# claims

claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:0e4344600d02d35df862
claim_id: claim:0e4344600d02d35df862
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
We also included NKG7 and GNLY as these are the most differentially expressed genes (DEGs) in NK cells compared to other lineages in the total peripheral blood mononuclear cell scRNA-seq dataset

summary:
In Homo sapiens, natural killer cells are marked by high expression of NKG7 and GNLY compared to other lineages.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:ab760a6d4fb8d16b0030
claim_id: claim:ab760a6d4fb8d16b0030
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
among these genes, we found several that belong to the immediate early genes (IEGs) category including NR4A2 , DUSP1 , FOSB , FOS , JUN , and JUNB

summary:
In Homo sapiens, active natural killer cells express immediate early genes including NR4A2, DUSP1, FOSB, FOS, JUN, and JUNB.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:5ba3f55cdad09d9dd7b7
claim_id: claim:5ba3f55cdad09d9dd7b7
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
We found the highest expression of cytolytic molecules in the “Mature NK” cluster, including perforin ( PRF1 ) and granzymes ( GZMA , GZMB , GZMH ).

summary:
In Homo sapiens, mature natural killer cells have the highest expression of cytolytic molecules including PRF1, GZMA, GZMB, and GZMH.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:473948331a73610430f5
claim_id: claim:473948331a73610430f5
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
We further demonstrate a high expression of B or dendritic cell-specific markers ( IGJ/MZB1/LILRA4 ) in cluster #8 and T cell-specific markers ( CD3D/E/G ) in cluster #9

summary:
In Homo sapiens, B cells or dendritic cells express IGJ, MZB1, and LILRA4, while T cells express CD3D, CD3E, and CD3G.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:f537e2999f6852e5c96e
claim_id: claim:f537e2999f6852e5c96e
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal: This cluster had high expression of IEGs, including FOS , FOSB , JUN , JUNB , and so on.
summary:
In Homo sapiens, active natural killer cells have high expression of immediate early genes including FOS, FOSB, JUN, and JUNB.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:5cadc7c64bc8334b917f
claim_id: claim:5cadc7c64bc8334b917f
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
Nearly half of them marked with high expression of CX3CR1 , HAVCR2 (TIM-3), and ZEB2 demonstrate unique transcriptional features and may comprise the terminal mature NK cells.

summary:
In Homo sapiens, terminal mature natural killer cells are marked by high expression of CX3CR1, HAVCR2 (TIM-3), and ZEB2.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:1101919aeb0bac4e55a2
claim_id: claim:1101919aeb0bac4e55a2
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
summary: In Homo sapiens, mature natural killer cells show peak expression of ACTB, ARPC2, CORO1A, and CFL1.
span_literal:
ACTB ), actin-related protein 2/3 complex subunit 2 ( ARPC2 , assist actin polymerization), and Coronin 1A ( CORO1A , remodel F-actin to enable granule release at the synapse), and Cofilin 1 ( CFL1 , depolymerize and remodel F-actin) peaked in the “Mature NK


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:c28a51514a09c112296a
claim_id: claim:c28a51514a09c112296a
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
summary: In Homo sapiens, mature natural killer cells show high expression of CST7 and PFN1.
span_literal:
We also found high expression of the negative regulators related to the cytotoxicity such as cystatin F ( CST7 ) and profilin 1 ( PFN1 )


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:c40bd285c0baa30e36dc
claim_id: claim:c40bd285c0baa30e36dc
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
Four of the top 10 up-regulated DEGs of the GATA2 T354M donor NK cells belonged to the GIMAP family and were shown in violin plots.

summary:
In Homo sapiens, natural killer cells from a donor with GATA2 T354M mutation show up-regulation of GIMAP family genes.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:ab61a4c71b27b79addf2
claim_id: claim:ab61a4c71b27b79addf2
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
summary: In Homo sapiens testis, spermatogonia are marked by UTF1 and FGFR3 expression.
span_literal:
Clusters 1–3 are germ cells, with C1 representing spermatogonia ( UTF1 + , FGFR3 + ), C2 consisting of spermatocytes ( SYCP3 + ), and C3 identifying post-meiotic spermatids ( PRM3 + ).


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:b152bcfa520fd17c22eb
claim_id: claim:b152bcfa520fd17c22eb
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
summary: In Homo sapiens testis, Sertoli cells are marked by SOX9 expression.
span_literal:
Clusters 4–8 correspond to a heterogenous mixture of Sertoli cells (C4; SOX9 + ), Leydig and myoid-like cells (C5; IGF1 + and/or ACTA2 + ), smooth muscle (C6; NOTCH3 + ), macrophages (C7: CD14 + ), and endothelial cells (C8; VWF + ), respectively (see Figures S1 D and S1E for additional markers).


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:9bcc793a7307bf286bea
claim_id: claim:9bcc793a7307bf286bea
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
slowly self-renewing and undifferentiated spermatogonia (referred to as States 0–1 in [ Guo et al., 2017 , Guo et al., 2018 ]) marked by UTF1 + and largely MKI67 – , differentiating spermatogonia (States 2–4) marked by KIT + and largely MKI67 + (note: State 4 is preparing to enter meiosis and lacks MKI67 ), spermatocytes (from STRA8 + to GPR85 + ), and spermatids ( PRM3 + )

summary:
In Homo sapiens testis, undifferentiated spermatogonia (States 0–1) are marked by positive UTF1 expression and largely negative MKI67 expression.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:17e2a9594c838c550d3e
claim_id: claim:17e2a9594c838c550d3e
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
slowly self-renewing and undifferentiated spermatogonia (referred to as States 0–1 in [ Guo et al., 2017 , Guo et al., 2018 ]) marked by UTF1 + and largely MKI67 – , differentiating spermatogonia (States 2–4) marked by KIT + and largely MKI67 + (note: State 4 is preparing to enter meiosis and lacks MKI67 ), spermatocytes (from STRA8 + to GPR85 + ), and spermatids ( PRM3 + )

summary:
In Homo sapiens testis, differentiating spermatogonia (States 2–4) are marked by positive KIT and positive MKI67 expression.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:0ae48b5df01dade76b62
claim_id: claim:0ae48b5df01dade76b62
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
However, in samples from 13 years old to adult, we observed a clear separation of Leydig (marked by DLK1 and IGF1 ) and myoid cells (marked by ACTA2 and MYH11 ).

