6.
summary:
In Homo sapiens cervical cancer, tumor cell cluster 1 shows high expression of CEACAM6, CD55, and GJB6.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:97d5b096d61f3ee461b6
claim_id: claim:97d5b096d61f3ee461b6
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
We found that cells in cluster 0 presented high levels of DEFB1, KRT5, CXCL10, WARS, LY6D, CRABP2, CXCL9, PHOV, C10orf99, and PYCARD and were enriched in a variety of features and metabolism-related signaling pathways, such as steroid biosynthesis, mismatch repair, and peroxisome

summary:
In Homo sapiens cervical cancer, tumor cell cluster 0 presents high levels of DEFB1, KRT5, CXCL10, WARS, LY6D, CRABP2, CXCL9, PHOV, C10orf99, and PYCARD.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:71bf1ca54cbd4e119aab
claim_id: claim:71bf1ca54cbd4e119aab
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
However, the cells in cluster 8 presented high expression of stem-related genes such as SOX2 and ALDHA1, and we presumed them to be the origin of cancer cells during tumor progression

summary:
In Homo sapiens cervical cancer, tumor cell cluster 8 (cancer stem cells) presents high expression of the stem-related genes SOX2 and ALDH1A1.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:8371829fa46d7463b731
claim_id: claim:8371829fa46d7463b731
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal: The CSC marker genes ALDH1A1 and SOX2 were significantly higher in cluster 8
summary:
In Homo sapiens cervical cancer, cancer stem cell marker genes ALDH1A1 and SOX2 are significantly higher in cluster 8 (cancer stem cells).


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:c1fff6e73654aa67456f
claim_id: claim:c1fff6e73654aa67456f
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
We found that SOX2 and ALDH1A1 presented a higher expression level in subcluster 1 than in other subclusters

summary:
In Homo sapiens cervical cancer, cancer stem cell subcluster 1 presents higher expression of SOX2 and ALDH1A1 than other subclusters.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:65c0387e392bbeb01fe1
claim_id: claim:65c0387e392bbeb01fe1
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
Further analysis revealed that arterial markers ELN and EGR1 were the most abundant in subclusters 0 and 6, while venous marker genes LRG1 and ICAM1 were identified in subclusters 1, 4, and 5

summary:
In Homo sapiens cervical cancer, arterial endothelial cells (subclusters 0 and 6) are marked by ELN and EGR1, while venous endothelial cells (subclusters 1, 4, and 5) are marked by LRG1 and ICAM1.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:666005e5e0edd02a0c55
claim_id: claim:666005e5e0edd02a0c55
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
Further analysis revealed that arterial markers ELN and EGR1 were the most abundant in subclusters 0 and 6, while venous marker genes LRG1 and ICAM1 were identified in subclusters 1, 4, and 5

summary:
In Homo sapiens cervical cancer, venous endothelial cells (subclusters 1, 4, and 5) are marked by LRG1 and ICAM1.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:4abedb53b7862ca70d35
claim_id: claim:4abedb53b7862ca70d35
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
Arteriolar ECs expressed both arterial and capillary markers (IGFBP3 and ARL15), which was consistent with their topographical location across the vascular tree (in between arteries and capillaries).

summary:
In Homo sapiens cervical cancer, arteriolar endothelial cells (capillary-arterial endothelial cells) express both arterial and capillary markers IGFBP3 and ARL15.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:146751ff5e7f158f30c4
claim_id: claim:146751ff5e7f158f30c4
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal: venular ECs express venous and capillary markers (EMCN and FOS
summary:
In Homo sapiens cervical cancer, venular endothelial cells (capillary-venous endothelial cells) express venous and capillary markers EMCN and FOS.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:ea751cae5654373eb695
claim_id: claim:ea751cae5654373eb695
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal: ABCB1 and ABCG2 were especially expressed in cluster 4, with higher level in TECs than in NECs
summary:
In Homo sapiens cervical cancer, ABCB1 and ABCG2 are especially expressed in the endothelial cell cluster, with higher levels in tumor-derived endothelial cells than in normal endothelial cells.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:aa53766c9b7f542f895a
claim_id: claim:aa53766c9b7f542f895a
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
we identified a cluster of cervical CSCs, which had outstanding levels of stem-related markers SOX2 and ALDH1A1.

summary:
In Homo sapiens cervical cancer, cervical cancer stem cells have outstanding levels of the stem-related markers SOX2 and ALDH1A1.


claim_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24:claim:b1b405fdb2d262ff4c04
claim_id: claim:b1b405fdb2d262ff4c04
paper_key: hca:0363_10.1016_j.omtn.2021.03.017_8083e53d24
span_literal:
In addition, several transcription factors, including TAGLN2, KLF5, STAT1, and STAT2, may be efficient markers for CC ECs, which have important diagnostic value and clinical significance for CC patients.

summary:
In Homo sapiens cervical cancer, TAGLN2, KLF5, STAT1, and STAT2 may be efficient markers for cervical cancer endothelial cells.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:1f595fabba763606a6b6
claim_id: claim:1f595fabba763606a6b6
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
The Contractile SMC cluster highly expressed contraction-related genes such as ACTC1 , ACTA2 , and MYL9 and the noncoding RNA CARMN

summary:
In Homo sapiens, contractile smooth muscle cells highly express contraction-related genes ACTC1, ACTA2, MYL9, and the noncoding RNA CARMN in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:f2ed0d3d158a83d63911
claim_id: claim:f2ed0d3d158a83d63911
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
However, Stressed SMC also expressed stress response genes, such as FOS , ATF3 , JUN , and HSPB8 , 12 suggesting activation of the stress response in this type of SMC

summary:
In Homo sapiens, stressed smooth muscle cells express stress response genes FOS, ATF3, JUN, and HSPB8 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:a204392752f9829bfff5
claim_id: claim:a204392752f9829bfff5
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Interestingly, the Proliferating SMC cluster highly expressed synthetic SMC marker genes MGP , TPM4 , and MYH10 13 , 14

summary:
In Homo sapiens, proliferating smooth muscle cells highly express synthetic smooth muscle cell marker genes MGP, TPM4, and MYH10 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:15d9c410b9e7e1f83d98
claim_id: claim:15d9c410b9e7e1f83d98
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
The Fibromyocyte cluster expressed contractile genes, such as ACTA2 and MYL9 , and ECM genes, such as COL1A2 and COL8A1

summary:
In Homo sapiens, fibromyocytes express contractile genes ACTA2 and MYL9 and extracellular matrix genes COL1A2 and COL8A1 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:f921a63c47c90239a04b
claim_id: claim:f921a63c47c90239a04b
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
We identified two types of fibroblasts (i.e., clusters Fibroblast1 and Fibroblast2) that highly expressed collagen and proteoglycan genes, such as COL1A2 , 16 DCN , 17 LUM , and CLU

summary:
In Homo sapiens, fibroblast 1 and fibroblast 2 highly express collagen and proteoglycan genes COL1A2, DCN, LUM, and CLU in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:e156a829e2aa80211452
claim_id: claim:e156a829e2aa80211452
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
We identified two types of fibroblasts (i.e., clusters Fibroblast1 and Fibroblast2) that highly expressed collagen and proteoglycan genes, such as COL1A2 , 16 DCN , 17 LUM , and CLU

summary:
In Homo sapiens, fibroblast 2 highly expresses collagen and proteoglycan genes COL1A2, DCN, LUM, and CLU in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:2a247da4f42c63547611
claim_id: claim:2a247da4f42c63547611
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
We identified two types of MSCs (i.e., clusters MSC1 and MSC2), which are sometimes referred to as pericytes, 18 that expressed the MSC marker genes CSPG4 (NG2), PDGFRB , and THY1 (CD90) 19 , 20

summary:
In Homo sapiens, mesenchymal stem cell 1 and mesenchymal stem cell 2 express the mesenchymal stem cell marker genes CSPG4, PDGFRB, and THY1 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:e35304fc76f4b77809b4
claim_id: claim:e35304fc76f4b77809b4
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
We identified two types of MSCs (i.e., clusters MSC1 and MSC2), which are sometimes referred to as pericytes, 18 that expressed the MSC marker genes CSPG4 (NG2), PDGFRB , and THY1 (CD90) 19 , 20

summary:
In Homo sapiens, mesenchymal stem cell 2 expresses the mesenchymal stem cell marker genes CSPG4, PDGFRB, and THY1 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:010fc36aaeefec02b48d
claim_id: claim:010fc36aaeefec02b48d
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: Inflammatory1 showed a T lymphocyte–like gene expression profile (such as CXCR4 and CCL4 )
summary:
In Homo sapiens, Inflammatory1 nonimmune cells express T lymphocyte-like genes CXCR4 and CCL4 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:e722307d83ac18e8183a
claim_id: claim:e722307d83ac18e8183a
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: Inflammatory2 expressed several macrophage-specific genes, such as C1QA and C1QB 21
summary:
In Homo sapiens, Inflammatory2 nonimmune cells express macrophage-specific genes C1QA and C1QB in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:b3f3ee70035f922aaa77
claim_id: claim:b3f3ee70035f922aaa77
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: Inflammatory3 expressed interferon-induced genes such as IFIT1 and IFI6
summary:
In Homo sapiens, Inflammatory3 nonimmune cells express interferon-induced genes IFIT1 and IFI6 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:cba7dcf4ab9c639c268a
claim_id: claim:cba7dcf4ab9c639c268a
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
We identified two clusters of endothelial cells (i.e., EC1 and EC2) that expressed endothelial marker genes VWF , PECAM1 , 17 and IFI27

summary:
In Homo sapiens, endothelial cell 1 and endothelial cell 2 express endothelial marker genes VWF, PECAM1, and IFI27 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:0cfa55b3012dfb2ce670
claim_id: claim:0cfa55b3012dfb2ce670
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
We identified two clusters of endothelial cells (i.e., EC1 and EC2) that expressed endothelial marker genes VWF , PECAM1 , 17 and IFI27

summary:
In Homo sapiens, endothelial cell 2 expresses endothelial marker genes VWF, PECAM1, and IFI27 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:4f7669f2d19c568ccd70
claim_id: claim:4f7669f2d19c568ccd70
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Expression analysis of well-defined M1 and M2 marker genes in each cluster demonstrated that M1 marker genes TNF , IL1B , and NFKB1 23 , 24 were highly expressed in 2 of 3 M1-like clusters, whereas M2 marker genes MERTK , MRC1 , STAB1 , and CD163 23 , 24 were highly expressed in all M2-like clusters

summary:
In Homo sapiens, M1-like macrophage clusters highly express M1 marker genes TNF, IL1B, and NFKB1, whereas M2-like macrophage clusters highly express M2 marker genes MERTK, MRC1, STAB1, and CD163 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:0f626f138ed8873c958f
claim_id: claim:0f626f138ed8873c958f
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Expression analysis of well-defined M1 and M2 marker genes in each cluster demonstrated that M1 marker genes TNF , IL1B , and NFKB1 23 , 24 were highly expressed in 2 of 3 M1-like clusters, whereas M2 marker genes MERTK , MRC1 , STAB1 , and CD163 23 , 24 were highly expressed in all M2-like clusters

summary:
In Homo sapiens, M2-like macrophage clusters highly express M2 marker genes MERTK, MRC1, STAB1, and CD163 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:890311072627b5a0ddee
claim_id: claim:890311072627b5a0ddee
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: The M1like1 cluster expressed several cytokine genes, including CCL3L1 , CCL4L2 , CCL4 , and TNF
summary:
In Homo sapiens, M1-like macrophage 1 expresses cytokine genes CCL3L1, CCL4L2, CCL4, and TNF in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:6137615442c059fc0d3b
claim_id: claim:6137615442c059fc0d3b
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
In addition to expressing M1 marker genes, M1like2 cells expressed epidermal growth factor–encoding genes EREG and AREG , metalloproteinase inhibitor–encoding gene TIMP1 , and chondroitin sulfate proteoglycan–encoding gene VCAN

summary:
In Homo sapiens, M1-like macrophage 2 expresses epidermal growth factor-encoding genes EREG and AREG, metalloproteinase inhibitor-encoding gene TIMP1, and chondroitin sulfate proteoglycan-encoding gene VCAN in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:1d1bd8ab5433668d4a6b
claim_id: claim:1d1bd8ab5433668d4a6b
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: The M1like3 cluster expressed transcription factor–encoding genes such as ETS1 and RUNX3
summary:
In Homo sapiens, M1-like macrophage 3 expresses transcription factor-encoding genes ETS1 and RUNX3 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:fb8ab0afda48cc68eaef
claim_id: claim:fb8ab0afda48cc68eaef
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: The M2like1 cluster expressed PDK4 , STAB1 , TXNIP , and MAF
summary:
In Homo sapiens, M2-like macrophage 1 expresses PDK4, STAB1, TXNIP, and MAF in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:4c869aadfd4aed66f2ba
claim_id: claim:4c869aadfd4aed66f2ba
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Conserved genes in M2like2 included C1QA , C1QB , C1QC , and RAB13 , which were mostly also expressed in M2like1

summary:
In Homo sapiens, M2-like macrophage 2 expresses conserved genes C1QA, C1QB, C1QC, and RAB13 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:3dc87ec9deb591de2189
claim_id: claim:3dc87ec9deb591de2189
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
The M_IFNresponse cluster expressed many interferon-induced genes including IFI44L , ISG15 , IFIT1 , and IFITM3

summary:
In Homo sapiens, interferon response macrophages express interferon-induced genes IFI44L, ISG15, IFIT1, and IFITM3 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:72eeb28df6e15d18bfe5
claim_id: claim:72eeb28df6e15d18bfe5
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
The M_remodeling cluster expressed several SMC or fibroblast genes including IGFBP7 , ADIRF , DSTN , TPM2 , MGP , and MYL9

summary:
In Homo sapiens, remodeling macrophages express smooth muscle cell or fibroblast genes IGFBP7, ADIRF, DSTN, TPM2, MGP, and MYL9 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:249dffea9b1bdca3b3d7
claim_id: claim:249dffea9b1bdca3b3d7
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: Active CD4 T lymphocytes (CD4_active) expressed CREM , CXCR6 , RGCC , MR3C1 , and GZMB
summary:
In Homo sapiens, active CD4 T lymphocytes express CREM, CXCR6, RGCC, MR3C1, and GZMB in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:c197a68bd8efcab28153
claim_id: claim:c197a68bd8efcab28153
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Resting CD4 T (CD4_EM_rest [effector memory rest CD4 T lymphocyte]) cells expressed CCR7 , IL7R , CCL20 , and KLRB1

summary:
In Homo sapiens, effector memory resting CD4 T lymphocytes express CCR7, IL7R, CCL20, and KLRB1 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:1982966c99bcc2e01cae
claim_id: claim:1982966c99bcc2e01cae
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Regulatory CD4 T lymphocytes (CD4_Treg) expressed Treg-defining genes IL2RA and CTLA4 , as well as TNFRSF18 , ID3 , and LTB

summary:
In Homo sapiens, regulatory CD4 T lymphocytes express regulatory T cell-defining genes IL2RA and CTLA4, as well as TNFRSF18, ID3, and LTB in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:d7c9d966c1aea5ee1c94
claim_id: claim:d7c9d966c1aea5ee1c94
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
Active CD8 T lymphocytes (CD8_active) expressed cytotoxicity-associated genes GZMK and CRTAM , inflammatory gene CCL4 , as well as CMC1

summary:
In Homo sapiens, active CD8 T lymphocytes express cytotoxicity-associated genes GZMK and CRTAM, inflammatory gene CCL4, and CMC1 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:d7d739765595b9e5be5f
claim_id: claim:d7d739765595b9e5be5f
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
CD8 terminally differentiated effector T lymphocytes (CD8_TEMRA) expressed cytotoxic genes GNLY , KLRD1 , and PRF1 , as well as CCL5 and HOPX

summary:
In Homo sapiens, CD8 terminally differentiated effector T lymphocytes express cytotoxic genes GNLY, KLRD1, and PRF1, as well as CCL5 and HOPX in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:88eb14bc619e86e514cb
claim_id: claim:88eb14bc619e86e514cb
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
T_GIMAP cells expressed GTPase of the immunity associated protein family genes, including GIMAP1 , GIMAP4 , and GIMAP7 , and lncRNA MALAT1

summary:
In Homo sapiens, T_GIMAP lymphocytes express GTPase of the immunity-associated protein family genes GIMAP1, GIMAP4, and GIMAP7, and long non-coding RNA MALAT1 in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:ff598341685373deebb0
claim_id: claim:ff598341685373deebb0
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal:
The T_proliferation cluster expressed microtubule-related genes TUBA1B and STMN1 , chromatin-associated non-histone protein genes HMGB1 and HMGN2 , and CKS1B , encoding cyclin-dependent kinases regulatory subunit 1

summary:
In Homo sapiens, proliferating T lymphocytes express microtubule-related genes TUBA1B and STMN1, chromatin-associated non-histone protein genes HMGB1 and HMGN2, and CKS1B in the ascending aortic wall.


claim_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c:claim:f66859ce778c11466a58
claim_id: claim:f66859ce778c11466a58
paper_key: hca:0364_10.1161_circulationaha.120.046528_00aa2deb4c
span_literal: T_switched cells expressed the contraction--related genes TAGLN , MYH11 , and TPM1
summary:
In Homo sapiens, T_switched lymphocytes express contraction-related genes TAGLN, MYH11, and TPM1 in the ascending aortic wall.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:3253a7b2543cda035f89
claim_id: claim:3253a7b2543cda035f89
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
summary: In Homo sapiens corpus cavernosum, endothelial cells are marked by VWF, PODXL, EMCN, and PECAM1.
span_literal:
Major cell type was annotated with selected marker gene listed: ECs ( VWF , PODXL, EMCN , PECAM1 ), SMCs ( ACTA2 , TAGLN , MYH11 ), fibroblasts ( DCN , LUM , COL1A2 , PDGFRA , IGF1 ), T cells ( CD2 , CD3D/E/G ), neutrophils ( S100A8/9 ), macrophages ( CD163 , C1QA , C1QB , C1QC ), monocytes ( CD14 , FCGR3A ), natural killer cells ( NKG7 , GZMA ), neural cells ( SOX10 , PLP1 ), mast cells ( TPSB2 , TPSAB1 ), B cells ( CD79A , IGHM , MZB1 ).


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:f1bd46723a7c4b227077
claim_id: claim:f1bd46723a7c4b227077
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal:
Major cell type was annotated with selected marker gene listed: ECs ( VWF , PODXL, EMCN , PECAM1 ), SMCs ( ACTA2 , TAGLN , MYH11 ), fibroblasts ( DCN , LUM , COL1A2 , PDGFRA , IGF1 ), T cells ( CD2 , CD3D/E/G ), neutrophils ( S100A8/9 ), macrophages ( CD163 , C1QA , C1QB , C1QC ), monocytes ( CD14 , FCGR3A ), natural killer cells ( NKG7 , GZMA ), neural cells ( SOX10 , PLP1 ), mast cells ( TPSB2 , TPSAB1 ), B cells ( CD79A , IGHM , MZB1 ).

summary:
In Homo sapiens corpus cavernosum, fibroblasts are marked by DCN, LUM, COL1A2, PDGFRA, and insulin-like growth factor 1 (IGF1).


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:f3709189ac7e422a71c8
claim_id: claim:f3709189ac7e422a71c8
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal: Pan-endothelial markers ( PECAM1 , CDH5 , TIE1 ) were expressed in all populations of ECs.
summary:
In Homo sapiens corpus cavernosum, pan-endothelial markers PECAM1, CDH5, and TIE1 are expressed in all endothelial cell populations.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:940fd24a1b6fd36c24f2
claim_id: claim:940fd24a1b6fd36c24f2
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal:
A number of factors that are indispensable for arterial differentiation showed an abundant expression level in ECs III (e.g. SOX17 , HEY1 , SEMA3G ).

summary:
In Homo sapiens corpus cavernosum, endothelial cell type 3 shows abundant expression of SOX17, HEY1, and SEMA3G, which are factors for arterial differentiation.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:db2df2d43d2bbeee3c53
claim_id: claim:db2df2d43d2bbeee3c53
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal:
In particular, the expression levels of arteriole markers ( HEY1 , SERPINE2 , SEMA3G , GJA5 ) were exclusively enriched in the endothelial sC5 and similar to the transcriptome profile of ECs III (C13).

summary:
In Homo sapiens corpus cavernosum, arteriole markers HEY1, SERPINE2, SEMA3G, and GJA5 are exclusively enriched in endothelial subcluster 5.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:2b489460b11d3e5ed562
claim_id: claim:2b489460b11d3e5ed562
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal:
Interestingly, our results showed a strong enrichment of canonical fibroblast-specific markers ( DCN , LUM , IGF1 ) in the endothelial sC6 ( Figure 2E ) .

summary:
In Homo sapiens corpus cavernosum, canonical fibroblast-specific markers DCN, LUM, and insulin-like growth factor 1 (IGF1) are strongly enriched in endothelial subcluster 6.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:053937f02704e621240b
claim_id: claim:053937f02704e621240b
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal: The SMCs in the sC5 displayed high levels of cell type-specific markers ( ACTA2 , TAGLN , MYH11 ).
summary:
In Homo sapiens corpus cavernosum, smooth muscle cells in subcluster 5 display high levels of cell type-specific markers ACTA2, TAGLN, and MYH11.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:c81878b45f95c4c8408b
claim_id: claim:c81878b45f95c4c8408b
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal:
In comparison with the other subclusters, endothelial signature genes ( EMCN, VWF , and PECAM1 ) were strongly enriched in a subset of fibroblasts (sC9) ( Figure 3C ) .

summary:
In Homo sapiens corpus cavernosum, endothelial signature genes EMCN, VWF, and PECAM1 are strongly enriched in fibroblast subcluster 9.


claim_key: hca:0365_10.3389_fendo.2022.874915_81de77d539:claim:9622f569c58a239178c0
claim_id: claim:9622f569c58a239178c0
paper_key: hca:0365_10.3389_fendo.2022.874915_81de77d539
span_literal:
Co-expression of PECAM1 , VWF , and EMCN in one subpopulation suggests differentiation into ECs-like fibroblasts from part of SMCs via a distinct cell fate.

summary:
In Homo sapiens corpus cavernosum, co-expression of PECAM1, VWF, and EMCN in one subpopulation suggests differentiation into endothelial cell-like fibroblasts from part of smooth muscle cells.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:83e400ac00b0da5b52ab
claim_id: claim:83e400ac00b0da5b52ab
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Among the CD8 + clusters, cluster 6 expressed genes indicating a canonical effector phenotype, including KLRG1

summary:
In Homo sapiens, intraepithelial CD8-positive T cells of cluster 6 express KLRG1, indicating a canonical effector phenotype.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:7fbd1a087dceb31ff995
claim_id: claim:7fbd1a087dceb31ff995
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 6 also expressed high level of KLF2 (Supplementary Fig. 2c ), a transcription factor that promotes lymphocytes circulation

summary:
In Homo sapiens, intraepithelial CD8-positive effector T cell cluster 6 expresses high levels of KLF2, a transcription factor that promotes lymphocyte circulation.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:5ac64301feca76b1cd01
claim_id: claim:5ac64301feca76b1cd01
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
In contrast, cluster 1 and cluster 0 shared expression of ITGAE , the receptor for E-cadherin, which is indicative of tissue residency 16 , and CD160 , a receptor for HVEM expressed on epithelial cells 17

summary:
In Homo sapiens, intraepithelial tissue-resident CD8-positive T cell clusters 0 and 1 express ITGAE and CD160, indicative of tissue residency.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:08d8451203173bf5e704
claim_id: claim:08d8451203173bf5e704
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Expression of ENTPD1 , which encodes the activation marker CD39, distinguished cluster 1 from cluster 0

summary:
In Homo sapiens, intraepithelial tissue-resident CD8-positive T cell cluster 1 is distinguished from cluster 0 by expression of ENTPD1, which encodes the activation marker CD39.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:d3d200ccc0aa99f76c4e
claim_id: claim:d3d200ccc0aa99f76c4e
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Within CD4 + cells, clusters 2 and 4 showed a T H 17 transcriptional profile, featuring RORC, CCR6 (Fig. 1d ), RORA, LTB, CCL20 , and KLRB1

summary:
In Homo sapiens, intraepithelial T helper 17 cells (clusters 2 and 4) show a transcriptional profile featuring RORC, CCR6, RORA, LTB, CCL20, and KLRB1.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:178180db2c7ebdc7a700
claim_id: claim:178180db2c7ebdc7a700
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Both subsets expressed CD40LG (Supplementary Fig. 2b ), which sustains T H 17 differentiation in vitro and in vivo

summary:
In Homo sapiens, both T helper 17 cell subsets express CD40LG, which sustains T helper 17 differentiation.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:8180e498b7fea1de3f82
claim_id: claim:8180e498b7fea1de3f82
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cells in cluster 3 corresponded to naïve CD4 + T cells expressing CCR7 (Fig. 1d ) , SELL, TCF7 , LEF1 , as well as KLF2

summary:
In Homo sapiens, intraepithelial naïve CD4-positive T cells (cluster 3) express CCR7, SELL, TCF7, LEF1, and KLF2.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:7f75a72133208fc56aa5
claim_id: claim:7f75a72133208fc56aa5
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
The left portion of cluster 5 expressed CXCL13 (Fig. 1d ), BCL6 and CXCR5 (Supplementary Fig. 2b, c ), pointing to a T FH phenotype.

summary:
In Homo sapiens, the T follicular helper cell portion of cluster 5 expresses CXCL13, BCL6, and CXCR5, pointing to a T follicular helper cell phenotype.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:61bfa943a43181392a9d
claim_id: claim:61bfa943a43181392a9d
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
The right portion of cluster 5 expressed the Treg markers FOXP3 , IL2RA , ENTPD1 (Fig. 1d ), CTLA4 , and IL10

summary:
In Homo sapiens, the regulatory T cell portion of cluster 5 expresses the markers FOXP3, IL2RA, ENTPD1, CTLA4, and IL10.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:fe6338f6682e3b12ab66
claim_id: claim:fe6338f6682e3b12ab66
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
In addition, the Treg side of cluster 5 expressed PRDM1 (Supplementary Fig. 2b ), which facilitates Treg over T FH differentiation

summary:
In Homo sapiens, the regulatory T cell side of cluster 5 expresses PRDM1, which facilitates regulatory T cell over T follicular helper cell differentiation.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:e459e370fb04e9058f62
claim_id: claim:e459e370fb04e9058f62
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 8 uniquely expressed BTLA (Fig. 1d ) and CD200 (Supplementary Fig. 2b ), which are markers of terminal T FH differentiation

summary:
In Homo sapiens, cluster 8 uniquely expresses BTLA and CD200, which are markers of terminal T follicular helper cell differentiation.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:8c23f469a6b655eabcab
claim_id: claim:8c23f469a6b655eabcab
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 0–1 0 corresponded to γδ T cells, as indicated by the expression of transcripts for γδTCR ( TRDC and TRGC1 ), as well as the transcription factors ID3 23 and HOPX

summary:
In Homo sapiens, intraepithelial gamma delta T cells (cluster 0-1 0) are indicated by expression of TRDC, TRGC1, ID3, and HOPX.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:696ba12eca8eb140e896
claim_id: claim:696ba12eca8eb140e896
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal: These γδ T cells selectively expressed the signaling adapter SH2D1B as well as PDGFD and CSF1
summary:
In Homo sapiens, intraepithelial gamma delta T cells selectively express the signaling adapter SH2D1B as well as PDGFD and CSF1.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:4a1dc5a8da4814fc4cd9
claim_id: claim:4a1dc5a8da4814fc4cd9
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 0–1 3 encompassed a CD8 + T cell subset that stood out for production of IFN-γ ( IFNG ), granzyme B ( GZMB ), and expression of the NK cell inhibitory receptor KLRC1

summary:
In Homo sapiens, intraepithelial CD8-positive T cell cluster 0-1 3 is marked by expression of IFNG, GZMB, and the NK cell inhibitory receptor KLRC1.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:cbbe2136cd0c155e07ca
claim_id: claim:cbbe2136cd0c155e07ca
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 0–1 1 expressed IL7R , IL2 , and TCF7 (Fig. 4b and Supplementary Fig. 4a ), which are indicative of long-lived and memory-like properties 24 , 25 , as well as lymphotoxin B ( LTB ), and the DC attracting chemokines XCL1 and XCL2

summary:
In Homo sapiens, intraepithelial tissue-resident CD8-positive T cell cluster 0-1 1 expresses IL7R, IL2, TCF7, LTB, XCL1, and XCL2, indicative of long-lived and memory-like properties.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:44d348324c79df48354b
claim_id: claim:44d348324c79df48354b
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 0–1 2 expressed the master transcription factor for tissue residency ZNF683 27 , and markers of cytotoxicity, such as GZMB , PRF1 , and TNFSF10

summary:
In Homo sapiens, intraepithelial tissue-resident CD8-positive T cell cluster 0-1 2 expresses the master transcription factor for tissue residency ZNF683 and cytotoxicity markers GZMB, PRF1, and TNFSF10.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:6f61b5750973731a67ec
claim_id: claim:6f61b5750973731a67ec
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
As opposed to clusters 0–1 0 and 0–1 3 , this cluster did not exhibit CD39 or NK cell receptors but expressed the epithelial membrane protein 3 ( EMP3 )

summary:
In Homo sapiens, tissue-resident CD8-positive T cell cluster 0-1 2 does not exhibit ENTPD1 (CD39) but expresses epithelial membrane protein 3 (EMP3).