summary:
In Homo sapiens testis, Leydig cells are marked by DLK1 and IGF1 expression, while myoid cells are marked by ACTA2 and MYH11 expression.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:ed6b4a3cbfde830fe529
claim_id: claim:ed6b4a3cbfde830fe529
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
Likewise, protein expression of CYP11A1, a marker for Leydig cell steroidogenesis, progressively appears as puberty proceeds

summary:
In Homo sapiens testis, CYP11A1 is a marker for Leydig cell steroidogenesis that progressively appears during puberty.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:a7d770421e4c90109cc4
claim_id: claim:a7d770421e4c90109cc4
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
Reclustering of C5 revealed that cells from the 11-year-old and younger samples largely overlapped and shared the expression of known markers of fetal Leydig and myoid precursors in the mouse (e.g., MAFB and NR4A1 ; Figures 4 A and 4B; DeFalco et al., 2011 , Wen et al., 2016 ), as well as heterogeneous co-expression of markers typically associated with both mature Leydig and myoid cells (e.g., DLK1 and ACTA2 , respectively)

summary:
In Homo sapiens testis, the common Leydig and myoid precursor cells express MAFB and NR4A1, as well as DLK1 and ACTA2.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:f8fc07ba17a1a7921c45
claim_id: claim:f8fc07ba17a1a7921c45
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
This is further supported by the upregulation of early Sertoli markers (including AMH and HES1 ), and downregulation of later Sertoli markers, including immune-related genes ( S100A6 , ISG15 )

summary:
In Homo sapiens, immature Sertoli cells are marked by upregulation of AMH and HES1, while mature Sertoli cells are marked by S100A6 and ISG15 expression.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:91e77d56330f7825e5b9
claim_id: claim:91e77d56330f7825e5b9
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
This is further supported by the upregulation of early Sertoli markers (including AMH and HES1 ), and downregulation of later Sertoli markers, including immune-related genes ( S100A6 , ISG15 )

summary:
In Homo sapiens, mature Sertoli cells are marked by S100A6 and ISG15 expression, which are downregulated in testosterone-suppressed testes.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:54669148954308a2a308
claim_id: claim:54669148954308a2a308
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
To confirm this, we performed IF/IHC staining and observed downregulation of the immature Sertoli marker AMH during puberty

summary:
In Homo sapiens testis, AMH is a marker of immature Sertoli cells that is downregulated during puberty.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:d7e92efd50ff3ae93a3c
claim_id: claim:d7e92efd50ff3ae93a3c
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
we observe that Sertoli cells downregulate INHA as they mature, while Leydig cells express high levels of INHBA after puberty

summary:
In Homo sapiens testis, Sertoli cells downregulate INHA as they mature, while Leydig cells express high levels of INHBA after puberty.


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:f1c2a8357139dd5f9b15
claim_id: claim:f1c2a8357139dd5f9b15
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
summary: In Homo sapiens testis, spermatogonia express activin receptors ACVR1B, BMPR1B, and ACVR2B.
span_literal:
activin receptors ( ACVR1B , BMPR1B , and ACVR2B ) are expressed in spermatogonia, whereas key inhibitors of Activin signaling ( FST , BAMBI , and NOG ) are specifically expressed in the undifferentiated spermatogonia (States 0 and 1).


claim_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298:claim:05e596cef5f947ed65a4
claim_id: claim:05e596cef5f947ed65a4
paper_key: hca:0472_10.1016_j.stem.2019.12.005_97b804f298
span_literal:
activin receptors ( ACVR1B , BMPR1B , and ACVR2B ) are expressed in spermatogonia, whereas key inhibitors of Activin signaling ( FST , BAMBI , and NOG ) are specifically expressed in the undifferentiated spermatogonia (States 0 and 1).

summary:
In Homo sapiens testis, undifferentiated spermatogonia (States 0 and 1) specifically express the activin signaling inhibitors FST, BAMBI, and NOG.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:f1c3b83383511887eb9c
claim_id: claim:f1c3b83383511887eb9c
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
However, SLC5A7 , a choline transporter that is necessary for ACh synthesis in the mouse CNS ( Ferguson et al., 2004 ), was detected ( Figure 5D ).

summary:
In Homo sapiens, SLC5A7 is detected in human colon enteric neurons as evidence of acetylcholine synthesis capacity.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:22f79ad5e0d07884b2ce
claim_id: claim:22f79ad5e0d07884b2ce
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
For example, the shared program for PEMNs ( n = 51 genes) includes ACh, neurotransmitter receptors ( e.g., Gfra2 , Oprk1 , Htr4 ), transporters ( e.g. , Slc5a7 ), TFs ( e.g., Casz1 ), and Colq , which tethers acetylcholinesterase in the neuromuscular junction ( Legay, 2000 ) ( Figure 5G , Table S4 ).

summary:
In Homo sapiens, the conserved transcriptional program for putative excitatory motor neurons includes GFRA2, OPRK1, HTR4, SLC5A7, CASZ1, and COLQ.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:d27d2d52142305cf69ab
claim_id: claim:d27d2d52142305cf69ab
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
We also defined shared programs for PIMNs, ( n = 42 genes; e.g., Nos1 , Gfra1 , Etv1 , Oprd1 , Dgkb ), PINs ( n = 59 genes; e.g., Penk , Adra2a , Bmpr1b ), PSNs ( n = 149 genes; e.g., Calcb , Nmu , Nog , Sst , Vipr2 ), and PSVNs ( n = 48 genes; e.g., Vip , Gal , Scgn , Calb2 ) ( Figure 5G , Table S4 ).

summary:
In Homo sapiens, the conserved transcriptional program for putative inhibitory motor neurons includes NOS1, GFRA1, ETV1, OPRD1, and DGKB.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:2bc525cd5a71aedbcc7e
claim_id: claim:2bc525cd5a71aedbcc7e
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
We also defined shared programs for PIMNs, ( n = 42 genes; e.g., Nos1 , Gfra1 , Etv1 , Oprd1 , Dgkb ), PINs ( n = 59 genes; e.g., Penk , Adra2a , Bmpr1b ), PSNs ( n = 149 genes; e.g., Calcb , Nmu , Nog , Sst , Vipr2 ), and PSVNs ( n = 48 genes; e.g., Vip , Gal , Scgn , Calb2 ) ( Figure 5G , Table S4 ).

summary:
In Homo sapiens, the conserved transcriptional program for putative interneurons includes PENK, ADRA2A, and BMPR1B.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:cde39d94140689a5dabd
claim_id: claim:cde39d94140689a5dabd
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
We also defined shared programs for PIMNs, ( n = 42 genes; e.g., Nos1 , Gfra1 , Etv1 , Oprd1 , Dgkb ), PINs ( n = 59 genes; e.g., Penk , Adra2a , Bmpr1b ), PSNs ( n = 149 genes; e.g., Calcb , Nmu , Nog , Sst , Vipr2 ), and PSVNs ( n = 48 genes; e.g., Vip , Gal , Scgn , Calb2 ) ( Figure 5G , Table S4 ).

summary:
In Homo sapiens, the conserved transcriptional program for putative sensory neurons includes CALCB, NMU, NOG, SST, and VIPR2.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:8d00d47ee7754ca70e70
claim_id: claim:8d00d47ee7754ca70e70
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
summary:
In Homo sapiens, the conserved transcriptional program for putative secretomotor/vasodilator neurons includes VIP, GAL, SCGN, and CALB2.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:bd9270018ef786fb3d47
claim_id: claim:bd9270018ef786fb3d47
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
summary: In Homo sapiens, enteric neurons are strongly enriched for the melanocortin 1 receptor MC1R.
span_literal:
Both human and mouse neurons were strongly enriched for the melanocortin receptor ( MC1R ) and its antagonist ( Agrp ), respectively ( Figure 5H , I ).


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:0a04c5d006d548db7e82
claim_id: claim:0a04c5d006d548db7e82
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
The leptin receptor ( LEPR ) and the enzyme for serotonin synthesis ( TPH2 ) we strongly expressed in human neurons, but not in mouse ( Figure 5H , I ).

summary:
In Homo sapiens, the leptin receptor LEPR and the serotonin synthesis enzyme TPH2 are strongly expressed in enteric neurons but not in mouse enteric neurons.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:0a3c83aef92138414677
claim_id: claim:0a3c83aef92138414677
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
summary: In Homo sapiens, mucosal glia are enriched for ferritin genes FTH1 and FLT.
span_literal:
Mucosal glia were enriched for ferritin genes ( e.g., FTH1, FLT ), myenteric glia expressed cell adhesion molecules ( e.g., NRXN1 , CADM2 ) ( Figure 5I ), and each myenteric subset expressed unique genes ( Figure 5I ), such as the purinergic receptor, P2Y12R in Glia2 cells, which may explain varying responses to adenosine triphosphate ( Boesmans et al., 2015 ).


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:8971c08c400a2510f151
claim_id: claim:8971c08c400a2510f151
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
For example, most HSCR risk genes were specifically expressed by enteric neurons, including RET , PHOX2B , GFRA1 , and ECE1 ( Figure 7B ; RET and PHOX2B validated in situ ; Figure S4L , M ); two exceptions, EDN3 and EDNRB , are expressed in the neural crest ( Pla and Larue, 2003 ).

summary:
In Homo sapiens, most Hirschsprung's disease risk genes are specifically expressed by enteric neurons, including RET, PHOX2B, GFRA1, and ECE1.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:720bed1ea227201ae31c
claim_id: claim:720bed1ea227201ae31c
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
While most IBD risk genes were enriched in mucosal cell subsets, a few were enriched in enteric neurons: BTBD8 , GRP , JAZF1 , NDFIP1 , PLA2R1 , and CNTNAP2 ( GRP validated in situ ; Figure 7B and S4N ).

summary:
In Homo sapiens, inflammatory bowel disease risk genes BTBD8, GRP, JAZF1, NDFIP1, PLA2R1, and CNTNAP2 are enriched in enteric neurons.


claim_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4:claim:8cd37b80ddae2c43c0c2
claim_id: claim:8cd37b80ddae2c43c0c2
paper_key: hca:0473_10.1016_j.cell.2020.08.003_9ae06495c4
span_literal:
Risk genes for ASD and PD were mainly expressed in the ENS relative to other cells in the colon ( Figure 7B ), including NRXN1 , ANK2 , DSCAM , and GABRB3 for ASD, and DLG2 , SNCA , and SCN3A for PD ( DSCAM and SNC3A validated in situ , Figure 7B and S4O , P ).

summary:
In Homo sapiens, autism spectrum disorder risk genes NRXN1, ANK2, DSCAM, and GABRB3 are mainly expressed in the enteric nervous system relative to other cells in the colon. In Homo sapiens, Parkinson's disease risk genes DLG2, SNCA, and SCN3A are mainly expressed in the enteric nervous system relative to other cells in the colon.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:23cd42c68a0a95bbd6a7
claim_id: claim:23cd42c68a0a95bbd6a7
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
summary: In Homo sapiens decidua, decidual natural killer cells are marked by KLRC1 and KLRD1.
span_literal:
dNK cells (markers: KLRC1 , KLRD1) , T cells (markers: CD3D , CD8A ), macrophages (markers: CD14 , FOLR2 ), monocytes (markers: FCN1 , VCAN ), DCs (markers: XCR1 , CLEC9A ), B cells (markers: CD20 , CD79A ), and mast cells (markers: TPSAB1 , MS4A2 ) were readily recognized and annotated by the expression of their feature genes and literature evidence