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:1390bac9b9ae51ff3553
claim_id: claim:1390bac9b9ae51ff3553
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
The small cluster 0–1 4 contained CD8 + T cells marked by CD40LG and a network of p53 regulators, such as EIF5A, MDM4 , and SET

summary:
In Homo sapiens, intraepithelial CD8-positive T cell cluster 0-1 4 is marked by CD40LG and p53 regulators EIF5A, MDM4, and SET.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:21e1eb1084b95d758812
claim_id: claim:21e1eb1084b95d758812
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Clusters 5–8 1 and 5–8 4 represented two distinct clusters of T FH , both of which expressed the chemokine CXCL13 and the T FH master transcription factor BCL6

summary:
In Homo sapiens, T follicular helper cell clusters 5-8 1 and 5-8 4 both express the chemokine CXCL13 and the master transcription factor BCL6.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:d571d10c8d872e81478b
claim_id: claim:d571d10c8d872e81478b
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal: However, 5–8 1 uniquely expressed CXCR5 , TNFSF8 , and the G-protein-coupled receptor P2RY8
summary:
In Homo sapiens, T follicular helper cell cluster 5-8 1 uniquely expresses CXCR5, TNFSF8, and the G-protein-coupled receptor P2RY8.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:170702d5241bfc033450
claim_id: claim:170702d5241bfc033450
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 5–8 4 also expressed BTLA 29 , as well as unique genes, such as amyloid precursor protein ( APP ), MS4A6A , and SERPINE2

summary:
In Homo sapiens, T follicular helper cell cluster 5-8 4 also expresses BTLA, amyloid precursor protein (APP), MS4A6A, and SERPINE2.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:d3b5f26db9c6b720ed63
claim_id: claim:d3b5f26db9c6b720ed63
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 5–8 0 encompassed Treg and contained both FOXP3 + Treg (right side), as well as LAG3 + Tr1 producing IL-10 (left side)

summary:
In Homo sapiens, cluster 5-8 0 encompasses regulatory T cells expressing FOXP3 and type 1 regulatory T cells expressing LAG3.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:deb720609f6a8feaa939
claim_id: claim:deb720609f6a8feaa939
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 2–4 0 corresponded to activated cytokine-secreting IL23R + T H 17, whereas cluster 2–4 1 expressed CXCR4 , GPR183 , and CXCR3 , which indicate quiescent T H 17

summary:
In Homo sapiens, activated T helper 17 cell cluster 2-4 0 expresses IL23R, whereas quiescent T helper 17 cell cluster 2-4 1 expresses CXCR4, GPR183, and CXCR3.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:69f9c82d09f827ebc34c
claim_id: claim:69f9c82d09f827ebc34c
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
These cells expressed RORC , IL17A , and IL26 , explaining the initial co-clustering with T H 17 cells and suggesting that they may represent a discrete subpopulation of γδ T cells with a type 17 polarization (Fig. 4f ).

summary:
In Homo sapiens, a discrete subpopulation of gamma delta T cells with type 17 polarization (cluster 2-4 2) expresses RORC, IL17A, and IL26.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:57bafb099ce8ca0e3a83
claim_id: claim:57bafb099ce8ca0e3a83
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal: This γδ T cell subset was also marked by NCR3
summary:
In Homo sapiens, the gamma delta T cell subset with type 17 polarization is also marked by NCR3 (NKp30).


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:745096a44a85d67e4883
claim_id: claim:745096a44a85d67e4883
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Within CD8A + clusters, cluster 1 showed the hallmarks of effector CD8 + T cells: KLRG1 (Fig. 5d ) , EOMES, TBX21 , CCL4, CCL3, CCL5, IFNG, PRF1, GZMB, GZMA, GZMH , and GZMK

summary:
In Homo sapiens, lamina propria effector CD8-positive T cells (cluster 1) show hallmark expression of KLRG1, EOMES, TBX21, CCL4, CCL3, CCL5, IFNG, PRF1, GZMB, GZMA, GZMH, and GZMK.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:07f8d7ae62f22a9587ed
claim_id: claim:07f8d7ae62f22a9587ed
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Among CD4 T cells, cluster 0 corresponded to T H 17 based on expression of CCR6, RORA (Fig. 5d ), KLRB1, LTB , and CCL20

summary:
In Homo sapiens, lamina propria T helper 17 cells (cluster 0) are identified based on expression of CCR6, RORA, KLRB1, LTB, and CCL20.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:8aa7df73394011fb0774
claim_id: claim:8aa7df73394011fb0774
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 5 and 6 were both T FH based on TOX2 and CXCR5 expression (Fig. 5d and Supplementary Fig. 5c ); cluster 6 was further distinguishable from cluster 5 based on the selective expression of CXCL13 (Fig. 5d ), PDCD1 , BTLA , and CD200

summary:
In Homo sapiens, lamina propria T follicular helper cells (clusters 5 and 6) express TOX2 and CXCR5; cluster 6 is further distinguished by selective expression of CXCL13, PDCD1, BTLA, and CD200.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:c670481559e88c078d86
claim_id: claim:c670481559e88c078d86
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Cluster 4 corresponded to Treg expressing FOXP3, IL2RA (Fig. 5d ), ENTPD1 , BATF, IL10, LAIR2, TNFRSF4 (for OX40), and TNFRSF9 (for CD137)

summary:
In Homo sapiens, lamina propria regulatory T cells (cluster 4) express FOXP3, IL2RA, ENTPD1, BATF, IL10, LAIR2, TNFRSF4, and TNFRSF9.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:8023d79656c1133ed8be
claim_id: claim:8023d79656c1133ed8be
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
The Treg subset was enriched in GPX1 (Fig. 5d ) and GLRX (Supplementary Fig. 5b ), which are induced by FOXP3 and encode molecules protecting from oxidative stress

summary:
In Homo sapiens, the lamina propria regulatory T cell subset is enriched in GPX1 and GLRX, which are induced by FOXP3 and encode molecules protecting from oxidative stress.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:c75519c064b981f1a93e
claim_id: claim:c75519c064b981f1a93e
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal:
Finally, cluster 7 identified a unique cluster of CD4 + T cells exhibiting a heat-shock stress-activated pathway, as indicated by expression of HSP family members ( HSPA1A, HSPA1B , and DNAJB1 ) , JUN , TNF , and IL2

summary:
In Homo sapiens, lamina propria CD4-positive T cell cluster 7 exhibits a heat-shock stress-activated pathway indicated by expression of HSPA1A, HSPA1B, DNAJB1, JUN, TNF, and IL2.


claim_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f:claim:aef7a6afd45325a5f678
claim_id: claim:aef7a6afd45325a5f678
paper_key: hca:0366_10.1038_s41467-021-22164-6_097f05776f
span_literal: One subset expressed T H 17 markers, such as RORC , IL-23R , IL-22 , and IL-26
summary:
In Homo sapiens, a gamma delta T cell subset expresses T helper 17 markers such as RORC, IL23R, IL22, and IL26.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:24c04c68fae0b420bea2
claim_id: claim:24c04c68fae0b420bea2
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
summary: In Homo sapiens, proximal tubule cells express the known marker PDZK1IP1.
span_literal:
Proximal tubule (PT) cells comprising clusters 1, 2, and 3 (henceforth labeled PT-A, PT-B, and PT-C) expressed known PT markers, including PDZK1IP1


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:0486a15478e86c30c807
claim_id: claim:0486a15478e86c30c807
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
summary: In Homo sapiens, proximal tubule B cells are characterized by expression of ITGB8 and PIGR.
span_literal:
Notably, both PT-B and PT-C cells were characterized by distinct marker expression, such as ITGB8 and PIGR in PT-B and CFH and KLK6 in PT-C cells


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:667c592fcbbcc7663926
claim_id: claim:667c592fcbbcc7663926
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Interestingly, PT-B and PT-C cells showed high expression of various renal stem cell marker genes, such as ICAM1 , VIM , and VCAM1

summary:
In Homo sapiens, proximal tubule B cells show high expression of renal stem cell marker genes ICAM1, VIM, and VCAM1.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:d1b4e72cffc409356f0d
claim_id: claim:d1b4e72cffc409356f0d
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Interestingly, PT-B and PT-C cells showed high expression of various renal stem cell marker genes, such as ICAM1 , VIM , and VCAM1

summary:
In Homo sapiens, proximal tubule C cells show high expression of renal stem cell marker genes ICAM1, VIM, and VCAM1.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:ec3d0a5f1ba665dfe9d4
claim_id: claim:ec3d0a5f1ba665dfe9d4
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
The neoplastic cells representing ccRCC in our cohort overexpressed classic biomarkers of this disease like CA9 , ANGPTL4 , NDUFA4L2 , and NNMT

summary:
In Homo sapiens, clear cell renal cell carcinoma tumor epithelial cells overexpress classic biomarkers CA9, ANGPTL4, NDUFA4L2, and NNMT.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:40662b64a3bac9616446
claim_id: claim:40662b64a3bac9616446
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal: while chRCC tumor epithelia overexpressed KIT , RHCG , and FOXI1
summary:
In Homo sapiens, chromophobe renal cell carcinoma tumor epithelial cells overexpress KIT, RHCG, and FOXI1.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:9cce056656d428eec3d6
claim_id: claim:9cce056656d428eec3d6
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
only endothelial cells (afferent/efferent arterioles/descending vasa recta [AEA-DVR]) in the benign kidney showed EPO expression

summary:
In Homo sapiens benign kidney, endothelial cells of afferent/efferent arterioles/descending vasa recta show EPO expression.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:5829dfd7aacd261404fb
claim_id: claim:5829dfd7aacd261404fb
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Four of the clusters were annotated as AEA/DVR ( CLDN5 + / AQP1 + ), AVR (ascending vasa recta, PLVAP + ), pericyte ( PDGFB + , RGS5 + ), and GC (glomerular capillaries, ITGA8 + ).

summary:
In Homo sapiens, afferent/efferent arterioles/descending vasa recta endothelial cells are positive for CLDN5 and AQP1.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:425c1b520b5947a1a8f4
claim_id: claim:425c1b520b5947a1a8f4
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
The fifth endothelial subpopulation was uncharacterized (UC), as it expressed both the general endothelial marker PECAM1 and the cell adhesion gene POSTN

summary:
In Homo sapiens, the uncharacterized endothelial subpopulation expresses the general endothelial marker PECAM1 and the cell adhesion gene POSTN.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:3d85ddc4d5eb795e7fe4
claim_id: claim:3d85ddc4d5eb795e7fe4
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
We also identified other markers for these subtypes, including IGF2 and SERPINE2 for AEA/DVR, DNASE1L3 for AVR, and SOST and CRHBP for GC

summary:
In Homo sapiens, afferent/efferent arterioles/descending vasa recta endothelial cells express markers IGF2 and SERPINE2.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:fc792f4ff00076466add
claim_id: claim:fc792f4ff00076466add
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
The major cluster in ccRCC, ccRCC-AVR-1, was similar to the AVR population in benign tissue, while the minor cluster, ccRCC-AVR-2, specifically expressed ACKR1 and SELP

summary:
In Homo sapiens, the clear cell renal cell carcinoma ascending vasa recta 2 endothelial cell population specifically expresses ACKR1 and SELP.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:becff4dcbc7fa577bb81
claim_id: claim:becff4dcbc7fa577bb81
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Curiously, ccRCC-AVR-1 cells had higher expression of VEGF receptor mRNAs FLT1 , KDR , and FLT4 compared with ccRCC-AVR-2 cells

summary:
In Homo sapiens, clear cell renal cell carcinoma ascending vasa recta 1 endothelial cells have higher expression of vascular endothelial growth factor receptor mRNAs FLT1, KDR, and FLT4 compared with clear cell renal cell carcinoma ascending vasa recta 2 endothelial cells.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:9cf7a0fdd0d2b95a59b8
claim_id: claim:9cf7a0fdd0d2b95a59b8
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
we observed up-regulation of endothelial genes, such as endothelin receptor type B ( EDNRB ), von Willebrand factor ( VWF ) involved in hemostasis and possibly angiogenesis ( 40 , 41 ), and heparan sulfate proteoglycan 2 ( HSPG2 ) that can stimulate endothelial growth and regeneration

summary:
In Homo sapiens, the clear cell renal cell carcinoma ascending vasa recta 1 endothelial cell population shows up-regulation of endothelin receptor type B (EDNRB), von Willebrand factor (VWF), and heparan sulfate proteoglycan 2 (HSPG2).


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:fda4e4fec7f792f4f581
claim_id: claim:fda4e4fec7f792f4f581
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
The macrophage-A cluster showed higher expression of proinflammatory genes like IL1B , CCL3 , CCL4 , CCL20 , and IL23A compared with the macrophage-B population.

summary:
In Homo sapiens, macrophage-A cells show higher expression of proinflammatory genes IL1B, CCL3, CCL4, CCL20, and IL23A compared with the macrophage-B population.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:9c2414137901a262eae2
claim_id: claim:9c2414137901a262eae2
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Expression of oncostatin M receptor ( OSMR ) in the ccRCC compartment and its ligand OSM in macrophage is of particular significance.

summary:
In Homo sapiens, clear cell renal cell carcinoma tumor epithelial cells express oncostatin M receptor (OSMR), while macrophages express its ligand OSM.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:61b4d5e73d00b28d8a73
claim_id: claim:61b4d5e73d00b28d8a73
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Expression of oncostatin M receptor ( OSMR ) in the ccRCC compartment and its ligand OSM in macrophage is of particular significance.

summary:
In Homo sapiens, macrophages in the clear cell renal cell carcinoma tumor microenvironment express OSM.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:cca10cff6baaf77ebcbb
claim_id: claim:cca10cff6baaf77ebcbb
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
we observed expression of endothelin ligand 1 ( EDN1 ) in tumor epithelia in sync with its cognate receptor EDNRB expressed in endothelial cells of the tumor vasculature visualized by RNA-ISH

summary:
In Homo sapiens, clear cell renal cell carcinoma tumor epithelial cells express endothelin ligand 1 (EDN1), while endothelial cells of the tumor vasculature express its cognate receptor EDNRB.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:e3a01a5f0f8ab40b3b20
claim_id: claim:e3a01a5f0f8ab40b3b20
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
we observed expression of endothelin ligand 1 ( EDN1 ) in tumor epithelia in sync with its cognate receptor EDNRB expressed in endothelial cells of the tumor vasculature visualized by RNA-ISH

summary:
In Homo sapiens, endothelial cells of the tumor vasculature express endothelin receptor type B (EDNRB).


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:0130dece5bddd195ee4a
claim_id: claim:0130dece5bddd195ee4a
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
Violin plots depicting gene expression patterns of select cell type markers: PDZK1IP1 (all PT cells), ITGB8 (PT-B and -C), PIGR (PT-B and -C), CFH (PT-C), KLK6 (PT-C), CALB1 (IC-PC, CNT), AQP2 (PC), FOXI1 (IC-PC, IC-A, IC-B), and SLC4A1 (IC-PC, IC-A).

summary:
In Homo sapiens, CALB1 is a marker of intercalated-principal cells and connecting tubule cells. In Homo sapiens, FOXI1 is a marker of intercalated-principal cells, intercalated cell type A, and intercalated cell type B. In Homo sapiens, SLC4A1 is a marker of intercalated-principal cells and intercalated cell type A.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:670cdffbd2379fd8bdaa
claim_id: claim:670cdffbd2379fd8bdaa
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
summary:
In Homo sapiens, FOXI1 is a marker of intercalated cell type A. In Homo sapiens, SLC4A1 is a marker of intercalated cell type A.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:e42acdb9c8c7a3a3dbc0
claim_id: claim:e42acdb9c8c7a3a3dbc0
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
The tumor endothelium contains two distinct subpopulations which include the major AVR-1 ( EDNRB + ) and minor AVR-2 ( ACKR1 + ) groups.

summary:
In Homo sapiens, the major tumor endothelium ascending vasa recta 1 subpopulation is EDNRB-positive, while the minor ascending vasa recta 2 subpopulation is ACKR1-positive.


claim_key: hca:0367_10.1073_pnas.2103240118_fda266512b:claim:78227518aae2173a3645
claim_id: claim:78227518aae2173a3645
paper_key: hca:0367_10.1073_pnas.2103240118_fda266512b
span_literal:
The tumor endothelium contains two distinct subpopulations which include the major AVR-1 ( EDNRB + ) and minor AVR-2 ( ACKR1 + ) groups.

summary:
In Homo sapiens, the minor tumor endothelium ascending vasa recta 2 subpopulation is ACKR1-positive.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:c73d7b5fd6ecb6eec084
claim_id: claim:c73d7b5fd6ecb6eec084
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal: DC genes, including FLT3
summary:
In Homo sapiens, dendritic cells express the hallmark receptor FLT3, while macrophages express the core macrophage gene signature containing MERTK, CTSC, CTSD, GLUL, and PLD3.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:3f6b00817151a240e503
claim_id: claim:3f6b00817151a240e503
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal: macrophage gene signature,” which contains MERTK , CTSC , CTSD , GLUL , and PLD3
summary:
In Homo sapiens, macrophages express the core macrophage gene signature containing MERTK, CTSC, CTSD, GLUL, and PLD3.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:7d228ba1f1691a916fd3
claim_id: claim:7d228ba1f1691a916fd3
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal: DC ( CD14 , CD68 , and FCGR3A
summary:
In Homo sapiens, macrophages express CD14, CD68, and FCGR3A, which are not expressed by dendritic cells.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:d7dedfd3099bb5728299
claim_id: claim:d7dedfd3099bb5728299
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal: MAFB , M-CSF receptor ( CSF1R
summary:
In Homo sapiens, gut-resident macrophages express high levels of the transcription factor MAFB and the macrophage colony-stimulating factor receptor CSF1R.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:1237ce734eacfccc1658
claim_id: claim:1237ce734eacfccc1658
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal: DNASE1L3 , C1Qs
summary:
In Homo sapiens, gut-resident macrophages express genes required for apoptotic cell clearance including DNASE1L3 and C1Qs.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:c215365495b525b87ab2
claim_id: claim:c215365495b525b87ab2
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
A third DC cluster annotated as activated conventional DCs expressed transcripts enriched in migratory DCs on their way to tissue draining lymph node (DLN) and included the activation marker DC-LAMP ( LAMP3 ), co-stimulatory molecules ( CD40 , CD86 ), checkpoint molecule PD-L1, and the chemokine receptor CCR7

summary:
In Homo sapiens, activated conventional dendritic cells express the activation marker DC-LAMP (LAMP3), co-stimulatory molecules CD40 and CD86, checkpoint molecule PD-L1, and the chemokine receptor CCR7.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:d42df1d3e5589225f3bf
claim_id: claim:d42df1d3e5589225f3bf
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
FLT3 and the DC2 markers CD1c and FCER1A together with CD207 (langerin), the TF MAFB , and MRC1 (CD206) as well as additional genes induced in monocyte-derived DCs (moDCs) cultured with GM-CSF and IL-4 such as CD209 (DC-SIGN), SEPP1 , STAB1 , and DAB2

summary:
In Homo sapiens, monocyte-derived dendritic cells express FLT3, CD1c, FCER1A, CD207, MAFB, MRC1, CD209, SEPP1, STAB1, and DAB2.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:a6fc0ab1b85c8775b41f
claim_id: claim:a6fc0ab1b85c8775b41f
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
We identified two subsets of endothelial cells that shared the expression of the vascular endothelial growth factor receptor 2 ( KDR ) and included lymphatic endothelial cells, defined by high levels of the lymphatic vessel endothelial hyaluronan receptor 1 ( LYVE1 ) and the CCR7 ligand CCL21 , and blood endothelial cells co-expressing PECAM1 (CD31) and Von Willebrand factor VWF

summary:
In Homo sapiens, lymphatic endothelial cells are defined by high levels of LYVE1 and CCL21, while blood endothelial cells co-express PECAM1 and VWF, and both share expression of KDR.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:40244e66d79e9be33b22
claim_id: claim:40244e66d79e9be33b22
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
We identified two subsets of endothelial cells that shared the expression of the vascular endothelial growth factor receptor 2 ( KDR ) and included lymphatic endothelial cells, defined by high levels of the lymphatic vessel endothelial hyaluronan receptor 1 ( LYVE1 ) and the CCR7 ligand CCL21 , and blood endothelial cells co-expressing PECAM1 (CD31) and Von Willebrand factor VWF

summary:
In Homo sapiens, blood endothelial cells co-express PECAM1 and VWF, and share expression of KDR with lymphatic endothelial cells.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:2a5b13f6570ed866ced3
claim_id: claim:2a5b13f6570ed866ced3
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
One subset of blood endothelial cells expressed high levels of the atypical chemokine receptor 1 ( ACKR1 ) and adhesion molecules SELE (E-selectin) and SELP (P-selectin) and was annotated as activated endothelial cells

summary:
In Homo sapiens, activated endothelial cells express high levels of the atypical chemokine receptor 1 ACKR1, SELE (E-selectin), and SELP (P-selectin).


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:97823eea8a4b2a32384e
claim_id: claim:97823eea8a4b2a32384e
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
summary: In Homo sapiens, smooth muscle cells express ACTG2, MYH11, and DES.
span_literal:
and smooth muscle cells, as suggested by their expression ACTG2 (actin gamma-2 enteric smooth muscle), MYH11 (myosin heavy chain 11), and DES (desmin)


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:20c0347a8f99bcc21465
claim_id: claim:20c0347a8f99bcc21465
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
fibroblasts were characterized by their expression of the two subunits of the platelet-derived growth factor receptors ( PDGFRA , PDGFRB ), the prostaglandin-H2 D-isomerase PTGDS , and several genes encoding extracellular matrix (ECM) proteins such as lumican ( LUM ) and ECM-remodeling proteins (e.g., matrix metallo-proteinase-2 [ MMP2

summary:
In Homo sapiens, fibroblasts are characterized by expression of PDGFRA, PDGFRB, PTGDS, LUM, and MMP2.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:5f54cba46e0409f0d325
claim_id: claim:5f54cba46e0409f0d325
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
One of the two subtypes of fibroblasts expressed a hallmark activation program including strong expression of THY1 (CD90), PDPN (podoplanin), CTHRC1 , and CHI3L1

summary:
In Homo sapiens, activated fibroblasts express a hallmark activation program including strong expression of THY1, PDPN, CTHRC1, and CHI3L1.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:abf4928f04096fdd859d
claim_id: claim:abf4928f04096fdd859d
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
summary: In Homo sapiens, glial cells express S100B.
span_literal:
The last cluster of non-hematopoietic cells (cluster 16) corresponded to S100B expressing glial cells


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:618f6157b6142c4c6738
claim_id: claim:618f6157b6142c4c6738
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
C1Qs , GLUL , APOE , and ACP5 , while the second program included the IBD biomarker calprotectin ( S100A8 and S100A9 ) ( Konikoff and Denson, 2006 ), S100A12 , and versican ( VCAN

summary:
In Homo sapiens, inflammatory macrophages contain a program with macrophage markers C1Qs, GLUL, APOE, and ACP5, and a second program including S100A8, S100A9, S100A12, and VCAN.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:da94d03e2cd7fb42c16d
claim_id: claim:da94d03e2cd7fb42c16d
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
T cell cluster #17 expressed a strong cell cycle score and genes encoding for membrane proteins associated with human T cells activation such as HLA-DRA , CD38 and the high affinity IL-2 receptor chain IL2RA (CD25), and thus was annotated as highly activated T cells.

summary:
In Homo sapiens, highly activated T cells express HLA-DRA, CD38, and the high affinity interleukin-2 receptor chain IL2RA (CD25).


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:7b8dcb17155e5010baca
claim_id: claim:7b8dcb17155e5010baca
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
FOXP3, IL2RA (CD25), CTLA4 , together with genes which high expression was consistently associated with Tregs by recent scRNaseq studies, including TNFRSF18 , TNFRSF4 , and LAYN

summary:
In Homo sapiens, regulatory T cells express high levels of FOXP3, IL2RA, CTLA4, TNFRSF18, TNFRSF4, and LAYN.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:f589dc1c77be7d350795
claim_id: claim:f589dc1c77be7d350795
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
Cells in cluster #22 shared several genes with Tregs including TIGIT, BATF, ICA1 and TNFRSF4 (OX-40), but lacked Tregs-defining transcripts FOXP3, IL2RA , TNFRSF18 and IKZF2 (HELIOS) while they expressed high levels of CD40LG and the chemokine CXCL13 , and thus were referred to as T follicular helper-like (TFH-like) cells

summary:
In Homo sapiens, T follicular helper-like cells express TIGIT, BATF, ICA1, TNFRSF4, CD40LG, and CXCL13, but lack FOXP3, IL2RA, TNFRSF18, and IKZF2.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:4a4e0e811d195afcb0bf
claim_id: claim:4a4e0e811d195afcb0bf
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
Two cell clusters (#19, 29) expressed high levels of the naive/CM signature, including the chemokine receptor CCR7 and the selectin CD62L ( SELL ), known to promote the recruitment of naive and central memory (CM) T cells to the T cell areas of secondary lymphoid organs through the high endothelial venule

summary:
In Homo sapiens, naive and central memory T cells express high levels of the chemokine receptor CCR7 and the selectin SELL (CD62L).