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:371d0781f5ef08eeb434
claim_id: claim:371d0781f5ef08eeb434
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 1 dNK cells preferentially expressed KLRB1 and cytokines CCL5 , and Cluster 2 highly expressed cytolytic enzyme GZMB and cytokeratin cell surface proteins KRT81 , KRT86

summary:
In Homo sapiens decidua, cluster 1 decidual natural killer cells preferentially express KLRB1 and CCL5.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:c1710c2c1f59dd657601
claim_id: claim:c1710c2c1f59dd657601
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 1 dNK cells preferentially expressed KLRB1 and cytokines CCL5 , and Cluster 2 highly expressed cytolytic enzyme GZMB and cytokeratin cell surface proteins KRT81 , KRT86

summary:
In Homo sapiens decidua, cluster 2 decidual natural killer cells highly express GZMB, KRT81, and KRT86.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:df09c1b0ff175fb4633b
claim_id: claim:df09c1b0ff175fb4633b
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 3 preferentially expressed SPINK2 , CSF1 , SYNGR1 , CD59 , KIR2DL3 , KIR2DL1 , ID3 , CD39 , and STAT3 , most of which are potential regulators of immune responses

summary:
In Homo sapiens decidua, cluster 3 decidual natural killer cells preferentially express SPINK2, CSF1, SYNGR1, CD59, KIR2DL3, KIR2DL1, ID3, CD39, and STAT3.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:36ef63ac0954bcb71ab7
claim_id: claim:36ef63ac0954bcb71ab7
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal: Cluster 4 expressed STMN1 , CDK1 , indicating the proliferating properties of these cells
summary:
In Homo sapiens decidua, cluster 4 decidual natural killer cells express STMN1 and CDK1, indicating proliferating properties.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:95437a8d9f894954d4e6
claim_id: claim:95437a8d9f894954d4e6
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Specifically, cluster 3 cells uniquely expressed the dNK1 markers including KIR2DL1 , KIR2DL3 , LILRB1 , KIR3DL1 , KIR3DL2 , KIR3DL3 , and cytoplasmic granule proteins GNLY , PRF1 , GZMA , and GZMK

summary:
In Homo sapiens decidua, cluster 3 decidual natural killer cells uniquely express the dNK1 markers KIR2DL1, KIR2DL3, LILRB1, KIR3DL1, KIR3DL2, KIR3DL3, and cytoplasmic granule proteins GNLY, PRF1, GZMA, and GZMK.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:bab47abe98b2c4c66fcd
claim_id: claim:bab47abe98b2c4c66fcd
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal: cluster 2 CD4 + T cells expressed naïve and memory markers CCR7 , SELL , and IL7R
summary:
In Homo sapiens decidua, cluster 2 CD4-positive T cells express naïve and memory markers CCR7, SELL, and IL7R.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:806d1a2f831d0230685a
claim_id: claim:806d1a2f831d0230685a
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 3 cells were Tregs, which uniquely expressed IL2RA and FOXP3 with other well-defined Treg genes such as TNFRSF9 , TIGIT , and CTLA4

summary:
In Homo sapiens decidua, regulatory T cells uniquely express IL2RA and FOXP3 along with TNFRSF9, TIGIT, and CTLA4.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:058514bd0e043619d366
claim_id: claim:058514bd0e043619d366
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 1 CD8 + T cells were characterized by the high expression of the GZMK , GZMA , GZMM , XCL1 , XCL2 , and CCL4 genes

summary:
In Homo sapiens decidua, cluster 1 CD8-positive T cells are characterized by high expression of GZMK, GZMA, GZMM, XCL1, XCL2, and CCL4.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:4eecef8eaad8b44d2111
claim_id: claim:4eecef8eaad8b44d2111
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 4 T cells showed some common gene expression signatures in cluster 1, and highly expressed FGFBP2 , FCGR3A , PRF1 , and GNLY which indicated effector CD8 + T cell properties

summary:
In Homo sapiens decidua, cluster 4 T cells highly express FGFBP2, FCGR3A, PRF1, and GNLY, indicating effector CD8-positive T cell properties.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:6f3ff8fea9741c491122
claim_id: claim:6f3ff8fea9741c491122
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 3 monocytes were then characterized by specific expression of classical monocyte-associated gene FCN1 and pro-inflammatory IL1B , TIMP1 , TREM1 genes

summary:
In Homo sapiens decidua, cluster 3 monocytes are characterized by specific expression of FCN1, IL1B, TIMP1, and TREM1.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:d99e06e2b7087505f5c6
claim_id: claim:d99e06e2b7087505f5c6
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
In addition, these monocytes also expressed a set of neutrophil-associated genes S100A8 , S100A9 , VCAN , and EREG

summary:
In Homo sapiens decidua, monocytes also express neutrophil-associated genes S100A8, S100A9, VCAN, and EREG.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:9db5b5112a423d3f4cb2
claim_id: claim:9db5b5112a423d3f4cb2
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Clusters 1-3 expressed the cDC1 markers XCR1 , CLEC9A , SERPINF2 , CADM1 , and CPVL , whereas cluster 4 expressed cDC2 markers CD1A , CLEC4A , PLAC8 , PLD4 , GPR183

summary:
In Homo sapiens decidua, clusters 1-3 dendritic cells express the conventional dendritic cell type 1 markers XCR1, CLEC9A, SERPINF2, CADM1, and CPVL, whereas cluster 4 dendritic cells express conventional dendritic cell type 2 markers CD1A, CLEC4A, PLAC8, PLD4, and GPR183.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:871882dae18d14fe723b
claim_id: claim:871882dae18d14fe723b
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Clusters 1-3 expressed the cDC1 markers XCR1 , CLEC9A , SERPINF2 , CADM1 , and CPVL , whereas cluster 4 expressed cDC2 markers CD1A , CLEC4A , PLAC8 , PLD4 , GPR183

summary:
In Homo sapiens decidua, cluster 4 dendritic cells express conventional dendritic cell type 2 markers CD1A, CLEC4A, PLAC8, PLD4, and GPR183.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:8818f97c979b843f291f
claim_id: claim:8818f97c979b843f291f
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
cluster 3 DCs expressed a set of cell cycle associated genes such as BIRC5 , MKI67 , STMN1 , CKS1B , and CENPM , indicating a proliferating feature of this cell population

summary:
In Homo sapiens decidua, cluster 3 dendritic cells express cell cycle associated genes BIRC5, MKI67, STMN1, CKS1B, and CENPM, indicating a proliferating feature.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:e7bc3982a55916932cd6
claim_id: claim:e7bc3982a55916932cd6
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
In contrast, cluster 5 DCs expressed pro-inflammatory genes such as CCL19 , CCL22 , and cell migration associated factors FSCN1 , LAMP3 , RAB9A

summary:
In Homo sapiens decidua, cluster 5 dendritic cells express pro-inflammatory genes CCL19 and CCL22, and cell migration associated factors FSCN1, LAMP3, and RAB9A.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:59f4b42745e283cc49e5
claim_id: claim:59f4b42745e283cc49e5
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Human decidual macrophages are phenotypically defined as CD14 + FOLR2 + and predominantly express CCL2 , CCL3 , and CCL4

summary:
In Homo sapiens, decidual macrophages are phenotypically defined as CD14-positive and FOLR2-positive and predominantly express CCL2, CCL3, and CCL4.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:a5b071c7c23dbf7f9cca
claim_id: claim:a5b071c7c23dbf7f9cca
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Decidual macrophages are believed to exist as anti-inflammatory cells of an M2-like phenotype which highly express HAVCR2 (Tim-3)

summary:
In Homo sapiens, decidual macrophages highly express HAVCR2 (T-cell immunoglobulin and mucin domain-containing protein 3), consistent with an M2-like phenotype.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:b30b039d0d957aa92023
claim_id: claim:b30b039d0d957aa92023
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
leukocyte immunoglobulin-like receptors LILRB1 and LILRB2 , the inhibitory receptors for HLA-G which are expressed on invading extravillous trophoblast, are found to be expressed by decidual macrophages

summary:
In Homo sapiens, decidual macrophages express leukocyte immunoglobulin-like receptor B1 (LILRB1) and leukocyte immunoglobulin-like receptor B2 (LILRB2).


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:eadf33c24fbb4ff9d5e8
claim_id: claim:eadf33c24fbb4ff9d5e8
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
summary: In Homo sapiens decidua, macrophages are characterized by the expression of CD14, CD16, and CD68.
span_literal:
Macrophages are the second most abundant leukocyte population within the human decidua characterized by the expression of CD14 , CD16 , and CD68


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:aea1f0108c252d4164ab
claim_id: claim:aea1f0108c252d4164ab
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
cDC1s expressing cell surface markers XCR1 and CADM1 were efficient antigen cross-presenters to CD8 + T cells, while cDC2s expressing CD1A and CD172A preferentially interacted with CD4 + T cells

summary:
In Homo sapiens, conventional dendritic cell type 1 cells express cell surface markers XCR1 and CADM1, while conventional dendritic cell type 2 cells express CD1A and CD172A.


claim_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403:claim:737a989c45694f9f27b6
claim_id: claim:737a989c45694f9f27b6
paper_key: hca:0474_10.3389_fimmu.2021.689019_ff96e36403
span_literal:
Cluster 6 macrophages highly express the pro-inflammatory genes ( FABP5 and EIF5A ), and anti-inflammatory genes ( APOE and MS4A7 )

summary:
In Homo sapiens decidua, cluster 6 macrophages highly express the pro-inflammatory genes FABP5 and EIF5A, and anti-inflammatory genes APOE and MS4A7.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:654aed98b9f0b2846241
claim_id: claim:654aed98b9f0b2846241
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
These data recapitulate tissue-specific vascular markers such as LCN1 (tear lipocalin) in the eye, ABCG2 (transporter at the blood-testis barrier) in the prostate, and OIT3 (oncoprotein induced transcript 3) in the liver.

summary:
In Homo sapiens, endothelial cells in the eye express LCN1 (tear lipocalin) as a tissue-specific vascular marker. In Homo sapiens, endothelial cells in the prostate express ABCG2 as a tissue-specific vascular marker. In Homo sapiens, endothelial cells in the liver express OIT3 (oncoprotein induced transcript 3) as a tissue-specific vascular marker.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:a34f13807b87326971a2
claim_id: claim:a34f13807b87326971a2
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
Of the potential novel markers determined by this analysis, SLC14A1 (solute carrier family 14 member 1) appears to be a new specific marker for endothelial cells in the heart, whose expression was independently validated with data from the Human Protein Atlas (18) ([fig. S13](452956v3_figs13.tif)).

summary:
In Homo sapiens, SLC14A1 (solute carrier family 14 member 1) is a novel specific marker for endothelial cells in the heart.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:8d46bd0264556261d34d
claim_id: claim:8d46bd0264556261d34d
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
Notably, lung ECs formed two distinct populations, which is in line with the aerocyte (aCap-EDNRB+) and general capillary (gCap - PLVAP+) cells described in the mouse and human lung (19) ([fig. S12 C,D](452956v3_figs12.tif)).

summary:
In Homo sapiens, aerocyte capillary endothelial cells in the lung are positive for EDNRB, while general capillary endothelial cells in the lung are positive for PLVAP.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:24a2099b5ec8f858ec63
claim_id: claim:24a2099b5ec8f858ec63
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
Lastly, we detected two distinct populations of ECs in the muscle, including a MSX1+ population with strong angiogenic and endothelial cell proliferation signatures, and a CYP1B1+ population enriched in metabolic genes, suggesting the presence of functional specialization in the muscle vasculature ([fig. S12 E,F](452956v3_figs12.tif)).

summary:
In Homo sapiens, one population of endothelial cells in the muscle is positive for MSX1 with angiogenic and proliferation signatures. In Homo sapiens, one population of endothelial cells in the muscle is positive for CYP1B1 and enriched in metabolic genes.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:973229025d987c64dfb0
claim_id: claim:973229025d987c64dfb0
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
summary: In Homo sapiens, mucosal associated invariant T cells have characteristic expression of TRAV1-2.
span_literal:
these cells had characteristic expression of TRAV1-2 as they are thought to be innate-like effector cells (17).