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:55f78a7e04d399936f6b
claim_id: claim:55f78a7e04d399936f6b
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
Cluster #35 displayed a gene signature highly compatible with ILC3, the most abundant ILC population in human healthy gut ( Simoni et al., 2017 ), including KIT (CD117), IL23R, IL1R1, the TFs ID2, RORC (RORγt), RORA (RORα) and the cytokines IL22 and CSF2 (GM-CSF)

summary:
In Homo sapiens, group 3 innate lymphoid cells express KIT, IL23R, IL1R1, ID2, RORC, RORA, IL22, and CSF2.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:6ff2d9db5bd5373ff504
claim_id: claim:6ff2d9db5bd5373ff504
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
summary: In Homo sapiens, group 3 innate lymphoid cells express lower levels of PTPRC (CD45).
span_literal:
This cluster also expressed lower level of CD45 ( PTPRC ), a well-defined feature of both mouse and human ILC3


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:45584f8324e87307d533
claim_id: claim:45584f8324e87307d533
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
summary: In Homo sapiens, plasma cells express LGALS1, encoding galectin-1.
span_literal:
PC also expressed LGALS1 , encoding for galectin-1, a downstream gene of the PC TF BLIMP-1 important for PC differentiation, survival and Igs secretion


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:e2134f8c48996f97ba31
claim_id: claim:e2134f8c48996f97ba31
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
while IgM and IgA PC expressed higher levels of BCMA ( TNFRSF17 ), the receptor for a proliferation-inducing ligand (APRIL) and B cell activating factor of TNF family (BAFF), important for PC survival in the gut

summary:
In Homo sapiens, IgM and IgA plasma cells express higher levels of TNFRSF17 (BCMA), the receptor for a proliferation-inducing ligand and B cell activating factor of tumor necrosis factor family.


claim_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe:claim:e230ffd2a93c365f2cef
claim_id: claim:e230ffd2a93c365f2cef
paper_key: hca:0368_10.1016_j.cell.2019.08.008_98c14c4ebe
span_literal:
which expressed genes encoding PC-associated membrane proteins including CD138 ( SDC1 ), CD38 and CD27 as well as genes associated with protein folding, trafficking and secretion ( SSR4, FKBP2, FKBP11, HSP90B1, SEC11C ), degradation of misfolded protein ( SDF2L1, DERL3 ) and endoplasmic reticulum stress, including the IBD susceptibility TF gene XBP1

summary:
In Homo sapiens, plasma cells express SDC1, CD38, CD27, SSR4, FKBP2, FKBP11, HSP90B1, SEC11C, SDF2L1, DERL3, and XBP1.


claim_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038:claim:f086eb7c72e64eaf5010
claim_id: claim:f086eb7c72e64eaf5010
paper_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038
summary: In Homo sapiens, CD79A is a marker of B cells in bone marrow mononuclear cells.
span_literal:
Expression of cell surface marker genes used to assign cell types: CD79A (B cells), CST3 (monocytes), CD3D (T cells) and HBA1 (erythrocytes).


claim_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038:claim:40d4940239d1e191df78
claim_id: claim:40d4940239d1e191df78
paper_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038
summary: In Homo sapiens, CD34 is a marker of CD34+ cells in bone marrow mononuclear cells.
span_literal:
Cell types were identified using the expression of known cell surface marker genes ( CD34/ CD34+, CD79A/ B cells, MS4A1/ CD20+ B cells, CST3/ monocytes, SPN + KIT/ immature hematopoietic, HBA1 /erythrocytes, CD3D /T cells, NKG7 /NK cells, MZB1 /BCMA).


claim_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038:claim:5dbe687002902ee81ff8
claim_id: claim:5dbe687002902ee81ff8
paper_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038
summary:
In Homo sapiens, SPN and KIT are markers of immature hematopoietic cells in bone marrow mononuclear cells.


claim_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038:claim:4d50bd8edbeddd06e833
claim_id: claim:4d50bd8edbeddd06e833
paper_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038
span_literal:
We observed two distinct clusters of B-ALL and T-ALL cells as shown by the expression of the CD79A/B and CD3D surface markers

summary:
In Homo sapiens, CD79A and CD79B are markers of B cell acute lymphoblastic leukemia cells, while CD3D is a marker of T cell acute lymphoblastic leukemia cells.


claim_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038:claim:9175a3ec2f37bb724632
claim_id: claim:9175a3ec2f37bb724632
paper_key: hca:0369_10.1038_s41598-020-64929-x_0cb78e8038
span_literal:
We observed two distinct clusters of B-ALL and T-ALL cells as shown by the expression of the CD79A/B and CD3D surface markers

summary:
In Homo sapiens, CD3D is a marker of T cell acute lymphoblastic leukemia cells, while CD79A and CD79B are markers of B cell acute lymphoblastic leukemia cells.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:5d60a166bac8ce3f4719
claim_id: claim:5d60a166bac8ce3f4719
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: endothelial cell (EC; expressing PLVAP , KDR , PTPRB
summary:
In Homo sapiens, endothelial cells are marked by expression of PLVAP, KDR, and PTPRB in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:2cef88146da8e8399d7b
claim_id: claim:2cef88146da8e8399d7b
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: enteroendocrine cell (expressing CHGA , GAST, PROX1
summary:
In Homo sapiens, enteroendocrine cells are marked by expression of CHGA, GAST, and PROX1 in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:d70e816edf4c11fccd2a
claim_id: claim:d70e816edf4c11fccd2a
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: fibroblast (expressing MMP2 , PDGFRA , MYL9 , FN1 , CAV1
summary:
In Homo sapiens, fibroblasts are marked by expression of MMP2, PDGFRA, MYL9, FN1, and CAV1 in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:e4f411dcbf539d4e2f37
claim_id: claim:e4f411dcbf539d4e2f37
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: IM (intestinal metaplasia; expressing TFF3 , CDX1 , CDX2
summary:
In Homo sapiens, intestinal metaplasia cells are marked by expression of TFF3, CDX1, and CDX2 in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:6167c57fe13a3063c53c
claim_id: claim:6167c57fe13a3063c53c
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: metaplastic-stem cell (MSC; expressing OLFM4 , REG1A , CLDN3
summary:
In Homo sapiens, metaplastic stem cells are marked by expression of OLFM4, REG1A, and CLDN3 in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:e9a7ae49761d8bb1bdb6
claim_id: claim:e9a7ae49761d8bb1bdb6
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: proliferative cell (PC; expressing CDKN2A , MKI67 , RBP4
summary:
In Homo sapiens, proliferative cells are marked by expression of CDKN2A, MKI67, and RBP4 in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:b086092f6c1808cf62f9
claim_id: claim:b086092f6c1808cf62f9
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: pit mucous cell (PMC; expressing GKN1 , GKN2 , MUC5AC
summary:
In Homo sapiens, pit mucous cells are marked by expression of GKN1, GKN2, and MUC5AC in gastric tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:3a4a8078801c44c2ed47
claim_id: claim:3a4a8078801c44c2ed47
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: tumor cell (expressing EPCAM , CDH17 , COL3A1 , PDGFRB
summary:
In Homo sapiens, tumor cells are marked by expression of EPCAM, CDH17, COL3A1, and PDGFRB in gastric cancer.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:01cc9f481824d99aa5c9
claim_id: claim:01cc9f481824d99aa5c9
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
IGC markers ( CDH17 , REG4 , and MUC13 ) were highly expressed in the C1 and C2, and DGC markers ( COL1A1 and S100A4) were highly expressed the C0 and C3–C7, respectively

summary:
In Homo sapiens gastric cancer, intestinal gastric cancer markers CDH17, REG4, and MUC13 are highly expressed in tumor cell subcluster C1 and C2, while diffuse gastric cancer markers COL1A1 and S100A4 are highly expressed in tumor cell subcluster C0 and C3–C7.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:002c799c35b4f1bf7069
claim_id: claim:002c799c35b4f1bf7069
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
IGC markers ( CDH17 , REG4 , and MUC13 ) were highly expressed in the C1 and C2, and DGC markers ( COL1A1 and S100A4) were highly expressed the C0 and C3–C7, respectively

summary:
In Homo sapiens gastric cancer, intestinal gastric cancer markers CDH17, REG4, and MUC13 are highly expressed in tumor cell subcluster C2, while diffuse gastric cancer markers COL1A1 and S100A4 are highly expressed in tumor cell subcluster C0 and C3–C7.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:42055fe49fd69edaf10c
claim_id: claim:42055fe49fd69edaf10c
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
IGC markers ( CDH17 , REG4 , and MUC13 ) were highly expressed in the C1 and C2, and DGC markers ( COL1A1 and S100A4) were highly expressed the C0 and C3–C7, respectively

summary:
In Homo sapiens gastric cancer, diffuse gastric cancer markers COL1A1 and S100A4 are highly expressed in tumor cell subcluster C0.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:299f766261db700f6988
claim_id: claim:299f766261db700f6988
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
A group of cells (C5) that did not express EMT signatures (Fig. 3c and Supplementary Fig. 8d ), but highly expressed myofibroblast-associated genes such as TAGLN and EGR1 (Supplementary Fig. 8e ) was identified in the tumor cell clusters analysis

summary:
In Homo sapiens gastric cancer, tumor cell subcluster C5 highly expresses myofibroblast-associated genes TAGLN and EGR1.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:6a852e4186fad55c547d
claim_id: claim:6a852e4186fad55c547d
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
summary: In Homo sapiens, fibroblast cells are marked by expression of SFRP2 and CXCL12 in gastric tissue.
span_literal:
Fibroblast cell marker genes such as SFRP2 and CXCL12 were expressed in the gray region of the trajectory


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:6dd036dc70a3da61bab6
claim_id: claim:6dd036dc70a3da61bab6
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
Genes encoding cytokines ( IL6 , IL11 , and IL24 ), chemokines ( CXCL1 , CXCL2 , CXCL5 , and CXCL6 ) 39 , and matrix metalloproteinases ( MMP1 , MMP3 , and MMP10 ) 40 were uniquely upregulated in iCAFs

summary:
In Homo sapiens gastric cancer, inflammatory cancer-associated fibroblasts show upregulation of IL6, IL11, IL24, CXCL1, CXCL2, CXCL5, CXCL6, MMP1, MMP3, and MMP10.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:d548e2c609a4032ab0d4
claim_id: claim:d548e2c609a4032ab0d4
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal: myCAFs were identified by known marker genes such as TPM1 , TPM2 , MYL9 , TAGLN , and POSTN
summary:
In Homo sapiens gastric cancer, myofibroblastic cancer-associated fibroblasts are identified by marker genes TPM1, TPM2, MYL9, TAGLN, and POSTN.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:6e3409b8609112514dc5
claim_id: claim:6e3409b8609112514dc5
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
inCAFs were distinctly divided between iCAFs and myCAFs, with high expression of PDGFRA , POSTN , ID1 , and ID3

summary:
In Homo sapiens gastric cancer, intermediate cancer-associated fibroblasts show high expression of PDGFRA, POSTN, ID1, and ID3.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:0f8f232f48e771e8bc1e
claim_id: claim:0f8f232f48e771e8bc1e
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
IL6 , CXCL1 , and CXCL2 are biomarkers of pro-stemness CAFs 43 , and these markers were highly expressed in iCAFs

summary:
In Homo sapiens gastric cancer, IL6, CXCL1, and CXCL2 are biomarkers of pro-stemness cancer-associated fibroblasts and are highly expressed in inflammatory cancer-associated fibroblasts.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:f8aa098000e6a11f81d5
claim_id: claim:f8aa098000e6a11f81d5
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
The PC1 cluster showed high expression in TFF1 and TFF2 , where most cells were obtained from non-cancerous tissues.

summary:
In Homo sapiens, proliferative cell 1 cluster shows high expression of TFF1 and TFF2 in gastric non-cancerous tissue.


claim_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104:claim:f9f14308a5bc77079909
claim_id: claim:f9f14308a5bc77079909
paper_key: hca:0370_10.1038_s41698-022-00251-1_1483c4b104
span_literal:
The PC2 cluster showed high expression in TFF3 and REG4 , where cells were obtained from the cancer tissue of intestinal patients.

summary:
In Homo sapiens, proliferative cell 2 cluster shows high expression of TFF3 and REG4 in intestinal-type gastric cancer tissue.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:955c3cfdf10d7db05254
claim_id: claim:955c3cfdf10d7db05254
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
pDCs expressed transcripts associated with this lineage ( LILRA4 , IRF8 ; Figure 1C ) and known population-defining proteins (CD123; Figure 1D )

summary:
In Homo sapiens, plasmacytoid dendritic cells express LILRA4 and IRF8 transcripts and CD123 protein.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:c33052e75d51698abc13
claim_id: claim:c33052e75d51698abc13
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, conventional dendritic cell type 1 expresses IRF8, WDFY4, and CLEC9A transcripts.
span_literal:
Conventional DC1 (cDC1; cluster 45) expressing IRF8 , WDFY4 , and CLEC9A transcripts ( Figure 2A ) as well as CD141 and CD26 surface protein ( Figure 2B )


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:fc7f7b72ce639c2517f0
claim_id: claim:fc7f7b72ce639c2517f0
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
We furthermore identified clusters that expressed cDC2 markers such as CD1c and CLEC10A , but also expressed high levels of monocyte and MΦ genes including S100A8 , S100A9 , C1QA , and C1QB , lacked surface expression of the pre-DC surface marker CD5

summary:
In Homo sapiens, DC3 cells express CD1c, CLEC10A, S100A8, S100A9, C1QA, and C1QB, and lack CD5 surface expression.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:a818f0c01eac012cf249
claim_id: claim:a818f0c01eac012cf249
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, interstitial macrophages lack PPARG and express MERTK, CSF1R, LYVE1, and CX3CR1.
span_literal:
IMΦ lacked PPARG and expressed higher levels of MAF family transcription factors, MERTK , CSF1R , LYVE1 , and CX3CR1


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:6adff8efea7ab0f82716
claim_id: claim:6adff8efea7ab0f82716
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, CD14-positive monocytes express CD14 and lack MRC1, VSIG4, and SIGLEC1.
span_literal:
CD14+ and CD16+ monocytes (clusters 2, 49, 36, 58, and 23) expressed CD14 or FCGR3A respectively and lacked MΦ genes MRC1 , VSIG4 , and SIGLEC1


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:ed4c08c188d1e7d05b97
claim_id: claim:ed4c08c188d1e7d05b97
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, monocyte-derived macrophages express MAFB, CEBPD, FCGR2B, and CSF1R.
span_literal:
Other MΦ clusters expressed MAFB , CEBPD , FCGR2B , and CSF1R , which are shared by monocytes and IMΦ; therefore, these clusters (47, 5, 38, 32, 33, 42, 11, 35) were annotated as MoMΦ


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:20b4f6955004e0145c50
claim_id: claim:20b4f6955004e0145c50
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, AZU1-positive macrophages express AZU1, ELANE, and CTSG but lack MPO.
span_literal:
AZU1 + MΦ (cluster 16) expressed genes consistent with primary granule formation ( AZU1 , ELANE , CTSG ) but distinct from bone marrow progenitors due to lack of MPO


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:828286857fbf8efd0599
claim_id: claim:828286857fbf8efd0599
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
We identified one cluster (13) of NK cells based on their high level of expression of NCR1 , SPON2 , KLRD1 , PRF1 , and GZMB and lack of CD3D and TRAC transcripts

summary:
In Homo sapiens, natural killer cells express high levels of NCR1, SPON2, KLRD1, PRF1, and GZMB and lack CD3D and TRAC.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:90999be2b546986f6672
claim_id: claim:90999be2b546986f6672
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
CITE-seq analysis of T cells identified CD8 + cells that were characterized by a natural killer (NK)-like signature (TNK-like; cluster 20), elevated GZMK (T GZMK ; cluster 1), genes related to tissue residence ( ITGA1 transcript and CD103 and CD69 protein; CD8 + T rm ; cluster 48), and an apparently activated cluster enriched in IFNG , GZMB , LAG3 , CXCL13 , and HAVCR2 transcripts and with increased PD-1, ICOS, and CD39 protein (T activated ; cluster 44

summary:
In Homo sapiens, activated T cells are enriched in IFNG, GZMB, LAG3, CXCL13, and HAVCR2 transcripts.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:b1b53dfe468e8dbd4796
claim_id: claim:b1b53dfe468e8dbd4796
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, central memory or naive-like T cells type I express TCF7, SELL, LEF1, and MAL.
span_literal:
cells expressing a profile consistent with central memory or naive cells (T CM/naive-like-I ; clusters 51, 39; TCF7 , SELL , LEF1 , MAL , and CD127)


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:e54afb04d2d78e721d60
claim_id: claim:e54afb04d2d78e721d60
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, cycling T cells highly express MKI67 and STMN1.
span_literal:
a cluster highly expressing cell-cycle genes MKI67 and STMN1 and surface proteins HLA-DR and CD38 was also increased (Tcycle; cluster 18


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:ce0d232a2b865c8ff45a
claim_id: claim:ce0d232a2b865c8ff45a
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, B cells express high levels of MS4A1.
span_literal:
Eight clusters of B and Plasma cells (56, 43, 40, 31, 17, 9, 46, 28) expressed high levels of MS4A1 or MZB1 transcripts and high levels of CD19 protein


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:456c85bd4d08c6b19942
claim_id: claim:456c85bd4d08c6b19942
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
MoMΦ-II clusters expressed the highest levels of the tumor-enriched mod2 which included SPP1 and glycolysis genes ( GAPDH , ENO1 , LDHA , ALDOA , TPI1 ), and lower levels of C1Q and HLA class II transcripts

summary:
In Homo sapiens, monocyte-derived macrophage type II expresses the highest levels of SPP1, GAPDH, ENO1, LDHA, ALDOA, and TPI1.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:8da310e5b518022300c1
claim_id: claim:8da310e5b518022300c1
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
MoMΦ-III clusters were enriched in mod11 (including TREM2 and LILRB4 ) and mod14 (including APOE and GPNMB )

summary:
In Homo sapiens, monocyte-derived macrophage type III is enriched in TREM2, LILRB4, APOE, and GPNMB.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:0c06b88487394e59900a
claim_id: claim:0c06b88487394e59900a
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, activated T cells in the lung cancer activation module express PDCD1 and CXCL13.
span_literal:
We identified a cellular module consisting of PDCD1 + CXCL13 + activated T cells, IgG + plasma cells, and SPP1 + macrophages, referred to as the lung cancer activation module (LCAM hi ).


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:dd02492683ba8c98da6e
claim_id: claim:dd02492683ba8c98da6e
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
MoMΦ-II expressed the highest levels of inflammatory cytokines TNF and IL6 , transcripts encoding the pleiotropic factor SPP1, multiple matrix metallopeptidases, and CCR2/5 ligands CCL-2 , −8 , and −7

summary:
In Homo sapiens, monocyte-derived macrophage type II expresses the highest levels of TNF, IL6, SPP1, CCL2, CCL8, and CCL7.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:a47bfba8397f390c89b7
claim_id: claim:a47bfba8397f390c89b7
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
span_literal:
mregDC, meanwhile, expressed cytokines and chemotactic factors associated with T cell engagement including IL12B , EBI3 , CCL17 , CCL22 , and CCL19

summary:
In Homo sapiens, mature dendritic cell enriched in regulatory molecules expresses IL12B, EBI3, CCL17, CCL22, and CCL19.


claim_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa:claim:07c1f3f33c1a413dacc7
claim_id: claim:07c1f3f33c1a413dacc7
paper_key: hca:0372_10.1016_j.ccell.2021.10.009_d6ab4790aa
summary: In Homo sapiens, T cells express CD3D and TRAC.
span_literal:
12 T cell clusters (20, 1, 48, 44, 50, 59, 34, 53, 51, 39, 19, 18) expressed CD3D and TRAC by RNA and CD3 by CITEseq


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:389924b6c8b4bd570972
claim_id: claim:389924b6c8b4bd570972
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
span_literal:
At day 18, the most highly expressed genes included markers of podocytes, a key component of the forming glomerulus ( NPHS1 , NPHS2 , PTPRO , MAFB , SYNPO , ITIH5 , CLIC5 , NPNT )

summary:
In Homo sapiens kidney organoids, podocytes express NPHS1, NPHS2, PTPRO, MAFB, SYNPO, ITIH5, CLIC5, and NPNT as markers of the forming glomerulus.


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:0a2541a5e0ecddad0a6d
claim_id: claim:0a2541a5e0ecddad0a6d
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
span_literal:
Simultaneous with the upregulation of nephron markers between days 10 and 18 was the downregulation of the nephron progenitor markers LIN28A , MEOX1 , CITED1 , and EYA1 .

summary:
In Homo sapiens kidney organoids, nephron progenitor cells are marked by LIN28A, MEOX1, CITED1, and EYA1, which are downregulated as nephrons mature.


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:0a53b1481b647fc88f81
claim_id: claim:0a53b1481b647fc88f81
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
summary: In Homo sapiens kidney organoids, NPHS2, PTPRO, and NPHS1 are markers of podocytes.
span_literal:
Many of the highly variable genes were related to nephron maturation (for example, the podocyte markers NPHS2 , PTPRO , and NPHS1 )


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:a859b211785cf7a6f822
claim_id: claim:a859b211785cf7a6f822
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
span_literal:
The proportion of cells expressing highly variable cell-type-specific genes, such as NPHS2 , PTPRO , and MMP1 , also differed across the four organoids

summary:
In Homo sapiens kidney organoids, NPHS2 and PTPRO are cell-type-specific genes expressed in podocytes, while MMP1 is expressed in endothelial cells.


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:73dd71ef8e199848668e
claim_id: claim:73dd71ef8e199848668e
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
span_literal:
A greater proportion of cells in organoids 1, 2, and 3 had high expression of NPHS2 and PTPRO in the podocyte cluster and MMP1 in the endothelial cluster, while fewer cells in organoid 4 expressed these genes at high levels

summary:
In Homo sapiens kidney organoids, podocytes express NPHS2 and PTPRO, while endothelial cells express MMP1.


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:39e52c5d7bd26527d530
claim_id: claim:39e52c5d7bd26527d530
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
span_literal:
organoid 4 had more cells expressing PAX2 (clusters 4 (podocyte), 9 (nephron progenitor), and 10 (nephron)) but much reduced MAFB expression in the podocyte cluster

summary:
In Homo sapiens kidney organoids, podocytes express PAX2 and MAFB, nephron progenitor cells express PAX2, and nephron cells express PAX2.


claim_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48:claim:0a808780169e6e159653
claim_id: claim:0a808780169e6e159653
paper_key: hca:0373_10.1038_s41592-018-0253-2_ae3c4efc48
span_literal: only a few genes ( MMP1 , endothelium; DCN , stroma) selectively expressed in other cell types
summary:
In Homo sapiens kidney organoids, MMP1 is selectively expressed in endothelial cells and DCN is selectively expressed in stromal cells.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:03484a2e7119000e9ba8
claim_id: claim:03484a2e7119000e9ba8
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
summary: In Homo sapiens lung, SPP1-high macrophages are marked by expression of SPP1, CCL2, and MERTK.
span_literal:
Macrophages and monocytes were identified in seven separate clusters, which divided into three primary subgroups: the first expressing SPP1, CCL2 , and MERTK (SPP1 hi ), the second expressing FABP4, INHBA , and SERPING1 (FABP4 hi ), and the third a population of monocytes expressing FCN1, IL1B, and IL1R2 (FCN1 hi )


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:93999b61b6ee19f25b86
claim_id: claim:93999b61b6ee19f25b86
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
Macrophages and monocytes were identified in seven separate clusters, which divided into three primary subgroups: the first expressing SPP1, CCL2 , and MERTK (SPP1 hi ), the second expressing FABP4, INHBA , and SERPING1 (FABP4 hi ), and the third a population of monocytes expressing FCN1, IL1B, and IL1R2 (FCN1 hi )

summary:
In Homo sapiens lung, FABP4-high macrophages are marked by expression of FABP4, INHBA, and SERPING1.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:613755e247e489f1c651
claim_id: claim:613755e247e489f1c651
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
summary: In Homo sapiens lung, fibroblasts are robustly marked by expression of LUM, PDGFRA, and FBLN1.
span_literal:
Fibroblasts composed four clusters, as marked robustly by the expression of LUM, PDGFRA, and FBLN1 , with fibroblast subpopulations as detailed below.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:da81c6f12e16fb021a38
claim_id: claim:da81c6f12e16fb021a38
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
A distinct pericyte population, markedly expanded in SSc-ILD (p-value 0.0295), was identified by its expression of the known markers RGS5, PDGFRB, MCAM, CSPG4 ( NG2), and NES

summary:
In Homo sapiens lung, pericytes are identified by expression of the known markers RGS5, PDGFRB, MCAM, CSPG4, and NES.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:3abae47a09def12312c4
claim_id: claim:3abae47a09def12312c4
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
The identified pericyte population showed enhanced expression of FAM162B, CHN1, IGFBP2, and HIGD1B compared to other mesenchymal cells, with FAM162B the most specific identifier of this population.

summary:
In Homo sapiens lung, pericytes show enhanced expression of FAM162B, CHN1, IGFBP2, and HIGD1B compared to other mesenchymal cells, with FAM162B being the most specific identifier.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:9140eb769cf3585f6954
claim_id: claim:9140eb769cf3585f6954
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
The first major population was defined by expression of SPINT2, CD14, LMCD1, FGFR4 , and FIGF (SPINT2 hi fibroblasts).

summary:
In Homo sapiens lung, SPINT2-high fibroblasts are defined by expression of SPINT2, CD14, LMCD1, FGFR4, and FIGF.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:a58ef01922b8eaa65d6c
claim_id: claim:a58ef01922b8eaa65d6c
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
A second major population was defined by expression of MFAP5, CD34, THY1, SLPI, and PLA2G2A ( MFAP5 hi fibroblasts).

summary:
In Homo sapiens lung, MFAP5-high fibroblasts are defined by expression of MFAP5, CD34, THY1, SLPI, and PLA2G2A.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:e3c24449e4efb4e7211d
claim_id: claim:e3c24449e4efb4e7211d
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
summary: In Homo sapiens lung, WIF1-high fibroblasts are distinguished by expression of WIF1 and ITGA10.
span_literal:
A distinct minor population was distinguished by expression of WIF1 and ITGA10 (WIF1 hi fibroblasts).


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:1dde1b0dae21db5b94d1
claim_id: claim:1dde1b0dae21db5b94d1
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
This population did not express the smooth muscle specific markers MYH11 and DES, and had the highest expression of several collagen genes amongst the mesenchymal cells

summary:
In Homo sapiens lung, myofibroblasts do not express the smooth muscle specific markers MYH11 and DES.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:e7f9186cc26c3f8cd594
claim_id: claim:e7f9186cc26c3f8cd594
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
In myofibroblasts, 237 genes were up-regulated by greater than twofold, including COL10A1 (22.93 fold), DPEP1 (13.61 fold), TSPAN2 (6.45 fold), POSTN (6.39 fold), and CTHRC1 (5.18 fold)

summary:
In Homo sapiens lung, myofibroblasts show upregulation of COL10A1, DPEP1, TSPAN2, POSTN, and CTHRC1 compared to other fibroblast subpopulations.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:d718fe3480335de832af
claim_id: claim:d718fe3480335de832af
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
Within the SPINT2 hi fibroblasts, GRIA1 (13.74 fold), KANK3 (8.44 fold), FIGF (7.13 fold), SPINT2 (6.16 fold), FGFR4 (5.27 fold), and TCF21 (2.97 fold) were among 98 genes with greater than twofold increased expression

summary:
In Homo sapiens lung, SPINT2-high fibroblasts show increased expression of GRIA1, KANK3, FIGF, SPINT2, FGFR4, and TCF21 compared to other fibroblast subpopulations.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:f7d55184d07abee347a1
claim_id: claim:f7d55184d07abee347a1
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
In the MFAP5 hi fibroblasts, TNNT3 (39.89 fold), MFAP5 (26.34 fold), PI16 (18.87 fold), IGF2 (18.49 fold), and ACKR3 (16.16 fold) were among 114 genes with greater than twofold increased expression

summary:
In Homo sapiens lung, MFAP5-high fibroblasts show increased expression of TNNT3, MFAP5, PI16, IGF2, and ACKR3 compared to other fibroblast subpopulations.


claim_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f:claim:c195d6d9f41594bf6179
claim_id: claim:c195d6d9f41594bf6179
paper_key: hca:0374_10.1136_annrheumdis-2018-214865_9f6cd4034f
span_literal:
Three members of the Wnt-related secreted frizzled-related protein (SFRP) family: SFRP1 (13.45 fold), SFRP4 (3.34 fold), and SFRP2 (2.52 fold) were up-regulated, though none were exclusive to this fibroblast subset.

summary:
In Homo sapiens lung, MFAP5-high fibroblasts show upregulation of secreted frizzled-related protein 1 (SFRP1), secreted frizzled-related protein 4 (SFRP4), and secreted frizzled-related protein 2 (SFRP2).


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:566f5eb751285f9bd346
claim_id: claim:566f5eb751285f9bd346
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
span_literal:
Currently, ILCs are phenotypically defined as CD45 + Lin – CD3 – CD161 + CD127 + cells and are subdivided into 3 subsets, namely, group 1 ILCs (ILC1s) (CD117 – CRTH2 – ), group 2 ILCs (ILC2s) (CRTH2 + ), and group 3 ILCs (ILC3s) (CD117 + CRTH2 – ).

summary:
In Homo sapiens, innate lymphoid cells are phenotypically defined as CD45-positive, lineage-negative, CD3-negative, CD161-positive, CD127-positive cells, subdivided into group 1 innate lymphoid cells (CD117-negative, CRTH2-negative), group 2 innate lymphoid cells (CRTH2-positive), and group 3 innate lymphoid cells (CD117-positive, CRTH2-negative).


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:86c5b6cbd1eeba41ef0f
claim_id: claim:86c5b6cbd1eeba41ef0f
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
summary: In Homo sapiens, innate lymphoid cells express PTPRC (CD45), KLRB1 (CD161), and IL7R (CD127).
span_literal:
ILCs expressing PTPRC (CD45), KLRB1 (CD161), and IL7R (CD127) were located in clusters 0, 4, and 5; KLRD1 (CD94) + NK cells were present in cluster 2; CD3D + T cells predominated in cluster 7; KRT1 + and KRT5 + keratinocytes (KC) resided in clusters 1, 3, 6, 8, 10, and 15; a minor subset of CD79A - and IGHG 1 -expressing cells of B-cell lineage were found in cluster 11; LYZ + phagocytes (PH) were present in cluster 12; CLEC14A - and PECAM 1 -expressing endothelial cells (EC) were located in cluster 13; TAGLN + and ACTA2 + smooth muscle cells (SMC) were present in cluster 14; MLANA + melanocytes (MEL) were found in cluster 16; and COL6A1 + fibroblasts (FB) were located in cluster 9


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:3f5ed20d7cd413dd180c
claim_id: claim:3f5ed20d7cd413dd180c
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
summary: In Homo sapiens, innate lymphoid cells are characterized by expression of KLRB1 and IL7R.
span_literal:
we identified the top 10 genes characteristic for each of the attributed cell types, such as KLRB1 and IL7R for ILCs; KLRD1 and GNLY for NK cells; CD3D for T cells; JCHAIN and IGKC for the B-cell lineage; HLA-DQB1 , LYZ, and CD74 for phagocytes; ACTA2 and TAGLN for smooth muscle cells; PMEL , MLANA, and KIT for melanocytes; RAMP2 and PECAM1 for endothelial cells; COL1A2 and COL6A2 for fibroblasts; and KRT14 for keratinocytes


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:976fd7d310c1c21734a1
claim_id: claim:976fd7d310c1c21734a1
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
span_literal:
EOMES + and TBX21 + cells from cluster 1 were assigned to NK cells (NK), and FCER1G + and KLRC1 + cells from cluster 2 were assigned to ILC1s.

summary:
In Homo sapiens, natural killer cells express EOMES and TBX21, while group 1 innate lymphoid cells express FCER1G and KLRC1.


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:14b9c5986cc97a000911
claim_id: claim:14b9c5986cc97a000911
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
span_literal:
Cluster 5 ILCs, which expressed NCR1 (NKp46) and CCR10 , demonstrated a mixture of type 1 and type 3 markers and were, thus, attributed to the ILC1_3 subset

summary:
In Homo sapiens, the group 1/group 3 innate lymphoid cell subset (ILC1_3) expresses NCR1 (NKp46) and CCR10.


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:d7d6b0a848305c11596d
claim_id: claim:d7d6b0a848305c11596d
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
span_literal:
we subdivided cluster 3 into the subgroups 3a and 3b to detect a potential precursor population within cluster 3. We observed indeed that the subset 3a demonstrated a combination of markers ZBTB16 (PLZF), ID2 , KIT , and IL1R1 , which are characteristic of ILC precursors (ILC_pre)

summary:
In Homo sapiens, innate lymphoid cell precursors are characterized by expression of ZBTB16 (PLZF), ID2, KIT, and IL1R1.


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:5edf3f3d3912ff69ef75
claim_id: claim:5edf3f3d3912ff69ef75
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
span_literal:
The subset 3b was assigned to ILC3s because these cells expressed IL23R , IL1R2 as well as RORC and AHR .

summary:
In Homo sapiens, group 3 innate lymphoid cells express IL23R, IL1R2, RORC (RAR related orphan receptor C), and AHR (aryl hydrocarbon receptor).


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:8a12f3053e0294e6b004
claim_id: claim:8a12f3053e0294e6b004
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
span_literal:
Cluster 0 ILCs expressing GATA3 , RORA , PTGDR2 (CRTH2), CRLF2 (TSLPR), IL1RL1 (ST2), and IL17RB were assigned to ILC2s.

summary:
In Homo sapiens, group 2 innate lymphoid cells express GATA3 (GATA binding protein 3), RORA (RAR related orphan receptor A), PTGDR2 (CRTH2), CRLF2 (thymic stromal lymphopoietin receptor), IL1RL1 (ST2), and IL17RB.


claim_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b:claim:fa5f26a30e55f6a501a4
claim_id: claim:fa5f26a30e55f6a501a4
paper_key: hca:0375_10.1016_j.jaci.2021.07.025_bdc966c89b
summary: In Homo sapiens, proliferating natural killer cells express MKI67 and NMUR1.
span_literal:
Within cluster 4 we noticed the expression of MKI67 and NMUR1 and would conclude that they represent proliferating NK cells (NK_pro)


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:8113f952f93b349fecaf
claim_id: claim:8113f952f93b349fecaf
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
summary: In Homo sapiens, hematopoietic stem cells are associated with expression of HLF, MECOM, and NFIB.
span_literal:
The loadings plot for the PCA using the ANOVA define 300 most DEG identified stem- ( HLF , MECOM , NFIB ), lymphoid- ( IGJ , IRF8 , MME ) and erythroid-megakaryocytic-affiliated genes ( HBD , HPGDS )


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:0d440cd68bd56920ac7a
claim_id: claim:0d440cd68bd56920ac7a
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
The loadings plot for the PCA using the ANOVA define 300 most DEG identified stem- ( HLF , MECOM , NFIB ), lymphoid- ( IGJ , IRF8 , MME ) and erythroid-megakaryocytic-affiliated genes ( HBD , HPGDS )

summary:
In Homo sapiens, erythroid-megakaryocytic progenitor cells are associated with expression of HBD and HPGDS.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:715b62a28abd83ca55be
claim_id: claim:715b62a28abd83ca55be
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
LMPP and MLP shared expression of many lymphoid-affiliated genes (e.g. IL7R , LCK , SYK , ADA , HLX , LST1 and ITGAL

summary:
In Homo sapiens, lymphoid-primed multipotent progenitor and multi-lymphoid progenitor share expression of lymphoid-affiliated genes IL7R, LCK, SYK, ADA, HLX, LST1, and ITGAL.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:048d271ce29c7ae2fc9a
claim_id: claim:048d271ce29c7ae2fc9a
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
MLP shared expression of many lymphoid-affiliated genes (e.g. IL7R , LCK , SYK , ADA , HLX , LST1 and ITGAL

summary:
In Homo sapiens, multi-lymphoid progenitor shares expression of lymphoid-affiliated genes IL7R, LCK, SYK, ADA, HLX, LST1, and ITGAL.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:f771617745494c1a47b6
claim_id: claim:f771617745494c1a47b6
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
The GMP signature contained many myeloid genes and the MLP signature many lymphoid genes ( Fig. 4d ). By contrast, the LMPP signature contained both lymphoid ( ETS1 , EBF1 , CYTIP ) and myeloid genes ( TRPM2 , S100A8 , PADI4 , ALOX15B ).

summary:
In Homo sapiens, the lymphoid-primed multipotent progenitor gene signature contains both lymphoid genes ETS1, EBF1, CYTIP and myeloid genes TRPM2, S100A8, PADI4, ALOX15B.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:cce0b385b661ae856e30
claim_id: claim:cce0b385b661ae856e30
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
In both analyses, GMP expressed mainly myeloid TFs (e.g. ERG , GATA2 , MYB , EGR1 ), while lymphoid TFs (e.g. HES1 , RUNX3 , POU2F2 , LEF1 , IKZF1 , IRF8 , TCF4 ) showed highest expression in MLP.

summary:
In Homo sapiens, granulocyte-macrophage progenitor expresses mainly myeloid transcription factors ERG, GATA2, MYB, and EGR1.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:41d4b7727cda332e62a3
claim_id: claim:41d4b7727cda332e62a3
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
In both analyses, GMP expressed mainly myeloid TFs (e.g. ERG , GATA2 , MYB , EGR1 ), while lymphoid TFs (e.g. HES1 , RUNX3 , POU2F2 , LEF1 , IKZF1 , IRF8 , TCF4 ) showed highest expression in MLP.

summary:
In Homo sapiens, multi-lymphoid progenitor shows highest expression of lymphoid transcription factors HES1, RUNX3, POU2F2, LEF1, IKZF1, IRF8, and TCF4.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:a0002917f623750a6519
claim_id: claim:a0002917f623750a6519
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
Cluster 1 showed high expression of lymphoid-affiliated genes (e.g. MME , JCHAIN and ABCA1) . Cluster 3 showed increased expression of myeloid genes (e.g. CPA3, MPO and VIM ). Cluster 2 showed a mixed transcriptional signature and increased expression of hematopoietic progenitor gene KIT .

summary:
In Homo sapiens, the lymphoid-affiliated single cell cluster 1 (mostly multi-lymphoid progenitor) shows high expression of MME, JCHAIN, and ABCA1.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:7959476f57c6ec05089e
claim_id: claim:7959476f57c6ec05089e
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
Cluster 1 showed high expression of lymphoid-affiliated genes (e.g. MME , JCHAIN and ABCA1) . Cluster 3 showed increased expression of myeloid genes (e.g. CPA3, MPO and VIM ). Cluster 2 showed a mixed transcriptional signature and increased expression of hematopoietic progenitor gene KIT .

summary:
In Homo sapiens, the myeloid-affiliated single cell cluster 3 (mostly granulocyte-macrophage progenitor) shows increased expression of CPA3, MPO, and VIM.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:44768c62c1dfc7efc1b2
claim_id: claim:44768c62c1dfc7efc1b2
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
Cluster 1 showed high expression of lymphoid-affiliated genes (e.g. MME , JCHAIN and ABCA1) . Cluster 3 showed increased expression of myeloid genes (e.g. CPA3, MPO and VIM ). Cluster 2 showed a mixed transcriptional signature and increased expression of hematopoietic progenitor gene KIT .

summary:
In Homo sapiens, the mixed lympho-myeloid single cell cluster 2 (lymphoid-primed multipotent progenitor and granulocyte-macrophage progenitor) shows increased expression of the hematopoietic progenitor gene KIT.


claim_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07:claim:b0067940f740724ba493
claim_id: claim:b0067940f740724ba493
paper_key: hca:0376_10.1038_s41590-017-0001-2_5fb0775c07
span_literal:
There was a significant positive correlation between CD38 expression and myeloid gene expression ( MPO ) and negative correlation between CD38 and lymphoid gene expression ( MME and SELL ) by single cell qRT-PCR

summary:
In Homo sapiens, granulocyte-macrophage progenitor cells with high CD38 expression show positive correlation with myeloid gene MPO and negative correlation with lymphoid genes MME and SELL.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:a1c062238825498e46d4
claim_id: claim:a1c062238825498e46d4
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal:
Based on the expression of glutamatergic markers and K-specific markers ( CALB1 , CAMK2A, and PRKCG , Figure 3A , Supplementary file 4 ), two K types, Kap and Kp, could be identified

summary:
In Homo sapiens dorsal lateral geniculate nucleus, koniocellular neurons are identified by expression of the K-specific markers CALB1, CAMK2A, and PRKCG.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:d6887ed8d14db07e22ce
claim_id: claim:d6887ed8d14db07e22ce
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal:
The remaining glutamatergic nuclei belong to a single cluster to which we assign the MP projection neuron identity based on the following observations: (1) it is the most numerous glutamatergic type that expresses the known M/P marker gene PVALB ( Figure 3A ; Yan et al., 1996 ), (2) it does not express K markers CALB1 , CAMK2A, and PRKCG, and (3) it contains cells derived from both M and P layer dissections

summary:
In Homo sapiens dorsal lateral geniculate nucleus, magnocellular/parvocellular projection neurons express the marker gene PVALB and do not express the koniocellular markers CALB1, CAMK2A, and PRKCG.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:4bd40dd9b404c854eec2
claim_id: claim:4bd40dd9b404c854eec2
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
summary: In Homo sapiens dorsal lateral geniculate nucleus, the koniocellular neuron type Kp expresses PENK.
span_literal:
Similar to the K types identified in macaque, the PENK -expressing K type (Kp) is limited to posterior K1 and K2 layers


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:e632433931d785c6935f
claim_id: claim:e632433931d785c6935f
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal: We confirmed expression of the pan-M/P marker gene BTNL9 .
summary:
In Homo sapiens dorsal lateral geniculate nucleus, BTNL9 is a pan-magnocellular/parvocellular marker gene expressed in magnocellular/parvocellular neurons.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:40ced47e8810215677b6
claim_id: claim:40ced47e8810215677b6
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal: We verified expression for M marker genes CRH and SUSD2 and P marker gene EPHA7 .
summary:
In Homo sapiens dorsal lateral geniculate nucleus, CRH and SUSD2 are marker genes for magnocellular neurons, and EPHA7 is a marker gene for parvocellular neurons.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:c361cd62df3a7c5cb988
claim_id: claim:c361cd62df3a7c5cb988
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal: We verified expression for M marker genes CRH and SUSD2 and P marker gene EPHA7 .
summary:
In Homo sapiens dorsal lateral geniculate nucleus, EPHA7 is a marker gene for parvocellular neurons.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:5c0f3b95b81e78e8e498
claim_id: claim:5c0f3b95b81e78e8e498
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal:
FOXP2 is a robust marker of P neurons ( Iwai et al., 2013 ) and is enriched in the macaque P cluster and overlapping nuclei in the human MP cluster

summary:
In Homo sapiens dorsal lateral geniculate nucleus, FOXP2 is a robust marker of parvocellular neurons and is enriched in the human magnocellular/parvocellular cluster.


claim_key: hca:0377_10.7554_elife.64875_32e53ae733:claim:1737c14558b8905fefb1
claim_id: claim:1737c14558b8905fefb1
paper_key: hca:0377_10.7554_elife.64875_32e53ae733
span_literal:
Confirmation of GABAergic SOX14 -positive and SOX14 -negative populations in human ( E ) and macaque ( F ) dorsal lateral geniculate nucleus (dLGN).

summary:
In Homo sapiens dorsal lateral geniculate nucleus, GABAergic neurons include SOX14-positive and SOX14-negative populations.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:b903b4b649792730191a
claim_id: claim:b903b4b649792730191a
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal: macrophages associated with lipid digestion and transport (NUPR1, RBP4) denoted as macro-lipid
summary:
In Homo sapiens, macro-lipid macrophages are marked by NUPR1 and RBP4, associated with lipid digestion and transport.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:107c4a9d8ba94d6734ba
claim_id: claim:107c4a9d8ba94d6734ba
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal:
macrophages expressing cholesterol biosynthesis related genes (MSM01, FDFT1) denoted as macro-cholesterol

summary:
In Homo sapiens, macro-cholesterol macrophages express cholesterol biosynthesis related genes MSM01 and FDFT1.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:0209c4b3b28b13a368e7
claim_id: claim:0209c4b3b28b13a368e7
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal:
macrophages expressing genes associated with; vesicle production (AZU1, PLAC8) denoted as macro-vesicle

summary:
In Homo sapiens, macro-vesicle macrophages express genes associated with vesicle production, including AZU1 and PLAC8.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:e6f424008ee91b809dcd
claim_id: claim:e6f424008ee91b809dcd
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal:
This cluster was characterised by expression of IFI27 and IGF1 and was enriched for REACTOME pathways including interferon-alpha-beta signalling.

summary:
In Homo sapiens, macro-interferon-alpha/beta macrophages are characterized by expression of IFI27 and IGF1.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:6201ea7ae76cb9c82685
claim_id: claim:6201ea7ae76cb9c82685
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal:
macro-CCL population in our dataset was enriched for the chemokine-receptor-bind-chemokines REACTOME pathway, and expressed genes for chemokines CCL4, CCL20, CCL23, CXCL5, CXCL8, CXCL9 and CXCL10

summary:
In Homo sapiens, macro-CCL macrophages express chemokine genes CCL4, CCL20, CCL23, CXCL5, CXCL8, CXCL9, and CXCL10.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:22cfe40ff1820e341883
claim_id: claim:22cfe40ff1820e341883
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal: cDC1 expressed CLEC9A gene and CD141 protein, whilst cDC2 expressed CD1c
summary:
In Homo sapiens, conventional dendritic cell type 1 expresses CLEC9A, whilst conventional dendritic cell type 2 expresses CD1C.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:66fbec5f1eaba97841a8
claim_id: claim:66fbec5f1eaba97841a8
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
summary: In Homo sapiens, plasmacytoid dendritic cells express marker genes CLEC4C and GZMB.
span_literal:
Plasmacytoid DC expressed plasmacytoid surface marker CD123, were negative for conventional markers CD1c and CD141, and marker genes included CLEC4C and GZMB.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:9d1b07f9e018a7266340
claim_id: claim:9d1b07f9e018a7266340
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
summary: In Homo sapiens, plasma B cells are characterized by marker genes JCHAIN, MZB1, and TNFRSF17.
span_literal:
Plasma B cells were also identified, characterised by key marker genes (JCHAIN, MZB1, TNFRSF17) as well as protein expression of plasma markers CD27 and CD38


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:5d6b097afdf5632423c9
claim_id: claim:5d6b097afdf5632423c9
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
summary: In Homo sapiens, goblet/club cells express marker genes MUC5AC, TFF1, AZGP1, FST, and SYT8.
span_literal:
One cluster, denoted as goblet/club cells, expressed marker genes including MUC5AC, TFF1, AZGP1, FST, and SYT8 which are expressed by club, goblet and mucus secreting cells.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:69e05eae2025d8bae8a7
claim_id: claim:69e05eae2025d8bae8a7
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
summary: In Homo sapiens, tracheobronchial goblet/club cells express the marker gene TSPAN8.
span_literal:
Another cluster, denoted as tracheobronchial goblet/club cells, expressed the marker gene TSPAN8 which is a HCLA marker gene for both club and goblet cells from the lower airway.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:92e6ab253cb951432c85
claim_id: claim:92e6ab253cb951432c85
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal:
Both CD8 Trm and CD8-GZMK subtypes expressed genes encoding for cytotoxic proteases GZMA, GZMB, GZMH, GZMM however CD8-GZMK was the only CD8 subtype to express GZMK.

summary:
In Homo sapiens, CD8 tissue-resident memory T cells and CD8-GZMK T cells express cytotoxic protease genes GZMA, GZMB, GZMH, and GZMM, while CD8-GZMK is the only CD8 subtype to express GZMK.


claim_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3:claim:91370c6e7ce143a1981d
claim_id: claim:91370c6e7ce143a1981d
paper_key: hca:0378_10.1101_2022.06.17.496207_92cb140ff3
span_literal:
Both CD8 Trm and CD8-GZMK subtypes expressed genes encoding for cytotoxic proteases GZMA, GZMB, GZMH, GZMM however CD8-GZMK was the only CD8 subtype to express GZMK.

summary:
In Homo sapiens, CD8-GZMK T cells express cytotoxic protease genes GZMA, GZMB, GZMH, GZMM, and uniquely express GZMK among CD8 subtypes.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:f2df8cc90b2f1c67dd09
claim_id: claim:f2df8cc90b2f1c67dd09
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
summary: In Homo sapiens, T cells are identified by expression of CD2 and CD3D in biliary tract cancer.
span_literal:
Based on expression of canonical genes, the identified immune cells included T cells ( CD2, CD3D ); NK cells ( KLRD1, NKG7 ); B cells ( MS4A1, CD79A ) and myeloid cells ( LYZ )


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:6c6a4805db092519891f
claim_id: claim:6c6a4805db092519891f
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
Based on expression of canonical genes, the identified immune cells included T cells ( CD2, CD3D ); NK cells ( KLRD1, NKG7 ); B cells ( MS4A1, CD79A ) and myeloid cells ( LYZ )

summary:
In Homo sapiens, natural killer cells are identified by expression of KLRD1 and NKG7 in biliary tract cancer.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:6691b5275ac856e8cb10
claim_id: claim:6691b5275ac856e8cb10
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
summary: In Homo sapiens, naïve unswitched B cells are characterized by the expression of IGHD and CR2.
span_literal:
For B cells, five kinds of cell types were obtained, including naïve unswitched B cells (characterized by the expression of IGHD and CR2 ), activated memory B cells, resting memory B cells, plasma blast cells and transitional B cells


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:3d43f791b79df1bebdd7
claim_id: claim:3d43f791b79df1bebdd7
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
Naïve CD4 + T cells were dominant in peripheral blood and lymph nodes (Fig. 2d ) and specifically expressed “naïve” marker genes such as TCF7 , IL7R and SELL

summary:
In Homo sapiens, naïve CD4-positive T cells specifically express the marker genes TCF7, IL7R, and SELL.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:103473a40e509147e3f8
claim_id: claim:103473a40e509147e3f8
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
memory, effector, and exhausted CD8 + T cells shared differentially expressed genes, containing a subset of cytotoxicity-associated genes including granzymes and perforins ( GZMB and PRF1 )

summary:
In Homo sapiens, memory CD8-positive T cells, effector CD8-positive T cells, and exhausted CD8-positive T cells share expression of the cytotoxicity-associated genes GZMB and PRF1.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:5f77440f82bed87ab1dd
claim_id: claim:5f77440f82bed87ab1dd
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
memory, effector, and exhausted CD8 + T cells shared differentially expressed genes, containing a subset of cytotoxicity-associated genes including granzymes and perforins ( GZMB and PRF1 )

summary:
In Homo sapiens, effector CD8-positive T cells share expression of the cytotoxicity-associated genes GZMB and PRF1.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:565081b66d2bb769acd9
claim_id: claim:565081b66d2bb769acd9
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
memory, effector, and exhausted CD8 + T cells shared differentially expressed genes, containing a subset of cytotoxicity-associated genes including granzymes and perforins ( GZMB and PRF1 )

summary:
In Homo sapiens, exhausted CD8-positive T cells share expression of the cytotoxicity-associated genes GZMB and PRF1.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:dfc53d605fe6772e6d07
claim_id: claim:dfc53d605fe6772e6d07
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
summary: In Homo sapiens, exhausted CD8-positive T cells express the exhaustion marker gene CXCL13.
span_literal:
exhausted CD8 + T cells alternatively expressed remarkably well-described exhausted genes such as CXCL13


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:6207f84ecce5980ea3ee
claim_id: claim:6207f84ecce5980ea3ee
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
naïve CD8 + T cells highly expressed TCF7 , and GZMK was differentially enriched in memory CD8 + T cells

summary:
In Homo sapiens, naïve CD8-positive T cells highly express TCF7, and GZMK is differentially enriched in memory CD8-positive T cells.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:c1b6ecdedee3b0845e23
claim_id: claim:c1b6ecdedee3b0845e23
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
In contrast, CTLA4 and CD80 were enriched only in Tregs, while PDCD1 and LAG3 were preferentially enriched in exhausted CD8 + T cells

summary:
In Homo sapiens, CTLA4 and CD80 are enriched only in regulatory T cells, while PDCD1 and LAG3 are preferentially enriched in exhausted CD8-positive T cells.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:57f2cd2d4b520f120546
claim_id: claim:57f2cd2d4b520f120546
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
In contrast, CTLA4 and CD80 were enriched only in Tregs, while PDCD1 and LAG3 were preferentially enriched in exhausted CD8 + T cells

summary:
In Homo sapiens, PDCD1 and LAG3 are preferentially enriched in exhausted CD8-positive T cells compared to regulatory T cells.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:d1983f426357d7ef9845
claim_id: claim:d1983f426357d7ef9845
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
some of these genes activated in Tregs overlapped with those features of exhausted CD8 + T cells (e.g., TNFRSF9 , and TIGIT )

summary:
In Homo sapiens, regulatory T cells express TNFRSF9 and TIGIT, which overlap with features of exhausted CD8-positive T cells.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:16d5127223d52e7257dd
claim_id: claim:16d5127223d52e7257dd
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
some of these genes activated in Tregs overlapped with those features of exhausted CD8 + T cells (e.g., TNFRSF9 , and TIGIT )

summary:
In Homo sapiens, exhausted CD8-positive T cells express TNFRSF9 and TIGIT, which overlap with features of regulatory T cells.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:dc97b55ca9ea31e0ddde
claim_id: claim:dc97b55ca9ea31e0ddde
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
Tex01 and Tex03 cells expressed high levels of PDCD1, LAYN, CTLA4 , and HAVCR2 but low levels of XBP1 , whereas Tex02 and Tex05 cells exhibited the opposite pattern

summary:
In Homo sapiens, exhausted CD8-positive T cell subtype Tex01 expresses high levels of PDCD1, LAYN, CTLA4, and HAVCR2 but low levels of XBP1.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:6260ef80b3b295eff65f
claim_id: claim:6260ef80b3b295eff65f
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
Tex01 and Tex03 cells expressed high levels of PDCD1, LAYN, CTLA4 , and HAVCR2 but low levels of XBP1 , whereas Tex02 and Tex05 cells exhibited the opposite pattern

summary:
In Homo sapiens, exhausted CD8-positive T cell subtype Tex03 expresses high levels of PDCD1, LAYN, CTLA4, and HAVCR2 but low levels of XBP1.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:60663262f4c26d5b0692
claim_id: claim:60663262f4c26d5b0692
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal:
Tex01 and Tex03 cells expressed high levels of PDCD1, LAYN, CTLA4 , and HAVCR2 but low levels of XBP1 , whereas Tex02 and Tex05 cells exhibited the opposite pattern

summary:
In Homo sapiens, exhausted CD8-positive T cell subtype Tex02 expresses high levels of XBP1 but low levels of PDCD1, LAYN, CTLA4, and HAVCR2.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:16cdcd218105d3d498f8
claim_id: claim:16cdcd218105d3d498f8
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
summary:
In Homo sapiens, exhausted CD8-positive T cell subtype Tex05 expresses high levels of XBP1 but low levels of PDCD1, LAYN, CTLA4, and HAVCR2.


claim_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6:claim:569e0db31f0951c3cb76
claim_id: claim:569e0db31f0951c3cb76
paper_key: hca:0379_10.1038_s41698-022-00300-9_7bb9a273c6
span_literal: although LAG3 and TIGIT were uniformly highly expressed among exhausted CD8 + T cell subtypes
summary:
In Homo sapiens, LAG3 and TIGIT are uniformly highly expressed among exhausted CD8-positive T cell subtypes.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:574ffe7b666ca785477e
claim_id: claim:574ffe7b666ca785477e
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
Feature plots of markers of broad progenitors ( SOX2 ), radial glia ( NES ), IPCs ( PPP1R17 ), and neurons ( BCL11B ) are shown.

summary:
In Homo sapiens, SOX2 is a marker of broad progenitors, NES (nestin) is a marker of radial glia, PPP1R17 is a marker of intermediate progenitor cells, and BCL11B is a marker of neurons in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:50a4d5aa472cccff7e2e
claim_id: claim:50a4d5aa472cccff7e2e
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
summary: In Homo sapiens, NHLH1 is a marker of newborn neurons derived from intermediate progenitor cells.
span_literal:
These included expected differences such as clusters marked by NHLH1 , which was significantly higher in the older samples, and has been associated with newborn neurons derived from IPCs 18 .