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:9038a4530b5b9a9adc9b
claim_id: claim:9038a4530b5b9a9adc9b
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
macrophages in the spleen were different from most other macrophages, and this was driven largely by higher expression of CD5L, a regulator of lipid synthesis ([fig. S11B](452956v3_figs11.tif)).

summary:
In Homo sapiens, macrophages in the spleen have higher expression of CD5L compared to most other macrophages.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:5cad5420679a6aafcb68
claim_id: claim:5cad5420679a6aafcb68
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
We also observed a shared signature of elevated EREG (epiregulin) expression in solid tissues such as the skin, uterus and mammary compared to circulatory tissues ([fig. S11B](452956v3_figs11.tif)).

summary:
In Homo sapiens, macrophages in solid tissues such as the skin, uterus, and mammary have elevated expression of EREG (epiregulin) compared to macrophages in circulatory tissues.


claim_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad:claim:b89d67241f2eecad23e6
claim_id: claim:b89d67241f2eecad23e6
paper_key: hca:0475_10.1101_2021.07.19.452956_e30bf05aad
span_literal:
For example, expression of the long non-coding RNA MALAT1, which impacts the regulatory function of T cells, and CCR9, which mediates T lymphocyte development and migration to the intestine (31), were high only in the small intestine, while GPR15 (colonic T cell trafficking), SELENBP1 (selenium transporter), ANXA1 (repressor of inflammation in T cells), KLRC2 (T cell lectin), CD24 (T cell survival), GDF15 (T cell inhibitor), and RARRES2 (T cell chemokine) exhibited much higher expression in the large intestine.

summary:
In Homo sapiens, T cells in the small intestine have high expression of MALAT1 and CCR9. In Homo sapiens, T cells in the large intestine have much higher expression of GPR15, SELENBP1, ANXA1, KLRC2, CD24, GDF15, and RARRES2 compared to T cells in the small intestine.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:47171009b3baa55c394e
claim_id: claim:47171009b3baa55c394e
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
macrophages in the spleen were different from most other macrophages, and this was driven largely by higher expression of CD5L, a regulator of lipid synthesis

summary:
In Homo sapiens, macrophages in the spleen show higher expression of CD5L compared with macrophages from most other tissues.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:0c732633b74eafd23be1
claim_id: claim:0c732633b74eafd23be1
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
summary: In Homo sapiens, mucosal-associated invariant T cells have characteristic expression of TRAV1-2.
span_literal:
several clones of mucosalassociated invariant T cells are shared across donors ( fig. S11C ); these cells had characteristic expression of TRAV1-2 because they are thought to be innate-like effector cells


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:886fddaf251cd07e9d01
claim_id: claim:886fddaf251cd07e9d01
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
These data recapitulate tissue-specific vascular markers, such as LCN1 (tear lipocalin) in the eye, ABCG2 (transporter at the blood-testis barrier) in the prostate, and OIT3 (oncoprotein-induced transcript 3) in the liver.

summary:
In Homo sapiens, LCN1 (tear lipocalin) is a tissue-specific marker for endothelial cells in the eye. In Homo sapiens, ABCG2 is a tissue-specific marker for endothelial cells in the prostate. In Homo sapiens, OIT3 (oncoprotein-induced transcript 3) is a tissue-specific marker for endothelial cells in the liver.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:fb6265dbb30e8b12c1cb
claim_id: claim:fb6265dbb30e8b12c1cb
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
Of the potential previously undescribed markers determined by this analysis, SLC14A1 (solute carrier family 14 member 1) appears to be a specific marker for endothelial cells in the heart, whose expression was independently validated with data from the Human Protein Atlas ( 18 ) ( fig. S13 ).

summary:
In Homo sapiens, SLC14A1 (solute carrier family 14 member 1) is a specific marker for endothelial cells in the heart.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:12c7cd1a09c8bdf11b0b
claim_id: claim:12c7cd1a09c8bdf11b0b
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
Lung ECs formed two distinct populations, which is in line with the aerocyte (aCap - EDNRB+) and general capillary (gCap - PLVAP+) cells described in the mouse and human lung ( 19 ) ( fig. S12 , C and D ).

summary:
In Homo sapiens, aerocyte capillary cells in the lung are positive for EDNRB, and general capillary cells in the lung are positive for PLVAP.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:25794f54296e445462b7
claim_id: claim:25794f54296e445462b7
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
Lastly, we detected two distinct populations of ECs in the muscle, including a MSX1+ population with strong angiogenic and endothelial cell proliferation signatures and a CYPIB1+ population enriched in metabolic genes, which suggests the presence of functional specialization in the muscle vasculature ( fig. S12 , E and F ).

summary:
In Homo sapiens, one population of endothelial cells in the muscle is positive for MSX1 with angiogenic and proliferation signatures, and another population is positive for CYP1B1 and enriched in metabolic genes.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:ef649a55d2e7eda9be8c
claim_id: claim:ef649a55d2e7eda9be8c
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
We also observed a shared signature of elevated epiregulin (EREG) expression in solid tissues, such as the skin, uterus, and mammary, compared with circulatory tissues ( fig. S11B ).