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:f650282deaca7eed9220
claim_id: claim:f650282deaca7eed9220
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
summary: In Homo sapiens, RELN marks Cajal-Retzius cells in the early developing cortex.
span_literal:
The remaining clusters consisted of expected early-born neuronal populations including Cajal-Retzius cells marked by RELN ( SFig 10 ), and subplate cells marked by TLE4 and NR4A2 .


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:14414340e13115d8f284
claim_id: claim:14414340e13115d8f284
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
As expected, HES5 was strongly enriched in radial glia compared to other cell types, and FGF10 peaked in neuroepithelial populations ( SFig 15 ).

summary:
In Homo sapiens, HES5 is strongly enriched in radial glia compared to other cell types in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:15d5560ba2ca213f9829
claim_id: claim:15d5560ba2ca213f9829
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
As expected, HES5 was strongly enriched in radial glia compared to other cell types, and FGF10 peaked in neuroepithelial populations ( SFig 15 ).

summary:
In Homo sapiens, FGF10 expression peaks in neuroepithelial cell populations in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:3dbeb3e46991c822e0a5
claim_id: claim:3dbeb3e46991c822e0a5
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
NTRK3 was a highly specific marker of Progenitor Cluster 3, and intrigued us because it is commonly described as a TrkC receptor that enables survival of specific neuronal populations 34 and has broad neocortical expression at later stages of mouse cortex development 35 .

summary:
In Homo sapiens, NTRK3 is a highly specific marker of Progenitor Cluster 3 in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:4ad21169029846605ba2
claim_id: claim:4ad21169029846605ba2
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
Both in our initial clustering and in the more focused progenitor analysis, a mesenchymal-like population labelled by the gene LUM was distinctly segregated from other progenitor populations.

summary:
In Homo sapiens, LUM labels a mesenchymal-like population that is distinctly segregated from other progenitor populations in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:a878d9d938bcddbff4cc
claim_id: claim:a878d9d938bcddbff4cc
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
summary: In Homo sapiens, ALX1 is a marker of the mesenchymal-like cell cluster in the developing cortex.
span_literal:
Another marker of this cluster was ALX1 , which also has one of the most correlated gene expression patterns to LUM ( Fig 3B ).


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:e40538da8e68c5e5bd5a
claim_id: claim:e40538da8e68c5e5bd5a
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
However, there were no high correlations for Progenitor Cluster 4 (marked most highly by C1orf61 ) or Progenitor Cluster 7 (marked most highly by ID4 ).

summary:
In Homo sapiens, C1orf61 most highly marks Progenitor Cluster 4 and ID4 most highly marks Progenitor Cluster 7 in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:1b8970838685fb2221f5
claim_id: claim:1b8970838685fb2221f5
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
newborn neurons marked by doublecortin (DCX, green), progenitors by SOX2 (red), IPCs by TBR2 (yellow), and maturing neurons by CTIP2 (cyan).

summary:
In Homo sapiens, doublecortin (DCX) marks newborn neurons, SOX2 marks progenitors, TBR2 marks intermediate progenitor cells, and CTIP2 marks maturing neurons in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:3525ece0443ede2307d1
claim_id: claim:3525ece0443ede2307d1
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
summary: In Homo sapiens, FN1 is a marker of endothelial cells in the developing cortex.
span_literal:
This is supported by further velocity analysis demonstrating an increase in velocity (indicated in red) of presumptive endothelial ( FN1 ) and pericyte ( RGS5 ) markers, but not markers of microglia identity ( AIF1 ) or the marker of the mesenchymal population ( LUM ) ( SFig 4D ).


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:d64cccd89bc23a1fff45
claim_id: claim:d64cccd89bc23a1fff45
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
Using NES as a marker of radial glia, TJP1 (ZO-1) as an indicator of neuroepithelial cells, and SOX2 as a label for all progenitor populations, we saw small numbers of nestin-positive radial glia at CS14, with substantial upregulation by CS22 that simultaneously corresponded to a waning of ZO-1 ( Fig 2A ).

summary:
In Homo sapiens, NES (nestin) is a marker of radial glia, TJP1 (ZO-1) is an indicator of neuroepithelial cells, and SOX2 labels all progenitor populations in the developing cortex.


claim_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47:claim:f41de1dfbc1738f999fa
claim_id: claim:f41de1dfbc1738f999fa
paper_key: hca:0380_10.1038_s41593-020-00794-1_0ecbc1eb47
span_literal:
From this analysis we identified 29 populations that were characterized by SOX2 (progenitor), TOP2A (dividing), LHX5-AS1 (previously uncharacterized cell population), and LUM (mesenchymal cells).

summary:
In Homo sapiens, TOP2A characterizes dividing cells and LUM characterizes mesenchymal cells in the early developing cortex.


claim_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127:claim:919f391a5ed5e8cc4e62
claim_id: claim:919f391a5ed5e8cc4e62
paper_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127
summary: In Homo sapiens, inflammatory macrophages group A are marked by IL6, IL1B, and CXCL8.
span_literal:
One of the inflammatory macrophage clusters, made up almost exclusively of NEC-associated macrophages (inflammatory macrophages group A), was marked by inflammatory cytokines and chemokines such as IL6 , IL1B , and CXCL8 , previously shown to be associated with NEC


claim_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127:claim:7f632f46b7aa0be0d0b3
claim_id: claim:7f632f46b7aa0be0d0b3
paper_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127
span_literal:
We next turned to analyze the changes in enterocyte cell identity in NEC. Our atlas included 1,203 enterocytes ( Fig 5A and 5B ), which we further classified by crypt-villus zones using landmark genes, such as the villus-top gene APOA4 and the crypt gene LGR5

summary:
In Homo sapiens, villus-top enterocytes are marked by APOA4 and crypt enterocytes are marked by LGR5.


claim_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127:claim:d1d848ee9fb3ceb141bc
claim_id: claim:d1d848ee9fb3ceb141bc
paper_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127
span_literal:
To validate the induction of proinflammatory endothelial cells in NEC, we performed single-molecule fluorescence in situ hybridization (smFISH) for the endothelial/lymphatic-specific marker CLDN5 along with SELE as a specific marker of endothelial activation, and identified elevation in SELE+ endothelial cells in NEC

summary:
In Homo sapiens, vascular and lymphatic endothelial cells are marked by CLDN5, and activated endothelial cells are specifically marked by SELE.


claim_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127:claim:033b8284bc7d9038457f
claim_id: claim:033b8284bc7d9038457f
paper_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127
span_literal: DGE analysis of the Tregs revealed an increase in SELL (CD62L), CCR7 , as well as SOCS1
summary:
In Homo sapiens, regulatory T cells in necrotizing enterocolitis tissue show increased expression of SELL, CCR7, and SOCS1.


claim_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127:claim:602cdb76ab7771a38f4d
claim_id: claim:602cdb76ab7771a38f4d
paper_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127
span_literal:
Interestingly, there was a reduction in the expression genes classically associated with Treg identity or suppression function such as CTLA-4 , TIGIT , iCOS , TNFRSF4 (encoding the Ox40 receptor found on intestinal Tregs and effector memory T cells), and IL2RA

summary:
In Homo sapiens, regulatory T cells are classically associated with expression of CTLA-4, TIGIT, ICOS, TNFRSF4, and IL2RA as markers of identity or suppressive function.


claim_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127:claim:f21597d06e1f8093515b
claim_id: claim:f21597d06e1f8093515b
paper_key: hca:0382_10.1371_journal.pbio.3002124_f92c982127
span_literal:
UMAPs colored by cell type and the expression of PDPN and CLDN5 in all cells in the atlas from Fig 1B and 1C . Vascular/lymphatic endothelial cells are marked by a red square.

summary:
In Homo sapiens, vascular and lymphatic endothelial cells are marked by expression of PDPN and CLDN5.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:59a12c8d21e44a059d73
claim_id: claim:59a12c8d21e44a059d73
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
span_literal: ITGA8/Itga8 reliably marks the Col13a1 + fibroblast population across species.
summary:
In Homo sapiens, ITGA8 is a positive marker of the Col13a1-positive fibroblast population, conserved across species.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:2e29d95ebf3326db4d8d
claim_id: claim:2e29d95ebf3326db4d8d
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
span_literal:
ATI cells were consistently identified as a major signaling hub at a level approaching that of mesenchymal cells. Initial investigations revealed that this high centrality of ATI cells was backed by their expression of key growth factor genes including BDNF, SEMA3E, VEGFA, and PDGFA, as well as multiple WNT ligand genes (violin plots demonstrating these species-conserved patterns are shown in fig. S6).

summary:
In Homo sapiens, alveolar type I cells express key growth factor genes including BDNF, SEMA3E, VEGFA, and PDGFA, as well as WNT ligand genes, in a species-conserved pattern.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:847e2105cc1ec1f22b1e
claim_id: claim:847e2105cc1ec1f22b1e
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
span_literal:
Capillary endothelia ( Fig. 4C ), on the other hand, strongly express receptors such as KDR, FLT1, and NRP1, and their niche plot therefore shows a large contribution from VEGF family signaling.

summary:
In Homo sapiens, capillary endothelial cells strongly express KDR, FLT1, and NRP1, receptors for VEGF family signaling.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:f30b2d909ff19daffc22
claim_id: claim:f30b2d909ff19daffc22
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
span_literal:
ATII cells display strong macrophage cross-talk based on CSF2, complement, GAS6, OSM, and APOE, aligning with known roles for ATII-macrophage cross-talk in surfactant handling and immune regulation

summary:
In Homo sapiens, alveolar type II cells express CSF2, GAS6, OSM, and APOE, mediating cross-talk with macrophages.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:491f86841b8fadd2e979
claim_id: claim:491f86841b8fadd2e979
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
summary: In Homo sapiens, endothelial cells strongly produce DLL4, a Notch ligand.
span_literal:
Notch ligand DLL4, a major regulator of vascular development ( 35 ), is produced strongly by endothelial cells in the adult and can be sensed by a variety of cells, including SMCs and fibroblasts.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:69f3bc4aeac7a83c43db
claim_id: claim:69f3bc4aeac7a83c43db
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
summary: In Homo sapiens, Col13a1-positive fibroblasts display elevated transcription of HGF and FGF10.
span_literal:
Gene-level exploration of the species-conserved connectome revealed that Col13a1 + fibroblasts display elevated transcription of the genes HGF and FGF10.


claim_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee:claim:72d659395286c48544bb
claim_id: claim:72d659395286c48544bb
paper_key: hca:0383_10.1126_sciadv.aaw3851_fd6802ffee
span_literal:
These ligands are known potent regulators of epithelial phenotype and interact with receptors encoded by MET and FGFR2 (respectively), both of which were expressed by ATII cells.

summary:
In Homo sapiens, alveolar type II cells express MET and FGFR2, receptors for HGF and FGF10 respectively.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:b7dd4fc60471fc9b93f1
claim_id: claim:b7dd4fc60471fc9b93f1
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
HSPC cluster was distinguished by the enrichment of stem and progenitor cells-related genes, such as CD34 , MYCN and MECOM .

summary:
In Homo sapiens, hematopoietic stem/progenitor cells are marked by enrichment of CD34, MYCN and MECOM.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:54d66c6137bde9692941
claim_id: claim:54d66c6137bde9692941
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Two lymphoid progenitor (LP) clusters, LP1 and LP2, were readily identified based on the expression of lymphoid-specific genes CD7 and IL7R .

summary:
In Homo sapiens, lymphoid progenitor 1 and lymphoid progenitor 2 are identified by expression of CD7 and IL7R.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:bc666d5eef48119dba78
claim_id: claim:bc666d5eef48119dba78
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
summary: In Homo sapiens, pre pro-B cells highly express CD79A and CD79B in addition to CD7 and IL7R.
span_literal:
In addition to CD7 and IL7R , B-lineage genes CD79A and CD79B were highly expressed in pre pro-B cells.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:2e9b76d7399d379a0fb6
claim_id: claim:2e9b76d7399d379a0fb6
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal: Meanwhile, enrichment of GATA3 and TCF7 in ETP cluster was in line with its T-lineage potential.
summary:
In Homo sapiens, early thymic progenitor cells are enriched for GATA3 and TCF7, consistent with T-lineage potential.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:751b04d32eac9cab1bc2
claim_id: claim:751b04d32eac9cab1bc2
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Precursors of plasmacytoid dendritic cells (pre pDC) were characterized by the expression of IRF7, CLEC4C and remaining expression of CD34 .

summary:
In Homo sapiens, precursors of plasmacytoid dendritic cells are characterized by expression of IRF7, CLEC4C and CD34.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:ff6f8494de5e7af7269f
claim_id: claim:ff6f8494de5e7af7269f
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
summary: In Homo sapiens, innate lymphoid cell progenitors are enriched for RORC expression.
span_literal:
Importantly, RORC , encoding the essential TF (RORγt) for all ILCs and especially ILC3 development, 21 , 30 was enriched in ILCP cluster.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:de2aa8e4bdcc01cf62ce
claim_id: claim:de2aa8e4bdcc01cf62ce
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Consistent with the expression of cell surface marker, Group 1 ILC showed lower expression of IL7R and KIT , but higher expression of KLRB1 , than other ILC groups.

summary:
In Homo sapiens, Group 1 innate lymphoid cells show lower expression of IL7R and KIT but higher expression of KLRB1 compared with other innate lymphoid cell groups.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:4f4e697d4904e4a53e64
claim_id: claim:4f4e697d4904e4a53e64
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
summary: In Homo sapiens, Group 1 innate lymphoid cells are confirmed by enrichment of EOMES and IFNG.
span_literal:
The identification of Group 1 ILC was also confirmed by the enriched EOMES , which encodes the signature TF for cytotoxic ILC, and IFNG (Fig. 2b, c ).


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:726d24eae034745440ec
claim_id: claim:726d24eae034745440ec
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal: Group 2 ILC cluster was annotated based on the expression of GATA3 and PTGDR2 (encoding CRTH2).
summary:
In Homo sapiens, Group 2 innate lymphoid cells are annotated based on expression of GATA3 and PTGDR2.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:21d7e903070f1038d6fc
claim_id: claim:21d7e903070f1038d6fc
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Group 3 ILC was featured by the expression of RORC , and the highest expression level of IL7R and KIT .

summary:
In Homo sapiens, Group 3 innate lymphoid cells are featured by expression of RORC and the highest expression of IL7R and KIT.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:fd3fb629437425af229f
claim_id: claim:fd3fb629437425af229f
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Group 1 ILC-featured genes, TBX21 , NFIL3 , EOMES and IFNG were highly expressed in all ILC1 sub-populations, suggestive of their identities (Fig. 4b ; Supplementary information, Table S 5 ).

summary:
In Homo sapiens, Group 1 innate lymphoid cell subpopulations highly express TBX21, NFIL3, EOMES and IFNG.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:435018cb5ba24d3f2e42
claim_id: claim:435018cb5ba24d3f2e42
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
CXCR4 , the gene encoding the receptor of chemokine CXCL12 (SDF-1) expressed on the primary human skin fibroblast, 72 , 73 was enriched in ILC1_b cluster that might be involved in the recruitment of ILC1_b to skin (Fig. 4d ).

summary:
In Homo sapiens, CXCR4 is enriched in the ILC1_b cluster and may be involved in recruitment of ILC1_b to skin.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:7516071dced18c09865e
claim_id: claim:7516071dced18c09865e
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
ILC1_c cells were preferably located in liver and spleen (Fig. 4e ), with high expression of molecular chaperone-coding genes such as HSPA1B , HSP90AA1 and HSPA1A , and their function needs further investigation.

summary:
In Homo sapiens, ILC1_c cells highly express HSPA1B, HSP90AA1 and HSPA1A and are preferably located in liver and spleen.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:7c23d79f467da4d0a2d1
claim_id: claim:7c23d79f467da4d0a2d1
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
cytotoxicity-related genes, FGFBP2 , FCGR3A (encoding CD16a) and GZMB , were enriched in ILC1_d cluster, highlighting their NK and/or ILC1 identities (Fig. 4d ).

summary:
In Homo sapiens, FGFBP2, FCGR3A and GZMB are enriched in the ILC1_d cluster, highlighting natural killer cell and/or ILC1 identities.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:57e18b37f030f9fa360c
claim_id: claim:57e18b37f030f9fa360c
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
In accordance with our previous study, IL7R was enriched in ILC1 subset, but not in NK cells, and FGFBP2 showed restricted expression in the NK subset (Fig. 4g ).

summary:
In Homo sapiens, IL7R is enriched in the ILC1 subset but not in natural killer cells, while FGFBP2 shows restricted expression in the natural killer cell subset.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:b325f2543c30b41ef5d9
claim_id: claim:b325f2543c30b41ef5d9
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
In accordance with our previous study, IL7R was enriched in ILC1 subset, but not in NK cells, and FGFBP2 showed restricted expression in the NK subset (Fig. 4g ).

summary:
In Homo sapiens, FGFBP2 shows restricted expression in the natural killer cell subset, distinguishing it from the ILC1 subset.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:9cbf9da4b9841918ff72
claim_id: claim:9cbf9da4b9841918ff72
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
The cluster was separated into five sub-clusters (Fig. 5a ; Supplementary information, Table S 5 ), all of which were characterized by the high expression of ILC2-featured TF coding genes, GATA3 and RORA (Fig. 5b ).

summary:
In Homo sapiens, all Group 2 innate lymphoid cell sub-clusters are characterized by high expression of GATA3 and RORA.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:a68a8a3fcfee9e80038e
claim_id: claim:a68a8a3fcfee9e80038e
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Cells in Pre-ILC2 sub-cluster were proposed to be ILC2 precursors, based on the enrichment of PRSS57 and SPINK2 , as well as the reduction of proportion from 8 to 12 PCW (Fig. 5c ; Supplementary information, Fig. S 8a ).

summary:
In Homo sapiens, Pre-ILC2 cells are proposed to be ILC2 precursors based on enrichment of PRSS57 and SPINK2.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:e8a62e2c90dd8e3215ce
claim_id: claim:e8a62e2c90dd8e3215ce
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Both of them expressed high level of PTGDR2 (encoding CRTH2), while the latter specifically overrepresented PTGS2 that is essential for human ILC2 activation in PB and tonsil (Fig. 5b, c ).

summary:
In Homo sapiens, CRTH2_ILC2 and PTGS2_ILC2 express high levels of PTGDR2, while PTGS2_ILC2 specifically overrepresents PTGS2.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:c663c011d9f154772e64
claim_id: claim:c663c011d9f154772e64
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
Highest expression of IL1RL1 (encoding IL-33 receptor) and IL13 in CRTH2_ILC2 (Fig. 5c, e ) indicated their mature status.

summary:
In Homo sapiens, CRTH2_ILC2 cells show the highest expression of IL1RL1 and IL13, indicating their mature status.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:11c93c732e88d5b6253f
claim_id: claim:11c93c732e88d5b6253f
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
summary: In Homo sapiens, PTGS2_ILC2 is enriched for NR4A2 and NR4A3.
span_literal:
Enrichment of NR4A2 and NR4A3 suggested that PTGS2_ILC2 might be transcriptionally correlated with the newly identified ILC2 subpopulation localized with the fibroblast-like adventitial stromal cells 76 (Fig. 5e ).


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:a2d84fa69e4e09fb59e1
claim_id: claim:a2d84fa69e4e09fb59e1
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
ILC3_a was a proliferating subset, showing the higher expression of DNA replication-regulated genes ( TUBA1B , TUBB and TOP2A ) and MKI67 , but lower expression of ILC3-related genes, such as RORC and KIT , than other subsets (Fig. 6b, c ; Supplementary information, Fig. S 9a ), indicative of its precursor identity.

summary:
In Homo sapiens, ILC3_a (Pre-ILC3) shows higher expression of TUBA1B, TUBB, TOP2A and MKI67 but lower expression of RORC and KIT than other ILC3 subsets, indicative of its precursor identity.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:df0f939459f407e659a7
claim_id: claim:df0f939459f407e659a7
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
summary: In Homo sapiens, ILC3_e highly expresses NKG7, CD3D, IKZF3 and BCL11B.
span_literal:
Intriguingly, ILC3_e also highly expressed genes encoding NK and T cell surface markers and TFs, such as NKG7 , CD3D , IKZF3 85 and BCL11B , as seen in CCR9_ILC2s identified above (Fig. 6d ).


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:d6d4731d8f6bd008a3c5
claim_id: claim:d6d4731d8f6bd008a3c5
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal: The LTi-featured genes LTB was expressed in both ILC3_b and ILC3_c cells (Fig. 6d ).
summary:
In Homo sapiens, the lymphoid tissue-inducer-featured gene LTB is expressed in both ILC3_b and ILC3_c cells.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:de393a6c704c3e5629d0
claim_id: claim:de393a6c704c3e5629d0
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
NRP1 , expressed by LTi-like group 3 ILCs in smokers’ lungs and associated with ectopic lymphoid aggregates, 86 was also enriched in ILC3_b and ILC3_c (Fig. 6h ).

summary:
In Homo sapiens, NRP1 is enriched in ILC3_b and ILC3_c, which form the lymphoid tissue-inducer-related cluster.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:b2a6014883ee299def74
claim_id: claim:b2a6014883ee299def74
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
NRP1 , expressed by LTi-like group 3 ILCs in smokers’ lungs and associated with ectopic lymphoid aggregates, 86 was also enriched in ILC3_b and ILC3_c (Fig. 6h ).

summary:
In Homo sapiens, NRP1 is enriched in ILC3_c, which forms part of the lymphoid tissue-inducer-related cluster.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:338fd178f5bf45cf40f4
claim_id: claim:338fd178f5bf45cf40f4
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
In coincidence with studies in mouse, 25 , 27 ILCP had the upregulated expression of NFIL3 , ID2 and TOX (Fig. 7b ), indicating that the multi-potent lymphoid progenitors had been specialized to the ILC lineages.

summary:
In Homo sapiens, innate lymphoid cell progenitors have upregulated expression of NFIL3, ID2 and TOX, indicating specialization to the innate lymphoid cell lineages.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:7ca5c1b58589ec3247cd
claim_id: claim:7ca5c1b58589ec3247cd
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
IL3RA was also enriched in LPs (LP1 and LP2), suggesting the potential function of IL-3RA on ILC lineage decision (Fig. 3d ).

summary:
In Homo sapiens, IL3RA is enriched in lymphoid progenitor 1 and lymphoid progenitor 2, suggesting a potential function of interleukin-3 receptor alpha on innate lymphoid cell lineage decision.


claim_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe:claim:23a2177e5a18ea2dbee4
claim_id: claim:23a2177e5a18ea2dbee4
paper_key: hca:0384_10.1038_s41422-021-00529-2_d6c8237ebe
span_literal:
IL3RA was also enriched in LPs (LP1 and LP2), suggesting the potential function of IL-3RA on ILC lineage decision (Fig. 3d ).

summary:
In Homo sapiens, IL3RA is enriched in lymphoid progenitor 2, suggesting a potential function of interleukin-3 receptor alpha on innate lymphoid cell lineage decision.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:3713b25eb2ddef15ded7
claim_id: claim:3713b25eb2ddef15ded7
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary: In Homo sapiens, CLDN5 is a marker of endothelial cells in the cerebrovasculature.
span_literal:
We confirmed robust differential expression for known marker genes in endothelial (CLDN5) , mural (TAGLN) , fibroblast (CEMIP) , ependymal (TTR) , astroglia (GFAP) , neurons (CAMK2A) , oligodendrocytes (PLP1) , and microglial (CSF1R) cell types


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:8a1c077a709c3973b791
claim_id: claim:8a1c077a709c3973b791
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
we identified markers for subtypes of these cells, separating endothelial cells into arteriole ( VEGFC, ARL15 ), capillary ( MFSD2A, SLC7A5 ), venule ( TSHZ2, ADGRG6 ), separating mural cells into aSMC ( ACTA2, MYH11 ), vSMC ( MRC1, CD74 ), pericytes ( GRM8, PDGFRB ), and separating fibroblasts into Type I ( ABCA10, FBLN1), Type II ( TRPM3, MYRIP ), and Type III ( KCNMA1, SLC4A4 ), which we discuss in detail below.

summary:
In Homo sapiens, VEGFC and ARL15 are markers of arteriole endothelial cells in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:51f4aa9dd516cb17e6e4
claim_id: claim:51f4aa9dd516cb17e6e4
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
we identified markers for subtypes of these cells, separating endothelial cells into arteriole ( VEGFC, ARL15 ), capillary ( MFSD2A, SLC7A5 ), venule ( TSHZ2, ADGRG6 ), separating mural cells into aSMC ( ACTA2, MYH11 ), vSMC ( MRC1, CD74 ), pericytes ( GRM8, PDGFRB ), and separating fibroblasts into Type I ( ABCA10, FBLN1), Type II ( TRPM3, MYRIP ), and Type III ( KCNMA1, SLC4A4 ), which we discuss in detail below.

summary:
In Homo sapiens, MFSD2A and SLC7A5 are markers of capillary endothelial cells in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:32f3323c7e4abbe31d18
claim_id: claim:32f3323c7e4abbe31d18
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
we identified markers for subtypes of these cells, separating endothelial cells into arteriole ( VEGFC, ARL15 ), capillary ( MFSD2A, SLC7A5 ), venule ( TSHZ2, ADGRG6 ), separating mural cells into aSMC ( ACTA2, MYH11 ), vSMC ( MRC1, CD74 ), pericytes ( GRM8, PDGFRB ), and separating fibroblasts into Type I ( ABCA10, FBLN1), Type II ( TRPM3, MYRIP ), and Type III ( KCNMA1, SLC4A4 ), which we discuss in detail below.

summary:
In Homo sapiens, TSHZ2 and ADGRG6 are markers of venule endothelial cells in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:3111a765b038c4f302ce
claim_id: claim:3111a765b038c4f302ce
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary:
In Homo sapiens, ACTA2 and MYH11 are markers of arterial smooth muscle cells in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:9455e9cf00f5b1e427f1
claim_id: claim:9455e9cf00f5b1e427f1
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary:
In Homo sapiens, ABCA10 and FBLN1 are markers of Type I perivascular fibroblasts in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:98e01c851a76595c286f
claim_id: claim:98e01c851a76595c286f
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary:
In Homo sapiens, TRPM3 and MYRIP are markers of Type II perivascular fibroblasts in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:18ec3feb1ec5c4d3d469
claim_id: claim:18ec3feb1ec5c4d3d469
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary:
In Homo sapiens, KCNMA1 and SLC4A4 are markers of Type III perivascular fibroblasts in the cerebrovasculature.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:f68941db9b4200e44f7c
claim_id: claim:f68941db9b4200e44f7c
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
Here, we confirm by indirect immunofluorescence staining the expression of FBLN1 , CEMIP , and KCNMA1 , as markers for Type I, II, and III fibroblasts, respectively

summary:
In Homo sapiens, FBLN1 is a marker for Type I perivascular fibroblasts, confirmed by indirect immunofluorescence staining.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:b24d8be703e37653397f
claim_id: claim:b24d8be703e37653397f
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
Here, we confirm by indirect immunofluorescence staining the expression of FBLN1 , CEMIP , and KCNMA1 , as markers for Type I, II, and III fibroblasts, respectively

summary:
In Homo sapiens, CEMIP is a marker for Type II perivascular fibroblasts, confirmed by indirect immunofluorescence staining.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:625942079b824da676fe
claim_id: claim:625942079b824da676fe
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
Here, we confirm by indirect immunofluorescence staining the expression of FBLN1 , CEMIP , and KCNMA1 , as markers for Type I, II, and III fibroblasts, respectively

summary:
In Homo sapiens, KCNMA1 is a marker for Type III perivascular fibroblasts, confirmed by indirect immunofluorescence staining.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:7083f36082deabd8f66f
claim_id: claim:7083f36082deabd8f66f
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
We confirm TLR2 enrichment in vc-astrocytes by indirect immunofluorescence staining to demonstrate that a subset of GFAP -expressing astrocytes in proximity to the vasculature express TLR2 , whereas GFAP -expressing astrocytes not in proximity to blood vessels do not express TLR2

summary:
In Homo sapiens, TLR2 is a positive marker of vasculature-coupled astrocytes, distinguishing them from canonical astrocytes not in proximity to blood vessels.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:a730c5e9201f8f2a265d
claim_id: claim:a730c5e9201f8f2a265d
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary: In Homo sapiens, TGFBR1, TGFBR2, and BMPR2 are highly expressed in vasculature-coupled microglia.
span_literal:
Predicted receptors TGFBR1 , TGFBR2 , and BMPR2 were highly expressed in vc-microglia, indicating they may act as mediating receptors.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:5c64bd01c5ecc26243a3
claim_id: claim:5c64bd01c5ecc26243a3
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
These receptors activate downstream targets ID1 , VEGFC , and ID3 , which were also highly expressed in vc-microglia

summary:
In Homo sapiens, ID1, VEGFC, and ID3 are highly expressed in vasculature-coupled microglia as downstream targets.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:f28161180466e9765db4
claim_id: claim:f28161180466e9765db4
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
summary: In Homo sapiens, NRGN, SLC17A7, and CAMK2A are canonical markers of excitatory neurons.
span_literal:
we checked the canonical markers (excitatory neuron: NRGN , SLC17A7 , and CAMK2A ; inhibitory neuron: GAD1 and GAD2 ; astrocyte: AQP4 and GFAP ; oligodendrocyte: MBP , MOBP , and PLP1 ; microglia: CSF1R , CD74 , and C3 ; OPC: VCAN , PDGFRA , and CSPG4 ; endothelial: FLT1 and CLDN5 ; pericyte: AMBP )


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:2b378578ed0a425e90bb
claim_id: claim:2b378578ed0a425e90bb
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal:
We found strong conservation between zonation markers of human and mouse arterioles ( VEGFC, BMX, EFNB2 ) and capillaries ( MFSD2A, TFRC ), but venule zonation markers differed between species.

summary:
In Homo sapiens, VEGFC, BMX, and EFNB2 are zonation markers of arteriole endothelial cells, and MFSD2A and TFRC are zonation markers of capillary endothelial cells.


claim_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2:claim:ff5f6a1e36d88d1323b4
claim_id: claim:ff5f6a1e36d88d1323b4
paper_key: hca:0385_10.1038_s41586-022-04521-7_37f1f319e2
span_literal: TSHZ2 and LRRC1 were both venule-zonated in human, but showed no expression in mouse endothelium.
summary:
In Homo sapiens, TSHZ2 and LRRC1 are venule-zonated markers of venule endothelial cells, with no expression in mouse endothelium.


claim_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824:claim:e507b604a0d52a0d9971
claim_id: claim:e507b604a0d52a0d9971
paper_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824
summary: In Homo sapiens, NR4A2 is a marker gene specific to midbrain dopamine neurons.
span_literal:
we identified the gene Nr4a2 encoding a transcription factor (TF) as specific to mammalian midbrain DA neurons


claim_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824:claim:15a63248f3db07e205fd
claim_id: claim:15a63248f3db07e205fd
paper_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824
span_literal:
Four DA clusters preferentially expressed SOX6 while the other six expressed CALB1 , recapitulating a well-defined developmental axis of variation within midbrain DA neurons

summary:
In Homo sapiens, four dopamine neuron clusters preferentially express SOX6 while six express CALB1 in the midbrain.


claim_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824:claim:3a83298ce4ae31a9b37f
claim_id: claim:3a83298ce4ae31a9b37f
paper_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824
span_literal:
A single subtype, marked by the expression of the gene AGTR1 and spatially confined to the ventral tier of SNpc, was highly susceptible to loss in PD

summary:
In Homo sapiens, a dopamine neuron subtype marked by expression of AGTR1 in the substantia nigra pars compacta is highly susceptible to loss in Parkinson's disease.


claim_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824:claim:c23ecf7e809dc4a5a12e
claim_id: claim:c23ecf7e809dc4a5a12e
paper_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824
summary: In Homo sapiens, the VIM_LHX2 astrocyte subtype expresses VIM and LHX2 as reactive markers.
span_literal:
We also identified an increase in the VIM_LHX2 astrocyte subtype (Extended Data Fig. 8d ), similarly robust to large losses in power due to sample size (Extended Data Fig. 8e ). The VIM_LHX2 population expresses reactive markers, namely VIM and LHX2


claim_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824:claim:dfb28e6da33a75494f55
claim_id: claim:dfb28e6da33a75494f55
paper_key: hca:0387_10.1038_s41593-022-01061-1_5c1bbb5824
summary: In Homo sapiens, TMEM200A is a marker enriched in the CALB1_TRHR dopamine neuron population.
span_literal:
in a second experiment, we identified cells in situ expressing TH , CALB1 and TMEM200A (Fig. 3d ), a marker enriched in the CALB1_TRHR, CALB1_GEM and CALB_RBP4 populations


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:e17e92e3c2ff55fd7c5c
claim_id: claim:e17e92e3c2ff55fd7c5c
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
the violin plots show the level of expression of the pan-epithelial specific genes EPCAM , CDH1(ECAD) , KRT8 , KRT10 , KRT17 and KRT19

summary:
In Homo sapiens, epithelial cells are marked by the pan-epithelial specific genes EPCAM, CDH1, KRT8, KRT10, KRT17 and KRT19.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:368d5a20069b494d2971
claim_id: claim:368d5a20069b494d2971
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
we scored these cells for canonical tissue-specific progenitor markers: LGR5 , OLFM4 , LRIG1 , CDX2 , CD44 , LYZ , SMOC2 and PROCR (gastrointestinal)

summary:
In Homo sapiens, gastrointestinal progenitor cells are marked by canonical progenitor markers LGR5, OLFM4, LRIG1, CDX2, CD44, LYZ, SMOC2 and PROCR.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:102d12381ad14da7b786
claim_id: claim:102d12381ad14da7b786
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal: PAX2 , PAX8 , LHX1 , JAG1 , SIX2 , RET , HNF4A , GATA3 , POU3F3 and WT1 (kidney)
summary:
In Homo sapiens, kidney progenitor cells are marked by canonical progenitor markers PAX2, PAX8, LHX1, JAG1, SIX2, RET, HNF4A, GATA3, POU3F3 and WT1.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:314e7b52218abf5e3ef2
claim_id: claim:314e7b52218abf5e3ef2
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal: NKX2-1 , SOX9 , ETV4 , ETV5 , GATA6 and ID2 (lung)
summary:
In Homo sapiens, lung progenitor cells are marked by canonical progenitor markers NKX2-1, SOX9, ETV4, ETV5, GATA6 and ID2.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:bce98cb56dc981ec38c7
claim_id: claim:bce98cb56dc981ec38c7
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Bulk RNA-seq of 23 SiAFOs showed expression of typical intestinal stem/progenitor ( LGR5 , OLMF4 , LRIG1 and SMOC2 ), Paneth ( LYZ ), goblet ( MUC2 and CLCA1 ), endocrine ( CHGA ) and enterocyte ( ALPI , FABP1 , VIL1 , EZR , KRT20 and ATP1A1 ) markers

summary:
In Homo sapiens, small intestinal amniotic fluid organoids express typical intestinal stem/progenitor cell markers LGR5, OLFM4, LRIG1 and SMOC2, Paneth cell marker LYZ, goblet cell markers MUC2 and CLCA1, enteroendocrine cell marker CHGA, and enterocyte markers ALPI, FABP1, VIL1, EZR, KRT20 and ATP1A1.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:cf09026d8964febb9f28
claim_id: claim:cf09026d8964febb9f28
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Immunofluorescent staining displays CHGA-positive enteroendocrine cells and MUC2-positive secretory cells.

summary:
In Homo sapiens, enteroendocrine cells are positive for CHGA and secretory cells are positive for MUC2.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:126cc04392110b35f88a
claim_id: claim:126cc04392110b35f88a
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Bulk RNA-seq of 54 KAFOs (19 AF samples; 18–34 weeks GA) showed expression of canonical developmental renal epithelial and nephron progenitor genes ( PAX2 , PAX8 , LHX1 and JAG1 ), while lacking cap mesenchyme markers ( SIX2 , CITED1 and GDNF ).

summary:
In Homo sapiens, nephron progenitor cells express canonical developmental renal epithelial and nephron progenitor genes PAX2, PAX8, LHX1 and JAG1, while lacking cap mesenchyme markers SIX2, CITED1 and GDNF.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:ec03a5f0519c6cf4b6e2
claim_id: claim:ec03a5f0519c6cf4b6e2
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Moreover, we detected distal ( PCBD1 , SLC41A3 and POU3F3 ) and proximal ( ABCC1 , ABCC3 , ABCC4 and CUBN ) tubule gene expression.

summary:
In Homo sapiens, distal tubule cells express PCBD1, SLC41A3 and POU3F3, while proximal tubule cells express ABCC1, ABCC3, ABCC4 and CUBN.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:3b84c42c6a898a693276
claim_id: claim:3b84c42c6a898a693276
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal: Collecting duct marker GATA3 was expressed, while the loop of Henle marker UMOD was not.
summary:
In Homo sapiens, collecting duct cells are marked by GATA3, and loop of Henle cells are marked by UMOD.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:669da1d5e96fb7e08eb9
claim_id: claim:669da1d5e96fb7e08eb9
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Immunofluorescent staining shows presence of nephron progenitor markers PAX8 and LHX1 counterstained with phalloidin (F-ACT) and positivity for distal tubule/collecting duct marker GATA3, proximal tubule marker LTL, ECAD and Ac-αTUB apical cilia, further confirming the renal epithelial identity of KAFOs

summary:
In Homo sapiens, nephron progenitor cells are marked by PAX8 and LHX1, distal tubule/collecting duct cells are marked by GATA3, and proximal tubule cells are marked by LTL.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:75ac12538bc87bdb4407
claim_id: claim:75ac12538bc87bdb4407
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Bulk RNA-seq indicated expression of multiple pulmonary markers in 43 LAFOs, manifesting stem/progenitor cell markers ( NKX2-1 , FOXA2 , SOX2 , SOX9 , TP63 and GATA6 ), alveolar type 1 ( HOPX , PDPN , AGER and AQP5 ) and alveolar type 2 cell-related genes ( SFTPA1 , SFTPA2 , SFTPB , SFTPC , SFTPD , ABCA3 and LAMP3 ).

summary:
In Homo sapiens, lung stem/progenitor cells are marked by NKX2-1, FOXA2, SOX2, SOX9, TP63 and GATA6, alveolar type 1 cells are marked by HOPX, PDPN, AGER and AQP5, and alveolar type 2 cells are marked by SFTPA1, SFTPA2, SFTPB, SFTPC, SFTPD, ABCA3 and LAMP3.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:9c7de4bd576197b34560
claim_id: claim:9c7de4bd576197b34560
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Bulk RNA-seq indicated expression of multiple pulmonary markers in 43 LAFOs, manifesting stem/progenitor cell markers ( NKX2-1 , FOXA2 , SOX2 , SOX9 , TP63 and GATA6 ), alveolar type 1 ( HOPX , PDPN , AGER and AQP5 ) and alveolar type 2 cell-related genes ( SFTPA1 , SFTPA2 , SFTPB , SFTPC , SFTPD , ABCA3 and LAMP3 ).

summary:
In Homo sapiens, alveolar type 2 cells are marked by SFTPA1, SFTPA2, SFTPB, SFTPC, SFTPD, ABCA3 and LAMP3.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:dd1dec8857e47f9046d9
claim_id: claim:dd1dec8857e47f9046d9
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Mature basal cell markers KRT5 , TROP2 and NGFR were rarely detected in LAFOs as well as the ciliated cell transcription factor FOXJ1 , which showed sporadic low expression in the expansion medium.

summary:
In Homo sapiens, mature basal cells are marked by KRT5, TROP2 and NGFR, and ciliated cells are marked by the transcription factor FOXJ1.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:11085fdff3f4f5aea112
claim_id: claim:11085fdff3f4f5aea112
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
Furthermore, the early secretory cell marker SCGB3A2 was highly expressed compared to the absent mature club cell marker SCGB1A1 .

summary:
In Homo sapiens, early secretory cells are marked by SCGB3A2, and mature club cells are marked by SCGB1A1.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:995ef37d797042e65580
claim_id: claim:995ef37d797042e65580
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
summary: In Homo sapiens, secretory goblet cells are marked by MUC5AC.
span_literal:
Secretory goblet cell marker MUC5AC was expressed in tissue-derived control FLOs, but several LAFO lines showed low/negligible expression.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:512948a12a2441c3cabe
claim_id: claim:512948a12a2441c3cabe
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
summary: In Homo sapiens, neuroendocrine cells are marked by ASCL1.
span_literal:
Last, while the neuroendocrine cell marker ASCL1 was expressed in almost all LAFOs, only a small number showed expression of CHGA


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:4af1cd7be35892e66a97
claim_id: claim:4af1cd7be35892e66a97
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
span_literal:
IF staining highlighting the presence in LAFOs of lung stem/progenitor cell markers NKX2-1 and SOX2 together with P63 basal cells

summary:
In Homo sapiens, lung stem/progenitor cells are marked by NKX2-1 and SOX2, and basal cells are marked by P63.


claim_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18:claim:3a5be1546e1be0d9b2ef
claim_id: claim:3a5be1546e1be0d9b2ef
paper_key: hca:0389_10.1038_s41591-024-02807-z_9d82b71a18
summary: In Homo sapiens, ciliated cells are marked by FOXJ1.
span_literal:
IF staining on proximally differentiated LAFOs reveals polarized expression of ciliary protein Ac-αTUB, and ciliated cell marker FOXJ1.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:050182794db7ad63bd83
claim_id: claim:050182794db7ad63bd83
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal: myeloid dendritic cells (mDCs) ( CD1C , CLEC9A
summary:
In Homo sapiens bronchoalveolar lavage fluid, myeloid dendritic cells are identified by CD1C and CLEC9A expression.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:fd89f27b47b971dd2663
claim_id: claim:fd89f27b47b971dd2663
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal: plasmacytoid dendritic cells (pDCs) ( LILRA4
summary:
In Homo sapiens bronchoalveolar lavage fluid, plasmacytoid dendritic cells are identified by LILRA4 expression.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:427fd2a17a1173ff1714
claim_id: claim:427fd2a17a1173ff1714
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal: natural killer (NK) cells ( KLRD1
summary:
In Homo sapiens bronchoalveolar lavage fluid, natural killer cells are identified by KLRD1 expression.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:eafcda8ffdfa7b512d9c
claim_id: claim:eafcda8ffdfa7b512d9c
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal: epithelial cells ( TPPP3 , KRT18
summary:
In Homo sapiens bronchoalveolar lavage fluid, epithelial cells are identified by TPPP3 and KRT18 expression.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:15bca32551523f47b2b3
claim_id: claim:15bca32551523f47b2b3
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal:
Group 1 expressed the peripheral monocyte-like markers S100A8 , FCN1 and CD14 , and group 2 expressed high levels of the chemokines CCL2 , CCL3 , CXCL10 and other genes.

summary:
In Homo sapiens, group 1 macrophages express the peripheral monocyte-like markers S100A8, FCN1, and CD14.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:603cc103b2a9a15d74fc
claim_id: claim:603cc103b2a9a15d74fc
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal:
Group 3 expressed the immunoregulatory genes A2M , GPR183 and CCL13 and the profibrotic genes TREM2 , TGFB1 and SPP1 , suggestive of alternative M2-like macrophages, a reparative but profibrotic subset

summary:
In Homo sapiens, group 3 macrophages express the immunoregulatory genes A2M, GPR183, and CCL13 and the profibrotic genes TREM2, TGFB1, and SPP1, suggestive of alternative M2-like macrophages.


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:f13132574d3c76c08bab
claim_id: claim:f13132574d3c76c08bab
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
summary: In Homo sapiens, group 4 alveolar macrophages express FABP4, APOC1, and MARCO.
span_literal:
Group 4 expressed the alveolar macrophage (AM) genes FABP4 , APOC1 , MARCO and genes associated with lipid metabolic functions


claim_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292:claim:434abb152fb9bb65c6ad
claim_id: claim:434abb152fb9bb65c6ad
paper_key: hca:0390_10.1038_s41591-020-0901-9_be86edb292
span_literal:
These expanded clones preferentially expressed tissue-residence genes, including XCL1 , CXCR6 and ITGAE

summary:
In Homo sapiens, expanded ZNF683-positive CD8-positive T cell clones preferentially express the tissue-residence genes XCL1, CXCR6, and ITGAE.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:20b5a7385ccfbe7620db
claim_id: claim:20b5a7385ccfbe7620db
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
summary: In Homo sapiens, secretory goblet cells in the nose and airways express ACE2 and TMPRSS2.
span_literal:
Consistent with previous reports 33 , double positive ACE2 + TMPRSS2 + cells in the nose and airways were largely secretory goblet and multiciliated cells, and double positive cells in the distal lung were largely AT2 cells


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:3a08c01896d3667c3fcc
claim_id: claim:3a08c01896d3667c3fcc
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
summary: In Homo sapiens, some alveolar type 2 cells marked by HTII-280 express ACE2 and TMPRSS2.
span_literal:
Co-staining with cell type-specific markers, showed ACE2 expression and TMPRSS2 expression in some HTII-280 + AT2 cells


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:02243948b50b207a745c
claim_id: claim:02243948b50b207a745c
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
TMPRSS2 protein was expressed at low levels in some AT1 cells (identified by AGER, Extended Data Fig. 7d )

summary:
In Homo sapiens, TMPRSS2 protein is expressed at low levels in some alveolar type 1 cells, which are identified by AGER.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:ded55c031ce51d69b7c1
claim_id: claim:ded55c031ce51d69b7c1
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
summary: In Homo sapiens, alveolar type 2 cells are specifically labeled by pro-SFTPC immunohistochemistry.
span_literal:
Immunohistochemistry with antibodies used previously to block cellular viral entry specifically labeled adult pro-SFTPC + AT2 cells


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:ffb5975e4403c69a722e
claim_id: claim:ffb5975e4403c69a722e
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
summary: In Homo sapiens, mucous cells of submucosal glands show enrichment of ACE2, TMPRSS2, and CTSL.
span_literal:
scRNA-seq of microdissected SMGs of healthy donors showed enrichment of ACE2 , TMPRSS2 and CTSL in mucous cells


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:e539a54ba9d1fca83ed2
claim_id: claim:e539a54ba9d1fca83ed2
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
PCSK1 and PCSK2 were mostly restricted to neuroendocrine cells 26 , and PCSK2 also detected in some AT2 cells

summary:
In Homo sapiens, PCSK1 and PCSK2 are mostly restricted to neuroendocrine cells in the lung, and PCSK2 is also detected in some alveolar type 2 cells.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:94bcf93d11cfe87c85cc
claim_id: claim:94bcf93d11cfe87c85cc
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
ACE2 + TMPRSS2 + PCSK7 + were the main TPs in multiciliated (0.75%) and secretory (0.72%) cells of proximal airways, and ACE2 + TMPRSS2 + FURIN + TPs were the most common within AT2 cells (0.36%)

summary:
In Homo sapiens, multiciliated cells and secretory cells of proximal airways are enriched for ACE2, TMPRSS2, and PCSK7 triple-positive cells, while alveolar type 2 cells are enriched for ACE2, TMPRSS2, and FURIN triple-positive cells.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:4dc64be325d5a949acd1
claim_id: claim:4dc64be325d5a949acd1
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
ACE2 + TMPRSS2 + PCSK7 + were the main TPs in multiciliated (0.75%) and secretory (0.72%) cells of proximal airways, and ACE2 + TMPRSS2 + FURIN + TPs were the most common within AT2 cells (0.36%)

summary:
In Homo sapiens, secretory cells of proximal airways are enriched for ACE2, TMPRSS2, and PCSK7 triple-positive cells.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:73396518214bc9cc9580
claim_id: claim:73396518214bc9cc9580
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
ACE2 + TMPRSS2 + PCSK7 + were the main TPs in multiciliated (0.75%) and secretory (0.72%) cells of proximal airways, and ACE2 + TMPRSS2 + FURIN + TPs were the most common within AT2 cells (0.36%)

summary:
In Homo sapiens, alveolar type 2 cells are enriched for ACE2, TMPRSS2, and FURIN triple-positive cells.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:d4a2c4f8115736bed1c9
claim_id: claim:d4a2c4f8115736bed1c9
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
ACE2 was expressed (1.4%) in maternal decidual/stromal cells, maternal pericytes, and fetal extravillous trophoblasts, cytotrophoblasts, and syncytiotrophoblast in both first-trimester and term placenta

summary:
In Homo sapiens, ACE2 is expressed in maternal decidual/stromal cells, maternal pericytes, fetal extravillous trophoblasts, cytotrophoblasts, and syncytiotrophoblast in the placenta.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:496ecf9e69168972ea4b
claim_id: claim:496ecf9e69168972ea4b
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
Cell programs ( Fig. 4c , d , Supplementary Fig. 12a - c , Supplementary Tables 7 - 10 ) were enriched in many of the same genes and pathways (e.g., CEACAM5 , CXCL17 , SLPI ), and further captured unique functions, including TNF signaling in lung secretory cells ( e.g. , RIPK3 47 ), lysosomal functions in lung secretory and multiciliated cells 48 , the immunoproteasome (AT1 cells, Fig. 4c ), cytokines, chemokines and their receptors (nasal goblet cells: CSF3 , CXCL1 , CXCL3 , IL19 , CCL20; AT1 cells: IL1R1 ), and genes that encode surfactant proteins (AT2 cells, SFTPA , SFTPA2 )

summary:
In Homo sapiens, ACE2+TMPRSS2+ nasal goblet cells are enriched for CSF3, CXCL1, CXCL3, IL19, and CCL20.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:612155aa14e710d85db1
claim_id: claim:612155aa14e710d85db1
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
Cell programs ( Fig. 4c , d , Supplementary Fig. 12a - c , Supplementary Tables 7 - 10 ) were enriched in many of the same genes and pathways (e.g., CEACAM5 , CXCL17 , SLPI ), and further captured unique functions, including TNF signaling in lung secretory cells ( e.g. , RIPK3 47 ), lysosomal functions in lung secretory and multiciliated cells 48 , the immunoproteasome (AT1 cells, Fig. 4c ), cytokines, chemokines and their receptors (nasal goblet cells: CSF3 , CXCL1 , CXCL3 , IL19 , CCL20; AT1 cells: IL1R1 ), and genes that encode surfactant proteins (AT2 cells, SFTPA , SFTPA2 )

summary:
In Homo sapiens, ACE2+TMPRSS2+ alveolar type 2 cells are enriched for surfactant protein genes SFTPA and SFTPA2.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:5f2c106aa408bad3e771
claim_id: claim:5f2c106aa408bad3e771
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
summary:
In Homo sapiens, ACE2+TMPRSS2+ lung secretory cells are enriched for RIPK3 expression related to tumor necrosis factor signaling.


claim_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5:claim:5ce41400c17436b7c532
claim_id: claim:5ce41400c17436b7c532
paper_key: hca:0392_10.1038_s41591-020-01227-z_dba0e013f5
span_literal:
MYRF is a transcription factor that induces expression of the myelin proteins MBP (myelin basic protein) and MOG (myelin oligodendrocyte glycoprotein)

summary:
In Homo sapiens, MYRF is a transcription factor that induces expression of myelin basic protein (MBP) and myelin oligodendrocyte glycoprotein (MOG).


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:d7e4f3543836c7f5dfed
claim_id: claim:d7e4f3543836c7f5dfed
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
summary: In Homo sapiens pancreatic islets, beta cells are marked by high expression of INS.
span_literal:
Beta cells ( INS high), alpha cells ( GCG high), delta cells ( SST high), PP cells ( PPY high), epsilon cells ( GHRL high), acinar cells ( CPA1 high), ductal cells ( KRT19 high), endothelial cells ( VWF high), stellate cells ( RSG10 high), and immune cells ( PTPRC , also known as CD45 or leukocyte common antigen, high).


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:fb5e729a2a1d97f2080c
claim_id: claim:fb5e729a2a1d97f2080c
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
summary:
In Homo sapiens pancreatic islets, immune cells are marked by high expression of PTPRC (also known as CD45 or leukocyte common antigen).