summary:
In Homo sapiens, macrophages in solid tissues such as the skin, uterus, and mammary show elevated expression of epiregulin (EREG) compared with macrophages in circulatory tissues.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:4519b15ed339688fead9
claim_id: claim:4519b15ed339688fead9
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
For example, expression of the long noncoding RNA MALAT1, which affects the regulatory function of T cells, and CCR9, which mediates T lymphocyte development and migration to the intestine ( 31 ), were high only in the small intestine, whereas GPR15 (colonic T cell trafficking), SELENBP1 (selenium transporter), ANXA1 (repressor of inflammation in T cells), KLRC2 (T cell lectin), CD24 (T cell survival), GDF15 (T cell inhibitor), and RARRES2 (T cell chemokine) exhibited much higher expression in the large intestine.

summary:
In Homo sapiens, T cells in the small intestine show high expression of MALAT1 and CCR9, whereas T cells in the large intestine show much higher expression of GPR15, SELENBP1, ANXA1, KLRC2, CD24, GDF15, and RARRES2. In Homo sapiens, T cells in the large intestine show much higher expression of GPR15, SELENBP1, ANXA1, KLRC2, CD24, GDF15, and RARRES2 compared with T cells in the small intestine.


claim_key: hca:0476_10.1126_science.abl4896_6d8fed9731:claim:e42939a82f917734173b
claim_id: claim:e42939a82f917734173b
paper_key: hca:0476_10.1126_science.abl4896_6d8fed9731
span_literal:
Consistent with this finding, the expression values of cyclin-dependent kinase (CDK) inhibitors (in particular the gene CDKN1A), which block the cell cycle, have the lowest overall expression in macrophages from tissues with high cycling indices ( fig. S16F ).

summary:
In Homo sapiens, macrophages from tissues with high cycling indices have the lowest expression of CDKN1A, a cyclin-dependent kinase inhibitor.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:210fdb91a0650975f9bd
claim_id: claim:210fdb91a0650975f9bd
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal:
Expression of AEC2 marker genes including SFTPC , SFTPA2 , SFTPB , and ABCA3 was downregulated in IPF AEC2s

summary:
In Homo sapiens, type 2 alveolar epithelial cells are marked by SFTPC, SFTPA2, SFTPB, and ABCA3, and these markers are downregulated in idiopathic pulmonary fibrosis type 2 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:4ab1ca1215b7f464518b
claim_id: claim:4ab1ca1215b7f464518b
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal:
Our scRNA-Seq data showed that among the SLC39 family genes, SLC39A8 (encoding ZIP8) was expressed at the highest level in healthy AEC2s

summary:
In Homo sapiens, SLC39A8 (encoding ZIP8) is expressed at the highest level among SLC39 family genes in healthy type 2 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:6f47c2ca0829d6bdf83e
claim_id: claim:6f47c2ca0829d6bdf83e
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal: Within lung epithelial cells, SLC39A8 was mainly expressed in AEC2s and AEC1s
summary:
In Homo sapiens lung, SLC39A8 is mainly expressed in type 2 alveolar epithelial cells and type 1 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:e6dd88c9a982314bb6bb
claim_id: claim:e6dd88c9a982314bb6bb
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal: Within lung epithelial cells, SLC39A8 was mainly expressed in AEC2s and AEC1s
summary:
In Homo sapiens lung, SLC39A8 is mainly expressed in type 1 alveolar epithelial cells and type 2 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:90ecf19ab20332446e7e
claim_id: claim:90ecf19ab20332446e7e
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal:
We found that SLC39A8 was mainly expressed in EpCAM + epithelial cells and its expression in EpCAM – mesenchymal cells was very low

summary:
In Homo sapiens lung, SLC39A8 is mainly expressed in EpCAM-positive epithelial cells, with very low expression in EpCAM-negative mesenchymal cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:969e8dbe9231c11d0609
claim_id: claim:969e8dbe9231c11d0609
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal:
Most interestingly, expression of SLC39A8 was dramatically decreased in IPF AEC2s, prompting further investigations

summary:
In Homo sapiens, expression of SLC39A8 is dramatically decreased in idiopathic pulmonary fibrosis type 2 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:081eb80924f001e3a670
claim_id: claim:081eb80924f001e3a670
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal: ZIP8 – AEC2s derived from 3D-cultured organoids showed decreased PDPN expression
summary:
In Homo sapiens, ZIP8-negative type 2 alveolar epithelial cells derived from 3D-cultured organoids show decreased PDPN expression.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:19be73afa8b877024267
claim_id: claim:19be73afa8b877024267
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal: By qPCR , we found that SIRT1 expression was decreased in both freshly isolated IPF AEC2s
summary:
In Homo sapiens, SIRT1 expression is decreased in freshly isolated idiopathic pulmonary fibrosis type 2 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:f95424b3940796974db3
claim_id: claim:f95424b3940796974db3
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal: Our results showed that ZIP8 – AEC2s had much lower SIRT1 expression than ZIP8 + AEC2s
summary:
In Homo sapiens, ZIP8-negative type 2 alveolar epithelial cells have much lower SIRT1 expression than ZIP8-positive type 2 alveolar epithelial cells.


claim_key: hca:0477_10.1172_jci157338_273d70a217:claim:0f07c0ed4cce8fe789f6
claim_id: claim:0f07c0ed4cce8fe789f6
paper_key: hca:0477_10.1172_jci157338_273d70a217
span_literal: NNMT , NAMPT , KYNU , and NQO1 , were downregulated in AEC2s from IPF relative to healthy lungs
summary:
In Homo sapiens, genes encoding NAD+ synthesis enzymes including NNMT, NAMPT, KYNU, and NQO1 are downregulated in idiopathic pulmonary fibrosis type 2 alveolar epithelial cells relative to healthy type 2 alveolar epithelial cells.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:cfe11c23f1cfc5022fd0
claim_id: claim:cfe11c23f1cfc5022fd0
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
The global immune cell clusters were identified using key marker genes: myeloid cells ( LYZ , C1QA , S100A9 , and CD1C )

summary:
In Homo sapiens neuroblastoma, myeloid cells are identified by the marker genes LYZ, C1QA, S100A9, and CD1C.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:ff046b38700f34ed6fa6
claim_id: claim:ff046b38700f34ed6fa6
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
summary: In Homo sapiens neuroblastoma, B cells are identified by the marker genes MS4A1, BANK1, and CD79A.
span_literal:
The global immune cell clusters were identified using key marker genes: myeloid cells ( LYZ , C1QA , S100A9 , and CD1C ), 34 , 35 B cells ( MS4A1 , BANK1 , and CD79A )