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:5a82c997d52e371d0e59
claim_id: claim:5a82c997d52e371d0e59
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
summary: In Homo sapiens pancreatic islets, stellate cells are marked by high expression of RGS5.
span_literal:
this population also contained stellate ( RGS5 high) and Schwann ( PLP1 high) cells along with immune cells ( PTPRC high)


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:4d10cf9d1f96fb4eecb2
claim_id: claim:4d10cf9d1f96fb4eecb2
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal:
the gene signatures of antigen-presenting cells (APCs) such as macrophages, for example CD68, SPI1, CD14 , and CD16 , were most frequently expressed in the immune cell subset

summary:
In Homo sapiens pancreatic islets, macrophages (antigen-presenting cells) express CD68, SPI1, CD14, and CD16.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:90d3bb67bd2451de02f0
claim_id: claim:90d3bb67bd2451de02f0
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal:
while cells in the Ductal-1 cluster were enriched for transcription factors (TFs) associated with the endocrine cell fate (i.e., PDX1 and NKX6-1 ), those in the Ductal-2 cluster expressed acinar TFs (i.e., PTF1A and GATA4 ).

summary:
In Homo sapiens pancreatic islets, Ductal-1 cells are enriched for PDX1 and NKX6-1, while Ductal-2 cells express PTF1A and GATA4.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:6837409ea128eb71fb9e
claim_id: claim:6837409ea128eb71fb9e
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal:
while cells in the Ductal-1 cluster were enriched for transcription factors (TFs) associated with the endocrine cell fate (i.e., PDX1 and NKX6-1 ), those in the Ductal-2 cluster expressed acinar TFs (i.e., PTF1A and GATA4 ).

summary:
In Homo sapiens pancreatic islets, Ductal-2 cells express PTF1A and GATA4, in contrast to Ductal-1 cells.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:dcae98092f8b8b47d610
claim_id: claim:dcae98092f8b8b47d610
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal: DC1 corresponds to the cross-presenting CD141/BDCA-3 + cDC1, which is best marked by CLEC9A 47 .
summary:
In Homo sapiens, conventional dendritic cell type 1 (DC1, CD141/BDCA-3 positive) is best marked by CLEC9A.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:3b686dfb1132caa9140e
claim_id: claim:3b686dfb1132caa9140e
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal:
We found that CD80 and CD86 were not expressed in T1D ductal cells, suggesting a lack of costimulatory signal in these dendritic cell-like ductal cells in T1D donors

summary:
In Homo sapiens, Type 1 Diabetes ductal cells do not express the costimulatory proteins CD80 and CD86.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:1ce4283425eea776a482
claim_id: claim:1ce4283425eea776a482
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal:
Ductal cells of T1D donors express interferon-associated genes including ISG20 , ICAM1 , and IRF7 compared with those of control donors.

summary:
In Homo sapiens, ductal cells of Type 1 Diabetes donors express interferon-associated genes including ISG20, ICAM1, and IRF7 compared with those of control donors.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:07e72289159d91303965
claim_id: claim:07e72289159d91303965
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
span_literal:
the inhibitory receptor VSIR, which negatively regulates T cell responses 49 , showed higher expression in T1D compared with control ductal cells

summary:
In Homo sapiens, the inhibitory receptor VSIR shows higher expression in Type 1 Diabetes ductal cells compared with control ductal cells.


claim_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e:claim:b17ea22603d5f08b72e8
claim_id: claim:b17ea22603d5f08b72e8
paper_key: hca:0393_10.1038_s42255-022-00531-x_b92878970e
summary: In Homo sapiens pancreatic islets, beta cells are marked by high INS expression.
span_literal:
beta cells ( INS high), alpha cells (GCG high), acinar cells ( CPA1 high), ductal cells ( KRT19 high), endothelial cells ( VWF high) stellate cells ( RSG10 high), and immune cells ( PTPRC , also known as CD45 or leukocyte common antigen, high)


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:0da4a5476b96b03ba02b
claim_id: claim:0da4a5476b96b03ba02b
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, nonclassical monocytes are marked by positive expression of CD16 and C1QA/B/C.
span_literal:
We identified expansion of nonclassical monocytes expressing complement transcripts ( CD16 + C1QA/B/C + ) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:9241a3e4fbbd7fe1f5b3
claim_id: claim:9241a3e4fbbd7fe1f5b3
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, hematopoietic stem/progenitor cells are marked by positive expression of CD34.
span_literal:
Early, uncommitted CD34 + hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:ea54e00038dfd763df2d
claim_id: claim:ea54e00038dfd763df2d
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Three CD14 + monocyte states were present (proliferating, classical CD14 + and activated CD83 + ) in addition to two CD16 + monocyte states (nonclassical CD16 + and C1QA/B/C + CD16 + ; Fig. 2a,b ).

summary:
In Homo sapiens, classical monocytes are marked by positive expression of CD14, and activated monocytes are marked by positive expression of CD83.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:d71b3fb87cf8f00dc26e
claim_id: claim:d71b3fb87cf8f00dc26e
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Three CD14 + monocyte states were present (proliferating, classical CD14 + and activated CD83 + ) in addition to two CD16 + monocyte states (nonclassical CD16 + and C1QA/B/C + CD16 + ; Fig. 2a,b ).

summary:
In Homo sapiens, nonclassical monocytes are marked by positive expression of CD16, and C1QA/B/C-positive CD16-positive monocytes are marked by positive expression of C1QA/B/C and CD16.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:575ff61bf3c53f787f93
claim_id: claim:575ff61bf3c53f787f93
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary:
In Homo sapiens, C1QA/B/C-positive CD16-positive monocytes are marked by positive expression of C1QA/B/C and CD16.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:0dda602ef4284417e40c
claim_id: claim:0dda602ef4284417e40c
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, proliferating monocytes and dendritic cells express MKI67 and TOP2A.
span_literal:
Proliferating monocytes and DCs expressing MKI67 and TOP2A were increased with disease severity (Fig. 2a,b ).


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:3684bc27825ae0ab1c50
claim_id: claim:3684bc27825ae0ab1c50
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Rare C1QA/B/C -expressing CD16 + monocytes were the only source of C1 complement components (Fig. 2b and Extended Data Fig. 3b ).

summary:
In Homo sapiens, C1QA/B/C-expressing CD16-positive monocytes are the only source of C1 complement components, marked by positive expression of C1QA/B/C and CD16.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:a68bc038beb85b1de2eb
claim_id: claim:a68bc038beb85b1de2eb
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, C1QA/B/C-positive CD16-positive monocytes express FCGR3A and C1QA/B/C.
span_literal:
Both BAL macrophages and C1QA/B/C + CD16 + monocytes express FCGR3A and C1QA/B/C and type I interferon response genes (Fig. 2a ).


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:19ca4a49d11554883d96
claim_id: claim:19ca4a49d11554883d96
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Genes differentially expressed by blood monocytes identified S100A8 , previously reported in COVID-19 as contributing to the cytokine storm in severe infection 24 .

summary:
In Homo sapiens, blood monocytes express S100A8, previously reported as contributing to the cytokine storm in severe COVID-19 infection.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:a3573908ff96683b25ac
claim_id: claim:a3573908ff96683b25ac
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
BAL macrophages contain a population of mature, migratory DCs that express CCR7 and LAMP3 but downregulate DC-specific markers, such as CD1C and CLEC9A (Extended Data Fig. 3c ).

summary:
In Homo sapiens, mature migratory dendritic cells express CCR7 and LAMP3 but downregulate CD1C and CLEC9A.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:b75021c786724e64bdae
claim_id: claim:b75021c786724e64bdae
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Absence of CD38 mRNA and protein expression marks the most immature cells within the CD34 + compartment, while expression of markers such as GATA1 , MPO and PF4 characterizes distinct erythroid, myeloid and megakaryocytic progenitor populations, respectively (Fig. 2i ).

summary:
In Homo sapiens, the most immature cells within the CD34-positive hematopoietic stem/progenitor cell compartment are marked by negative expression of CD38, while GATA1 marks erythroid progenitors, MPO marks myeloid progenitors, and PF4 marks megakaryocytic progenitors.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:8c95b5c33b6add04e03e
claim_id: claim:8c95b5c33b6add04e03e
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Proliferating CD4 + and CD8 + T cells coexpressed exhaustion marker genes LAG3 and TOX (Extended Data Fig. 5c ), in keeping with previous studies of patients with severe COVID-19 (ref. 5 ).

summary:
In Homo sapiens, proliferating CD4-positive T cells and proliferating CD8-positive T cells coexpress the exhaustion marker genes LAG3 and TOX.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:4c052071767e1f61cbbb
claim_id: claim:4c052071767e1f61cbbb
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Proliferating CD4 + and CD8 + T cells coexpressed exhaustion marker genes LAG3 and TOX (Extended Data Fig. 5c ), in keeping with previous studies of patients with severe COVID-19 (ref. 5 ).

summary:
In Homo sapiens, proliferating CD8-positive T cells coexpress the exhaustion marker genes LAG3 and TOX.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:e97b85a1a73e31cd39d5
claim_id: claim:e97b85a1a73e31cd39d5
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
We also found a large population of plasmablasts with negative expression of CD19 and CD20, with high expression of the proliferation marker MKI67 , consistent with previous reports on severe SARS-CoV-2 infection 15 , 24 , as well as IgM + , IgG + and IgA + plasma cells (Fig. 4a,b ).

summary:
In Homo sapiens, plasmablasts are marked by negative expression of CD19 and CD20 and high expression of the proliferation marker MKI67.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:beee15803b53f895bc95
claim_id: claim:beee15803b53f895bc95
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
Transcriptome and surface proteome analysis of blood mononuclear phagocytes (MPs) identified known DC subsets (pDC, ASDC ( AXL + SIGLEC6 + DC), DC1, DC2 and DC3) and several monocyte states (Fig. 2a,b ).

summary:
In Homo sapiens, AXL-positive SIGLEC6-positive dendritic cells (ASDC) are identified by positive expression of AXL and SIGLEC6.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:a9e65c0c39516a653d52
claim_id: claim:a9e65c0c39516a653d52
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, IFNAR2 is highly expressed by plasmablasts, monocytes, and dendritic cells.
span_literal:
IFNAR2 was both upregulated in individuals with COVID-19 compared to healthy controls in most circulating cell types and highly expressed by plasmablasts, monocytes and DCs (Extended Data Fig. 2i ).


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:8e7021cb5f19ee7b6c6b
claim_id: claim:8e7021cb5f19ee7b6c6b
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, type 1 helper T cells are marked by expression of IFNG, TBX21, and TNFA.
span_literal:
Polarized CD4 + T cell annotations were refined using the combination of transcription factor genes and expressed cytokines for the respective T H cell types: T H 1 ( IFNG , TBX21 and TNFA ), T H 2 ( GATA3 , IL4 and IL5 ) and T H 17 ( RORC , IL17A , IL17F and IL21 ).


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:cbe625e9b219b506e04a
claim_id: claim:cbe625e9b219b506e04a
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
summary: In Homo sapiens, gamma-delta T cells are annotated using markers TRGV9 and TRDV2.
span_literal:
Remaining clusters were annotated using a combination of canonical protein and mRNA markers for major αβ T cells (CD4, CD8, CCR7, CD45RA, CD45RO, CD62L, CD27, CD38, CD44, CXCR5, CD40LG, CCR7 , FOXP3 and IKZF2 ), γδ T cells (Vγ9, Vγ2, TRGV9 and TRDV2 ) and invariant T cells, MAIT (Vα24-Jα18 and TRAV1.2 ) and NK T (CD3, CD16, CD56, NCAM1 , NCR1 and FCGR3A ) cells.


claim_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c:claim:b2ceb2c9098b0a50a968
claim_id: claim:b2ceb2c9098b0a50a968
paper_key: hca:0394_10.1038_s41591-021-01329-2_7dcc6ae73c
span_literal:
We assessed the expression of genes associated with BCR activation, such as CD79A and CD79B , and downstream kinases such as BTK in B cell subsets.

summary:
In Homo sapiens, B cell receptor activation in B cell subsets is associated with expression of CD79A, CD79B, and BTK.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:3d64181d27c8309a2f99
claim_id: claim:3d64181d27c8309a2f99
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
summary: In Homo sapiens retina, PDE6A is a marker of rod photoreceptors.
span_literal:
we observed cell-type-specific expression of many genes, including PDE6A in rod photoreceptors, GRIK1 in OFF-cone bipolar cells, RLBP1 in Müller glia, GRM6 in ON-cone and rod bipolar cells, PRKCA in rod bipolar cells, ARR3 in cone photoreceptors, GAD1 in GABAergic (GABA-) amacrine cells, ONECUT1 in horizontal cells, SLC6A9 in AII- and other glycinergic (gly-) amacrine cells, NEFL in retinal ganglion cells, GJD2 in AII-amacrine cells, GFAP in astrocytes, and C1QA in microglia


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:dcf2eb7f0f28cb9ea639
claim_id: claim:dcf2eb7f0f28cb9ea639
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
summary:
In Homo sapiens retina, SLC6A9 is a marker of AII-amacrine cells and other glycinergic amacrine cells.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:db93b114c4e137df3b0c
claim_id: claim:db93b114c4e137df3b0c
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
span_literal:
we observed enrichment of binding motifs for TFs with known cell-type-specific functions, such as OTX2 in photoreceptors and bipolar cells

summary:
In Homo sapiens retina, OTX2 transcription factor binding motifs are enriched in photoreceptors and bipolar cells.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:7d8b7e2c6e19ee332583
claim_id: claim:7d8b7e2c6e19ee332583
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
span_literal: ONECUT family members in horizontal cells
summary:
In Homo sapiens retina, ONECUT family transcription factor binding motifs are enriched in horizontal cells.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:b94eef8e1e6e1eadedb9
claim_id: claim:b94eef8e1e6e1eadedb9
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
span_literal: POU4F family members in retinal ganglion cells
summary:
In Homo sapiens retina, POU4F family transcription factor binding motifs are enriched in retinal ganglion cells.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:179d97aad7f4c85b3964
claim_id: claim:179d97aad7f4c85b3964
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
summary: In Homo sapiens retina, LINC00461 is a predicted target gene active in Müller glia.
span_literal:
we also predicted rs17421627 to act on LINC00461, a long noncoding RNA. Consistent with these predictions, deletion of the locus containing rs17421627 in human retinal organoids has been shown to significantly downregulate LINC00461, with the strongest effect in Müller glia.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:e7219eb6a666d6ac7eed
claim_id: claim:e7219eb6a666d6ac7eed
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
span_literal:
we were able to locate a 3D loop connecting rs9966620 with a region 75 kb upstream. This region intersected the TSS of only one gene, TTC39C-AS1 , suggesting that rs9966620 may modulate DR risk by interacting with TTC39C-AS1 in rods.

summary:
In Homo sapiens retina, TTC39C-AS1 is a predicted target gene of the diabetic retinopathy-associated variant rs9966620 in rod photoreceptors.


claim_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e:claim:ffca3e076c8bfcdfcccc
claim_id: claim:ffca3e076c8bfcdfcccc
paper_key: hca:0395_10.1016_j.xgen.2022.100164_f07698cf8e
span_literal:
Our results suggest that rs1874459 may act on CDH11 in bipolar and amacrine cells by creating a new bHLH domain recognized by NEUROD4.

summary:
In Homo sapiens retina, NEUROD4 is specifically expressed in bipolar and amacrine cells, and CDH11 is a predicted target gene of rs1874459 in these cells.


claim_key: hca:0396_10.7554_elife.62522_10df7c4591:claim:30298a831efddc5c9be1
claim_id: claim:30298a831efddc5c9be1
paper_key: hca:0396_10.7554_elife.62522_10df7c4591
span_literal:
We detected ACE2 transcript in very few nuclei (total 80 nuclei) in the normal lungs and these nuclei were enriched within the epithelial lineage

summary:
In Homo sapiens lungs, ACE2 transcript is detected in very few nuclei enriched within the epithelial lineage.


claim_key: hca:0396_10.7554_elife.62522_10df7c4591:claim:f7b2d8457472d3c3beb2
claim_id: claim:f7b2d8457472d3c3beb2
paper_key: hca:0396_10.7554_elife.62522_10df7c4591
summary: In Homo sapiens lungs, alveolar type 2 cells had the highest number of ACE2-positive nuclei.
span_literal:
In our data, AT2 cells had the highest number of ACE2 + nuclei, accounting for 48.8% of all ACE2 -expressing nuclei (39 out of total 80 ACE2 + nuclei)


claim_key: hca:0396_10.7554_elife.62522_10df7c4591:claim:9179a01ca1a6269c46ec
claim_id: claim:9179a01ca1a6269c46ec
paper_key: hca:0396_10.7554_elife.62522_10df7c4591
span_literal:
Most TMPRSS2 -expressing cells were epithelial cells including AT1 and AT2 cells and airway cells such as club, ciliated and goblet cells

summary:
In Homo sapiens lungs, TMPRSS2 is expressed in alveolar type 1 cells, alveolar type 2 cells, club cells, ciliated cells, and goblet cells.


claim_key: hca:0396_10.7554_elife.62522_10df7c4591:claim:ac4565031f394f8d665f
claim_id: claim:ac4565031f394f8d665f
paper_key: hca:0396_10.7554_elife.62522_10df7c4591
summary: In Homo sapiens lungs, CTSL, BSG, and FURIN are expressed in alveolar type 1 cells.
span_literal:
The other three candidate genes of SARS-CoV-2 host cell entry CTSL , BSG and FURIN were expressed in a large number of AT1, AT2, matrix fibroblast1,2, and M1 macrophage cells, as well as a small number of cells in additional cell types


claim_key: hca:0396_10.7554_elife.62522_10df7c4591:claim:53def661dc26bb65122b
claim_id: claim:53def661dc26bb65122b
paper_key: hca:0396_10.7554_elife.62522_10df7c4591
summary: In Homo sapiens lungs, SLC6A20 is expressed predominantly in alveolar type 2 cells.
span_literal:
Among these genes, SLC6A20 , which encodes a proline transporter, was expressed predominantly in AT2 cells and had low expression in other cell types


claim_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911:claim:3a00ffcf2892d23ad22b
claim_id: claim:3a00ffcf2892d23ad22b
paper_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911
span_literal:
many identified TFs are previously shown to play cell type-specific role in the retina, such as OTX2, CRX, MEF2D in photoreceptor cells, ONECUT2 in HC, NFIA, NFIB, NFIX, and LHX2 in MG, supporting our findings

summary:
In Homo sapiens retina, OTX2, CRX, and MEF2D are markers of photoreceptor cells, playing cell type-specific roles.


claim_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911:claim:abf1a8fe4621c9806796
claim_id: claim:abf1a8fe4621c9806796
paper_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911
span_literal:
many identified TFs are previously shown to play cell type-specific role in the retina, such as OTX2, CRX, MEF2D in photoreceptor cells, ONECUT2 in HC, NFIA, NFIB, NFIX, and LHX2 in MG, supporting our findings

summary:
In Homo sapiens retina, NFIA, NFIB, NFIX, and LHX2 are markers of Müller glia cells, playing cell type-specific roles.


claim_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911:claim:9c425f73c4afe40e57d5
claim_id: claim:9c425f73c4afe40e57d5
paper_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911
summary: In Homo sapiens retina, FOXP2 is highly expressed in Müller glia cells.
span_literal:
This variant was predicted to enhance the binding of FOXP2 (highly expressed in MG), to a MG-specific LCRE of SLC27A6


claim_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911:claim:1c532ac18ad844ef36f5
claim_id: claim:1c532ac18ad844ef36f5
paper_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911
span_literal:
This variant likely disrupts the binding of NR3C1 , which is highly expressed in Rod but minimally in Cone, to a LCRE accessible in both Rod and Cone

summary:
In Homo sapiens retina, NR3C1 is highly expressed in rod photoreceptors but minimally expressed in cone photoreceptors.


claim_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911:claim:111953f0831706930df8
claim_id: claim:111953f0831706930df8
paper_key: hca:0397_10.1186_s13059-023-03111-8_05defe1911
span_literal:
the variant rs6859300 affects the chromatin accessibility of its residing OCR specifically in Rod, despite this OCR being accessible in multiple cell types (i.e., Rod, Cone, and BC), potentially through enhancing the binding of EPAS1, which is highly expressed in Rod but lowly expressed in Cone and BC

summary:
In Homo sapiens retina, EPAS1 is highly expressed in rod photoreceptors but lowly expressed in cone photoreceptors and bipolar cells.


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:cb95978301d3513059b7
claim_id: claim:cb95978301d3513059b7
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
span_literal:
A significant decrease in the non-classical monocyte genes ( C1AQ, C1BQ , and LSTB1 expression) and a corresponding relative increase of classical monocytes genes ( S100A8, S100A9 , and S100A12 expression) in the critical COVID-19 patients was also observed ( 5 ).

summary:
In Homo sapiens, non-classical monocytes are marked by C1QA, C1QB, and LYST expression, while classical monocytes are marked by S100A8, S100A9, and S100A12 expression.


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:4a9e2d611e41b1ba5785
claim_id: claim:4a9e2d611e41b1ba5785
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
summary: In Homo sapiens, TNFRSF13C is a pro-survival receptor expressed in class-switched memory B cells.
span_literal:
TNFRSF13C , a pro-survival receptor for B cells, was found to have increased expressed in the Class-switched memory B cells during active COVID-19 ( 38 ).


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:6eb16b7e92c72982705e
claim_id: claim:6eb16b7e92c72982705e
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
span_literal:
We observed increased expression of TNFRSF1B , also known as TNF receptor 2 ( TNFR2 ) in the Classical monocytes and NK cells during active COVID-19 ( Figure 2J ).

summary:
In Homo sapiens, TNFRSF1B (also known as tumor necrosis factor receptor 2) is expressed in classical monocytes during active COVID-19.


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:de20ad6f6d5eb434531c
claim_id: claim:de20ad6f6d5eb434531c
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
span_literal:
We observed increased expression of TNFRSF1B , also known as TNF receptor 2 ( TNFR2 ) in the Classical monocytes and NK cells during active COVID-19 ( Figure 2J ).

summary:
In Homo sapiens, TNFRSF1B (also known as tumor necrosis factor receptor 2) is expressed in natural killer cells during active COVID-19.


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:447a5d1424706d2a48c4
claim_id: claim:447a5d1424706d2a48c4
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
span_literal:
We observed higher expression of CD38, CD69 and CD40LG during active COVID-19 infection, indicating an activated phase of T cell population, compared to the healthy and the recovered, where the T cells are at resting phase in comparison to the active infection ( Figure 4A ).

summary:
In Homo sapiens, CD38, CD69, and CD40LG are T cell activation markers with higher expression during active COVID-19 infection.


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:f6e989e8fd7e4655a8ee
claim_id: claim:f6e989e8fd7e4655a8ee
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
span_literal:
We also observed higher expression of T cell exhaustion markers, i.e., TIM-3, LAG3, CD152 or CTLA4 and CD279 or PD-1 in the recovered individuals compared to the active COVID-19 and healthy individuals ( Figure 4B ).

summary:
In Homo sapiens, TIM-3, LAG3, CTLA4, and PD-1 are T cell exhaustion markers with higher expression in recovered individuals.


claim_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5:claim:2bc10da84f7ae54af8dd
claim_id: claim:2bc10da84f7ae54af8dd
paper_key: hca:0398_10.3389_fimmu.2022.1034159_e51dfc8bb5
span_literal:
Besides, the upregulation of S100A8 , TXNIP and MT2A genes in the monocytes indicate an inflammatory response upregulation in the infected individuals.

summary:
In Homo sapiens, S100A8, TXNIP, and MT2A are upregulated in monocytes during COVID-19 infection, indicating inflammatory response upregulation.


claim_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e:claim:a9c5f0371c2a41381d17
claim_id: claim:a9c5f0371c2a41381d17
paper_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e
span_literal:
Using CD88 and CD89 for monocytes and HLA-DQ and FcεRIα for cDC2s allowed for their specific identification in blood and tissues.

summary:
In Homo sapiens, monocytes are identified by CD88 and CD89, distinguishing them from conventional dendritic cell type 2 in blood and tissues.


claim_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e:claim:9b08b6b47a6ce31adf44
claim_id: claim:9b08b6b47a6ce31adf44
paper_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e
span_literal:
Using CD88 and CD89 for monocytes and HLA-DQ and FcεRIα for cDC2s allowed for their specific identification in blood and tissues.

summary:
In Homo sapiens, conventional dendritic cell type 2 is identified by HLA-DQ and FcεRIα, distinguishing them from monocytes in blood and tissues.


claim_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e:claim:8a61046630882048d8bd
claim_id: claim:8a61046630882048d8bd
paper_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e
span_literal:
We also showed that cDC2s could be subdivided into phenotypically and functionally distinct subsets based on CD5, CD163, and CD14 expression, including a distinct subset of circulating inflammatory CD5 - CD163 + CD14 + cells related to previously defined DC3s.

summary:
In Homo sapiens, conventional dendritic cell type 2 can be subdivided into distinct subsets based on CD5, CD163, and CD14 expression, including an inflammatory DC3 subset that is CD5 negative, CD163 positive, and CD14 positive.


claim_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e:claim:4ebc9da41edcb0f9c642
claim_id: claim:4ebc9da41edcb0f9c642
paper_key: hca:0399_10.1016_j.immuni.2019.08.008_d590b8282e
span_literal:
We also showed that cDC2s could be subdivided into phenotypically and functionally distinct subsets based on CD5, CD163, and CD14 expression, including a distinct subset of circulating inflammatory CD5 - CD163 + CD14 + cells related to previously defined DC3s.

summary:
In Homo sapiens, inflammatory DC3 is a distinct subset characterized by negative CD5, positive CD163, and positive CD14 expression.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:853cc5aeaa316654449a
claim_id: claim:853cc5aeaa316654449a
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
PT1, 4, and 6 are enriched for PT segment 1 (S1) marker SLC5A2 and S1/2-abundant genes ( SLC7A7 , ANK2 , SLC4A4 , SLC6A19 , SLC22A8 ), while PT2 shows increased expression of S3-abundant genes ( DCXR , AGXT , SLC22A7 , SLC7A13 )

summary:
In Homo sapiens kidney, proximal tubular cell cluster PT1 is enriched for proximal tubule segment 1 marker SLC5A2 and segment 1/2-abundant genes SLC7A7, ANK2, SLC4A4, SLC6A19, and SLC22A8.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:50dabdd38fa1fde3c082
claim_id: claim:50dabdd38fa1fde3c082
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
PT1, 4, and 6 are enriched for PT segment 1 (S1) marker SLC5A2 and S1/2-abundant genes ( SLC7A7 , ANK2 , SLC4A4 , SLC6A19 , SLC22A8 ), while PT2 shows increased expression of S3-abundant genes ( DCXR , AGXT , SLC22A7 , SLC7A13 )

summary:
In Homo sapiens kidney, proximal tubular cell cluster PT4 is enriched for proximal tubule segment 1 marker SLC5A2 and segment 1/2-abundant genes SLC7A7, ANK2, SLC4A4, SLC6A19, and SLC22A8.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:a5ae4437c676f0198440
claim_id: claim:a5ae4437c676f0198440
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
PT1, 4, and 6 are enriched for PT segment 1 (S1) marker SLC5A2 and S1/2-abundant genes ( SLC7A7 , ANK2 , SLC4A4 , SLC6A19 , SLC22A8 ), while PT2 shows increased expression of S3-abundant genes ( DCXR , AGXT , SLC22A7 , SLC7A13 )

summary:
In Homo sapiens kidney, proximal tubular cell cluster PT6 is enriched for proximal tubule segment 1 marker SLC5A2 and segment 1/2-abundant genes SLC7A7, ANK2, SLC4A4, SLC6A19, and SLC22A8.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:aacb4b56c5b6aeb9e2d3
claim_id: claim:aacb4b56c5b6aeb9e2d3
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
summary:
In Homo sapiens kidney, proximal tubular cell cluster PT2 shows increased expression of segment 3-abundant genes DCXR, AGXT, SLC22A7, and SLC7A13.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:8adcbac096a20bae639d
claim_id: claim:8adcbac096a20bae639d
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: PT5 ( VIM + S100A6 + VCAM1 + DCDC2 + ANXA4
summary:
In Homo sapiens kidney, proximal tubular cell cluster PT5 expresses VIM, S100A6, VCAM1, DCDC2, and ANXA4, displaying similarity to scattered tubular cells.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:ecf10339996dd161665a
claim_id: claim:ecf10339996dd161665a
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
summary: In Homo sapiens kidney, T cells are marked by CD3E expression.
span_literal:
T cells ( CD3E + ) , Natural Killer (NK) cells ( NKG7 + CD3E - ), and a small B cell population ( CD79A + ) mainly expressing the immunoglobulin chain IGHM were identified


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:17359c6dbffa5090ff35
claim_id: claim:17359c6dbffa5090ff35
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: T cell cluster T1 expressed CD4 + T helper (Th) cell genes ( IL7R + CD40LG + LTB
summary:
In Homo sapiens kidney, T cell cluster T1 (CD4-positive T helper cell) expresses IL7R, CD40LG, and LTB.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:5e6f072502985582d610
claim_id: claim:5e6f072502985582d610
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
T2 demonstrates expression of a cytotoxic program ( GZMA, GZMB, GZMH, GNLY, PRF1 ) alongside NK receptor genes ( KLRD1 , KLRG1 ), consistent with effector memory T cell or NKT cell identity

summary:
In Homo sapiens kidney, T cell cluster T2 expresses cytotoxic genes GZMA, GZMB, GZMH, GNLY, PRF1 and natural killer receptor genes KLRD1 and KLRG1, consistent with effector memory T cell or natural killer T cell identity.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:ac8b2061d39ebd82b2e4
claim_id: claim:ac8b2061d39ebd82b2e4
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
summary: In Homo sapiens kidney, gamma-delta T cells are marked by co-expression of TRDV2 and TRDC.
span_literal:
T2 also contained some gamma-delta (γδ) T cells, marked by co-expression of TCR chain components TRDV2 and TRDC


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:1387a012f42755ff8b0c
claim_id: claim:1387a012f42755ff8b0c
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: T3 had sparse expression of resident memory T cell (Trm) markers ( CXCR6 , ITGA1)
summary:
In Homo sapiens kidney, T cell cluster T3 has sparse expression of tissue-resident memory T cell markers CXCR6 and ITGA1.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:a36432514cf77781aae9
claim_id: claim:a36432514cf77781aae9
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: T4 was marked by high GZMK expression, a marker of circulating age-associated memory T cells
summary:
In Homo sapiens kidney, T cell cluster T4 is marked by high GZMK expression, a marker of circulating age-associated memory T cells.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:3b6db57762bef9dcfefd
claim_id: claim:3b6db57762bef9dcfefd
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
Cluster MP1 highly expressed complement components ( C1QA , C1QB , C1QC ) and markers of alternative macrophage activation or anti-inflammatory function ( CD163 , LYVE1 , STAB1 , MRC1 , VSIG4 , FOLR2 )

summary:
In Homo sapiens kidney, mononuclear phagocyte cluster MP1 highly expresses complement components C1QA, C1QB, C1QC and markers of alternative macrophage activation CD163, LYVE1, STAB1, MRC1, VSIG4, and FOLR2.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:49f823af4bce5e710aaf
claim_id: claim:49f823af4bce5e710aaf
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
MP3 contained cells expressing cDC2 markers ( CLEC10A , CD1C) , alongside a subgroup of cells co-expressing lipid-associated genes ( CD9 , TREM2 , APOE, APOC1 )

summary:
In Homo sapiens kidney, mononuclear phagocyte cluster MP3 expresses conventional dendritic cell type 2 markers CLEC10A and CD1C, alongside lipid-associated genes CD9, TREM2, APOE, and APOC1.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:fe12864251a9ebb8ee41
claim_id: claim:fe12864251a9ebb8ee41
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: MP2 and MP4 ( FCGR3A + SIGLEC10 + FCN1 + ) resemble CD16 + non-classical monocytes
summary:
In Homo sapiens kidney, mononuclear phagocyte clusters MP2 and MP4 express FCGR3A, SIGLEC10, and FCN1, resembling CD16-positive non-classical monocytes.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:9a2b61f07bf8fccafd2e
claim_id: claim:9a2b61f07bf8fccafd2e
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: MP5 expressed markers of classical CD14 + monocytes ( S100A8 , S100A9 , CD14 , VCAN )
summary:
In Homo sapiens kidney, mononuclear phagocyte cluster MP5 expresses markers of classical CD14-positive monocytes including S100A8, S100A9, CD14, and VCAN.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:b6074d7fbd20d551a387
claim_id: claim:b6074d7fbd20d551a387
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
CS2, which was almost entirely comprised of living donor kidney cells (Supplementary Fig. 14b ), is defined by expression of genes associated with alternatively activated macrophages ( C1QA/B/C + RNASE1 + CD163 + LYVE1 + FOLR2 + )

summary:
In Homo sapiens kidney, myeloid cell state CS2 (alternatively activated macrophages) is defined by expression of C1QA, C1QB, C1QC, RNASE1, CD163, LYVE1, and FOLR2.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:5c24b389ff91d2c015c4
claim_id: claim:5c24b389ff91d2c015c4
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
Kidney lymphocytes were distinguished from circulating lymphocytes by elevated expression of chemokine receptors ( CXCR4 , CXCR6 ), integrin components ( ITGB1 , ITGA4 ), and inhibitory NK receptors ( KLRD1 , KLRC1 )

summary:
In Homo sapiens kidney, kidney-resident lymphocytes are distinguished from circulating lymphocytes by elevated expression of CXCR4, CXCR6, ITGB1, ITGA4, KLRD1, and KLRC1.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:54f913fd09c6d89944fa
claim_id: claim:54f913fd09c6d89944fa
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
AREG, encoding the growth factor amphiregulin, was highly expressed by NK1 and validated by flow cytometry

summary:
In Homo sapiens kidney, natural killer cell cluster NK1 highly expresses AREG, encoding the growth factor amphiregulin.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:26c60a907e577bcaaa7a
claim_id: claim:26c60a907e577bcaaa7a
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
Endo2 ( SOX17 + SERPINE2 + CLDN5 + CXCL12 + ) represents afferent arterioles and vasa recta, exhibiting reduced KDR expression and increased expression of extracellular matrix-encoding genes

summary:
In Homo sapiens kidney, endothelial cell cluster Endo2 expresses SOX17, SERPINE2, CLDN5, and CXCL12, representing afferent arterioles and vasa recta, with reduced KDR expression.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:d7afda1888a1c076f322
claim_id: claim:d7afda1888a1c076f322
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
we identified two populations (Endo1, Endo3) of peritubular capillary cells ( PLVAP + TMEM88 + DNASE1L3 + )

summary:
In Homo sapiens kidney, peritubular capillary endothelial cell populations Endo1 and Endo3 express PLVAP, TMEM88, and DNASE1L3.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:e16c5dce4861f3111f86
claim_id: claim:e16c5dce4861f3111f86
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: Endo1 expressed ESM1 – required for VEGF-related maintenance of the peritubular capillary network
summary:
In Homo sapiens kidney, peritubular capillary endothelial cell Endo1 expresses ESM1, required for vascular endothelial growth factor-related maintenance of the peritubular capillary network.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:82a2c1b02fac9bab9511
claim_id: claim:82a2c1b02fac9bab9511
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: Endo3 expressed motility and angiogenesis markers MARCKS , CLU , ACKR1 , and SEMA3D
summary:
In Homo sapiens kidney, peritubular capillary endothelial cell Endo3 expresses motility and angiogenesis markers MARCKS, CLU, ACKR1, and SEMA3D.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:bd74d00983c2f13c4501
claim_id: claim:bd74d00983c2f13c4501
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
Endo4 expresses the glomerular microvascular endothelial cell markers EDH3, SOST , and TBX3 , a transcriptional regulator critical to fenestrated glomerular endothelial development

summary:
In Homo sapiens kidney, endothelial cell cluster Endo4 expresses glomerular microvascular endothelial cell markers EDH3, SOST, and TBX3.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:8953bc45bda4513c203c
claim_id: claim:8953bc45bda4513c203c
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal: FOXP3 + CD4 + regulatory T cells were notably absent from scRNAseq and flow cytometry analyses
summary:
In Homo sapiens kidney, FOXP3-positive CD4-positive regulatory T cells are notably absent at steady state, as shown by single-cell RNA sequencing and flow cytometry.


claim_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9:claim:3b24da038cace4468f9e
claim_id: claim:3b24da038cace4468f9e
paper_key: hca:0400_10.1038_s41467-022-35297-z_0eab5d0ba9
span_literal:
MP4 had elevated expression of IL1B , MHC Class-II genes, and CX3CR1 while MP2 had higher expression of CXCR4 and FPR1

summary:
In Homo sapiens kidney, mononuclear phagocyte cluster MP4 has elevated expression of IL1B and CX3CR1, while mononuclear phagocyte cluster MP2 has higher expression of CXCR4 and FPR1.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:48530d7c04b526f1c871
claim_id: claim:48530d7c04b526f1c871
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
We identified three microglia clusters, viz. Microglia 1, Microglia 2, and Microglia 3 as they expressed canonical microglia markers ( e.g. CX3CR1 and AIF1 )

summary:
In Homo sapiens, microglia clusters from the subventricular zone express canonical markers CX3CR1 and AIF1.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:c6a87ebb1375ceac8cb6
claim_id: claim:c6a87ebb1375ceac8cb6
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
We identified two clusters as progenitor clusters ( i.e. Progenitors 1 and Progenitors 2), which expressed markers for progenitors ( e.g . SOX2 and SOX10 ), and lacked expression of markers for ependymal cells ( FOXJ1 and AQP4 ), radial glial cells ( HOPX ), or astrocytes ( VIM , GFAP and ALDH1A1 )

summary:
In Homo sapiens, progenitor cells from the subventricular zone express SOX2 and SOX10, and lack expression of ependymal cell markers FOXJ1 and AQP4, radial glial cell marker HOPX, and astrocyte markers VIM, GFAP, and ALDH1A1.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:9854791c1eb0a7513a2c
claim_id: claim:9854791c1eb0a7513a2c
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
They expressed the marker for early progenitor/astrocyte CD9 12 , but did not express markers for activated progenitors NES and EGFR 23 , and neither PROM1 (not shown) or markers for late neuronal progenitors ( e.g. PAX6 and ASCL1 ).

summary:
In Homo sapiens, progenitor cells from the subventricular zone express the early progenitor/astrocyte marker CD9, but do not express activated progenitor markers NES, EGFR, and PROM1, or late neuronal progenitor markers PAX6 and ASCL1.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:463c9a5f8d4e8e53c52e
claim_id: claim:463c9a5f8d4e8e53c52e
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
summary: In Homo sapiens, oligodendrocyte progenitor cells express the markers SOX10 and RGCC.
span_literal:
Both clusters also expressed markers for the oligodendrocyte lineage including the oligodendrocyte progenitor cell (OPC) markers SOX10 and RGCC 37 .


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:50796bd48e02289c6576
claim_id: claim:50796bd48e02289c6576
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
The cluster Neuronal was negative for all the above markers, and instead, expressed SOX6 and neuronal markers ( e.g. MAP2, RBFOX1 , NRXN1 and CTNNA2 )

summary:
In Homo sapiens, the neuronal cluster from the subventricular zone expresses SOX6 and neuronal markers MAP2, RBFOX1, NRXN1, and CTNNA2.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:b6f8366315a46342dfd9
claim_id: claim:b6f8366315a46342dfd9
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
These subclusters corresponded to early OPCs ( PDGFRA and SOX6 ), late OPCs ( SOX10 and SOX2 ), and oligodendrocytes ( KLK6 and OPALIN )

summary:
In Homo sapiens, early oligodendrocyte progenitor cells are marked by PDGFRA and SOX6, late oligodendrocyte progenitor cells are marked by SOX10 and SOX2, and oligodendrocytes are marked by KLK6 and OPALIN.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:39a1fcca8df131874e1e
claim_id: claim:39a1fcca8df131874e1e
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
SFRP1 is mainly expressed in late OPCs (Figure 4b) and is the only member of the SFRP family that is expressed in aged OPCs (Figure S5a).

summary:
In Homo sapiens, SFRP1 is mainly expressed in late oligodendrocyte progenitor cells and is the only secreted frizzled-related protein family member expressed in aged oligodendrocyte progenitor cells.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:44310e099daef42d678d
claim_id: claim:44310e099daef42d678d
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal: In contrast, P57 is expressed in both late OPCs as well as oligodendrocytes (Figure 4a).
summary:
In Homo sapiens, CDKN1C (P57) is expressed in both late oligodendrocyte progenitor cells and oligodendrocytes.


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:0341ef0b98d3f0e2e841
claim_id: claim:0341ef0b98d3f0e2e841
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
summary: In Homo sapiens, NGFR (CD271) is a marker expressed by progenitors of the aged subventricular zone.
span_literal:
We have previously identified NGFR ( i.e. CD271) as a marker expressed by progenitors of the aged human SVZ 31 – 33 .


claim_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600:claim:8f62297bc69b0bee4712
claim_id: claim:8f62297bc69b0bee4712
paper_key: hca:0401_10.21203_rs.3.rs-151881_v1_d8e8733600
span_literal:
while markers for quiescence and cell cycle arrest were highly expressed in mid-aged and aged OPC lineage cells, in particular CDKN1B ( i.e. P27 ), CDKN1C ( i.e. P57 ) and SFRP1 (Figure 3c).

summary:
In Homo sapiens, markers for quiescence and cell cycle arrest CDKN1B (P27), CDKN1C (P57), and SFRP1 are highly expressed in mid-aged and aged oligodendrocyte progenitor cell lineage cells.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:280b7bc22aa4a1dc4410
claim_id: claim:280b7bc22aa4a1dc4410
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
summary: In Homo sapiens clear cell renal carcinoma, IL7R is a marker of CD4 T cells.
span_literal:
These data confirmed SingleR-inferred cellular identify of each cluster— including expression of IL7R in CD4 T cells, CD3 and granzyme in CD8 T cells, and S100A8/S100A9 in monocytes.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:37ffa1c8e2b782fc056a
claim_id: claim:37ffa1c8e2b782fc056a
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
For example, the most differentially active protein in the Treg cluster was FOXP3, consistent with well-established Treg biology ( Chao et al., 2018 ) ( Figure 1D ), and Cytotoxic T Lymphocyte Antigen–4 (CTLA-4), which is up-regulated on the surface of tumor infiltrating Tregs ( Vargas et al., 2017 ), was inferred as differentially active by VIPER.

summary:
In Homo sapiens clear cell renal carcinoma, FOXP3 and cytotoxic T lymphocyte antigen-4 (CTLA-4) are differentially active markers of regulatory T cells.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:7e2c52e03bafce1c5c6f
claim_id: claim:7e2c52e03bafce1c5c6f
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
VIPER identified a distinct CD8 T cell population with markers consistent with exhaustion, including differential activation of LAG-3, TOX2, and PD1, which had been missed by expression-based analysis ( Figure 1D , Figure 2A ).

summary:
In Homo sapiens clear cell renal carcinoma, exhausted CD8 T cells show differential activation of LAG-3, TOX2, and PD1.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:a872e4e4f92a5acd71a7
claim_id: claim:a872e4e4f92a5acd71a7
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
As shown, LILRB5 was identified as the most differentially active among VIPER-inferred markers of tumor-specific macrophages.

summary:
In Homo sapiens clear cell renal carcinoma, LILRB5 is the most differentially active marker of tumor-specific macrophages.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:7109fc215d8937a78b3a
claim_id: claim:7109fc215d8937a78b3a
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
Among T-cells, FOXP3 was identified as the most activated protein in TIL Treg; relative activation was also noted in tumor associated CD8 T cells.

summary:
In Homo sapiens clear cell renal carcinoma, FOXP3 is the most activated protein in tumor-infiltrating regulatory T cells.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:fd622b7048c8cd1bb286
claim_id: claim:fd622b7048c8cd1bb286
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
Violin plots of top transcriptional markers (C1Q, APOE, TREM2) specifically up-regulated in Tumor-Infiltrating Macrophages as compared to other cell populations as well as non-tumor macrophages.

summary:
In Homo sapiens clear cell renal carcinoma, C1Q, APOE, and TREM2 are transcriptional markers specifically upregulated in tumor-infiltrating macrophages.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:89746b0cde0705f694bd
claim_id: claim:89746b0cde0705f694bd
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
As above, protein activity analysis identified a novel, tumor-specific sub-population of macrophages and their top differentially active proteins (i.e., LILRB5, APOE, and TREM2) and differentially expressed genes (i.e., C1QA-C, APOE, and TREM2) ( Table S2 ).

summary:
In Homo sapiens clear cell renal carcinoma, the tumor-specific macrophage subpopulation is characterized by differentially active LILRB5, APOE, and TREM2 proteins and differentially expressed C1QA-C, APOE, and TREM2 genes.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:dab6f66ed99bf5c32687
claim_id: claim:dab6f66ed99bf5c32687
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
Specifically, we uncovered a tumor-specific macrophage subpopulation characterized by upregulation of TREM2/APOE/C1Q - validated by spatially-resolved, quantitative multispectral immunofluorescence.

summary:
In Homo sapiens clear cell renal carcinoma, a tumor-specific macrophage subpopulation is characterized by upregulation of TREM2, APOE, and C1Q.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:3623af2fddccf1b0f537
claim_id: claim:3623af2fddccf1b0f537
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
Additionally, the epithelial cluster showed upregulation of keratin 16 ( KRT16 ) and 8 ( KRT8 ), which have also been associated with poor prognosis in ccRCC ( Tan et al., 2017 ).

summary:
In Homo sapiens clear cell renal carcinoma, the epithelial cell cluster shows upregulation of keratin 16 (KRT16) and keratin 8 (KRT8).


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:ba51214fa45bc35d4525
claim_id: claim:ba51214fa45bc35d4525
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
summary: In Homo sapiens clear cell renal carcinoma, epithelial cells overexpress SERPINA1 and CD24.
span_literal:
Of note, epithelial cells overexpressed SERPINA1, a protease inhibitor upregulated in multiple cancer types, as well as CD24, recently described as a macrophage immune checkpoint protein ( Barkal et al., 2019 ), whose expression is associated with worse prognosis in ccRCC ( Arik et al., 2017 ).


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:585949b188cff59001e6
claim_id: claim:585949b188cff59001e6
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
To further understand the epithelial cell clusters, we assessed VIPER-inferred activity of PAX8, PAX2, and CAIX, proteins expressed in renal epithelium; these are upregulated in malignancy and commonly used as markers for ccRCC ( Farber at al., 2017 ).

summary:
In Homo sapiens, PAX8, PAX2, and CAIX are proteins expressed in renal epithelial cells and commonly used as markers for clear cell renal carcinoma.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:577cf87d364bcc5046fb
claim_id: claim:577cf87d364bcc5046fb
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
In exhausted CD8 T-cells, for instance, these included LAG-3, PD-1, and CTLA-4, while in Tregs, they included FOXP3 and CTLA-4.

summary:
In Homo sapiens clear cell renal carcinoma, exhausted CD8 T cells show differential activity of LAG-3, PD-1, and CTLA-4.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:e22c38d72e04381bd62d
claim_id: claim:e22c38d72e04381bd62d
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
In exhausted CD8 T-cells, for instance, these included LAG-3, PD-1, and CTLA-4, while in Tregs, they included FOXP3 and CTLA-4.

summary:
In Homo sapiens clear cell renal carcinoma, regulatory T cells show differential activity of FOXP3 and CTLA-4.


claim_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f:claim:010d2756863505f4c472
claim_id: claim:010d2756863505f4c472
paper_key: hca:0402_10.1016_j.cell.2021.04.038_26e3dc6d2f
span_literal:
tumor-specific macrophage subpopulation characterized by upregulation of C1Q, APOE, and TREM2 and high activity of the LILRB5

summary:
In Homo sapiens clear cell renal carcinoma, a tumor-specific macrophage subpopulation is characterized by upregulation of C1Q, APOE, and TREM2 and high activity of LILRB5.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:2d7aa78e5477901ccd7e
claim_id: claim:2d7aa78e5477901ccd7e
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
summary: In Homo sapiens adult ovary, granulosa cells are marked by AMH, HSD17B1, SERPINE2, and GSTA1.
span_literal:
To confirm the identity of these cell types in the tSNE, we colored the single cells according to the expression levels of several expected marker genes: AMH , HSD17B1 , SERPINE2 , GSTA1 for GC; DCN , LUM for TC and stroma; TAGLN and RGS5 for smooth muscle cells; VWF and CLDN5 for endothelial cells; and CD53 and CXCR4 for immune cells (Fig. 2e ).


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:8155ab1a130fb0acc805
claim_id: claim:8155ab1a130fb0acc805
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
summary: In Homo sapiens adult ovary, endothelial cells express PECAM1, CD34, CTGF, TXNIP, and ANGPT2.
span_literal:
We identified three separate clusters (CL) of endothelial cells (CL7, CL9, CL16) expressing markers associated with lymph and blood vascular system (such as PECAM1 , CD34 , CTGF ), but also associated with remodeling and inflammatory response (such as TXNIP , ANGPT2 )


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:16edaf73bf1da46af237
claim_id: claim:16edaf73bf1da46af237
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
span_literal: DEGs of CL14 (such as ACTA2 , PLN , ADIRF, and MYH11 ) associated with mature smooth muscle cells
summary:
In Homo sapiens adult ovary, mature smooth muscle cells are associated with ACTA2, PLN, ADIRF, and MYH11.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:817c328bbaf011b7343d
claim_id: claim:817c328bbaf011b7343d
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
span_literal:
The GC of small antral follicles (1–2 mm diameter) clustered pronouncedly in cluster (CL15) showing WT1 high / EGR4 high / VCAN low / FST low expression (Fig. 4b ), suggesting that at that stage mural and cumulus GC still have a common progenitor (pGC) signature.

summary:
In Homo sapiens adult ovary, progenitor granulosa cells show high WT1 and EGR4 expression and low VCAN and FST expression.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:7c9743adccd428d353b4
claim_id: claim:7c9743adccd428d353b4
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
span_literal:
GC from selectable follicles (2–5 mm diameter) separated into two main cell types: cumulus GC ( VCAN high / FST high / IGFBP2 high / HTRA1 high / INHBB high / IHH high ) and mural GC ( WT1 low / EGR4 low / KRT18 high / CITED2 high / LIHP high / AKIRIN1 high ) (Fig. 4b ) 7 , 17 .

summary:
In Homo sapiens adult ovary, cumulus granulosa cells show high expression of VCAN, FST, IGFBP2, HTRA1, INHBB, and IHH.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:8492f33ee6bf0c9a4a01
claim_id: claim:8492f33ee6bf0c9a4a01
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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GC from selectable follicles (2–5 mm diameter) separated into two main cell types: cumulus GC ( VCAN high / FST high / IGFBP2 high / HTRA1 high / INHBB high / IHH high ) and mural GC ( WT1 low / EGR4 low / KRT18 high / CITED2 high / LIHP high / AKIRIN1 high ) (Fig. 4b ) 7 , 17 .

summary:
In Homo sapiens adult ovary, mural granulosa cells show low WT1 and EGR4 expression and high KRT18, CITED2, LIHP, and AKIRIN1 expression.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:69c88640a5da5b589318
claim_id: claim:69c88640a5da5b589318
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
summary: In Homo sapiens adult ovary, atretic granulosa cells are negative for VCAN, FST, and KRT18.
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The GC of CL10 were negative for several GC markers, such as VCAN and FST (Fig. 4b ), but were also negative for KRT18 (Fig. 4b ), similarly to pan-KRT-negative GC in atretic follicles (Fig. 4d ).


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:cf5092b8d0a6699a46bf
claim_id: claim:cf5092b8d0a6699a46bf
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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The GC in CL10 expressed lower levels of GJA1 and CDH2 compared to the other GC clusters (Fig. 5a, b ).

summary:
In Homo sapiens adult ovary, atretic granulosa cells express lower levels of GJA1 and CDH2 compared to other granulosa cells.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:f86eebdfd5a3465074b0
claim_id: claim:f86eebdfd5a3465074b0
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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Those included TC present in samples with follicles (Supplementary Fig. 2a, b ) and in stromal samples without visible follicles, but that could contain TC from follicle walls, corpus luteum or albicans (Supplementary Fig. 2c ). TC from (healthy) follicles, such as follicles A, B, and C, were mainly clustered in CL5 (Fig. 4a ), characterized by expression of known markers PTH1 , APOD , APOC1 , and several genes not earlier associated with TC, such as WFDC1 , MATN2 , COLEC11 (Fig. 7a ).

summary:
In Homo sapiens adult ovary, theca cells from healthy follicles are characterized by expression of PTH1, APOD, APOC1, WFDC1, MATN2, and COLEC11.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:702aaefbb2cbbe165676
claim_id: claim:702aaefbb2cbbe165676
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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The TC in CL2 and CL6 expressed IFITM3 , lower levels of COL3A1 and higher levels of FOS and IGFBP5 compared to the TC in CL5 (Fig. 8a ).

summary:
In Homo sapiens adult ovary, atretic theca cells express IFITM3, lower levels of COL3A1, and higher levels of FOS and IGFBP5 compared to healthy theca cells.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:2c7689d19a4e42e71dd2
claim_id: claim:2c7689d19a4e42e71dd2
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
summary: In Homo sapiens adult ovary, stromal cells show high expression of GNL3 and ARID5B.
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Although stromal clusters (CL0, CL1) showed high expression of GNL3 and ARID5B (Fig. 8d ), CL0 expressed high levels of XBP1 and SELK (Fig. 8e ), both involved in endoplasmic reticulum (ER)-stress-induced apoptosis, whereas CL1 expressed high levels of GPRC5A and TNFRS12A (Fig. 8f ).


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:6d033a4b8a0f8397eacd
claim_id: claim:6d033a4b8a0f8397eacd
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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Interestingly, both the TC clusters (CL2, CL5, CL6) and stroma (CL1) showed pronounced expression of several components of the complement system, such as C1R, C1S, and C7 (Fig. 9a ).

summary:
In Homo sapiens adult ovary, theca cells show pronounced expression of complement components C1R, C1S, and C7.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:acba53ed2bed8122cbc4
claim_id: claim:acba53ed2bed8122cbc4
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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Interestingly, both the TC clusters (CL2, CL5, CL6) and stroma (CL1) showed pronounced expression of several components of the complement system, such as C1R, C1S, and C7 (Fig. 9a ).

summary:
In Homo sapiens adult ovary, stromal cells show pronounced expression of complement components C1R, C1S, and C7.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:c61347eed6c1a985d120
claim_id: claim:c61347eed6c1a985d120
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
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On the other hand, pGC, mural GC, and other cell populations in the ovary expressed CD55 and CD59 , known to protect against targeting and damage by the complement cascade (Fig. 9a ), suggesting a concerted mechanism involving the complement system to allow growth and degeneration of the different follicular compartments in a timely manner.

summary:
In Homo sapiens adult ovary, progenitor granulosa cells and mural granulosa cells express CD55 and CD59, known to protect against complement cascade damage.