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:66e01a0c08a35933da77
claim_id: claim:66e01a0c08a35933da77
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal: T cells ( CD3D ), 38 and NK cells ( CMC1 and GNLY )
summary:
In Homo sapiens neuroblastoma, natural killer cells are identified by the marker genes CMC1 and GNLY.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:5021442f367cfdd4d7fe
claim_id: claim:5021442f367cfdd4d7fe
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Focusing on Mono-1/2 subclusters, we annotated these clusters based on the expression of the key monocyte marker genes CLEC7A , NLRP3 , and BST1.

summary:
In Homo sapiens neuroblastoma, monocytes (Mono-1/2) are annotated based on expression of the marker genes CLEC7A, NLRP3, and BST1.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:02b8f5e8f853a90f7bde
claim_id: claim:02b8f5e8f853a90f7bde
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Both monocyte clusters expressed the pro-inflammatory cytokine IL1B , the monocyte genes TIMP1 , CD44 , and G0S2 , and several inflammatory-related S100A genes

summary:
In Homo sapiens neuroblastoma, monocyte clusters express the marker genes IL1B, TIMP1, CD44, and G0S2.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:63791491c5613aee8dde
claim_id: claim:63791491c5613aee8dde
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Mono-1 appeared to consist of two subpopulations within: a small population of non-classical monocytes with expression of FCGR3A , FCGR3B , and IFITM3 , and a larger population of cells that exhibited specific expression of TIMP1 , S100A4 , S100A12 , and CD55

summary:
In Homo sapiens neuroblastoma, non-classical monocytes within Mono-1 express FCGR3A, FCGR3B, and IFITM3.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:d2db1f18deb65e22be32
claim_id: claim:d2db1f18deb65e22be32
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Mono-1 appeared to consist of two subpopulations within: a small population of non-classical monocytes with expression of FCGR3A , FCGR3B , and IFITM3 , and a larger population of cells that exhibited specific expression of TIMP1 , S100A4 , S100A12 , and CD55

summary:
In Homo sapiens neuroblastoma, the larger subpopulation within Mono-1 exhibits specific expression of TIMP1, S100A4, S100A12, and CD55.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:e0e3e8b2b2f315425f4d
claim_id: claim:e0e3e8b2b2f315425f4d
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
This population might be differentiating into Macro-2 since part of the population displayed expression of the macrophage marker genes CD68 and APOE

summary:
In Homo sapiens neuroblastoma, Mono-2 displays expression of the macrophage marker genes CD68 and APOE.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:94d7f3bfa29a383a92d8
claim_id: claim:94d7f3bfa29a383a92d8
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Further investigation of the macrophage populations showed that the macrophage clusters had high expression of the classic macrophage marker gene CD68

summary:
In Homo sapiens neuroblastoma, macrophage clusters have high expression of the classic macrophage marker gene CD68.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:08173b793b8ccd31caaf
claim_id: claim:08173b793b8ccd31caaf
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Furthermore, Macro-1 displayed a population-specific gene expression pattern of tumor-associated macrophage markers, such as TREM2 , FABP5 , and FABP4

summary:
In Homo sapiens neuroblastoma, Macro-1 displays expression of tumor-associated macrophage markers TREM2, FABP5, and FABP4.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:03ee4c9ac87f19ac46b3
claim_id: claim:03ee4c9ac87f19ac46b3
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
summary: In Homo sapiens neuroblastoma, Macro-2 expresses high levels of CXCL2, CXCL3, and CXCL8.
span_literal:
Macro-2 expressed high levels of neutrophil-attracting chemokines, including CXCL2 , CXCL3 , and CXCL8.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:73f63d1c345c557aba0e
claim_id: claim:73f63d1c345c557aba0e
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
summary: In Homo sapiens neuroblastoma, Macro-2 exhibits high expression of GPR183, DUSP2, and CD83.
span_literal:
In addition, this population exhibited high expression of GPR183 , DUSP2 , CD83 , and HLA class II genes


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:a992f7d2f8441d0141e6
claim_id: claim:a992f7d2f8441d0141e6
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal: Macro-3 displayed expression of other macrophage genes, such as LYVE1 , CSF1R , and MRC1
summary:
In Homo sapiens neuroblastoma, Macro-3 displays expression of macrophage genes LYVE1, CSF1R, and MRC1.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:60ed036cf3e35792a653
claim_id: claim:60ed036cf3e35792a653
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
CLEC9A+ mDCs expressed high levels of CLEC9A , RAB7B , BATF3 , WDFY4 , and CADM1 , which phenotypically corresponded to DC1 cells

summary:
In Homo sapiens neuroblastoma, CLEC9A-positive myeloid dendritic cells (DC1) express high levels of CLEC9A, RAB7B, BATF3, WDFY4, and CADM1.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:e4b8dd5825ad194ca96c
claim_id: claim:e4b8dd5825ad194ca96c
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
CD1C+ mDCs were identified by the high expression of CD1C , CLEC10A , and FCER1A , but also exhibited high expression of HLA class II antigen-presenting genes, and therefore had a similar phenotype to previously described DC2.

summary:
In Homo sapiens neuroblastoma, CD1C-positive myeloid dendritic cells (DC2) are identified by high expression of CD1C, CLEC10A, and FCER1A.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:3081fe87f2fa476cd765
claim_id: claim:3081fe87f2fa476cd765
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal: Mature-LAMP3+ mDCs showed high expression of CCR7 and CD83
summary:
In Homo sapiens neuroblastoma, mature LAMP3-positive myeloid dendritic cells show high expression of CCR7 and CD83.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:bc25cbdb3c7aa2ea8427
claim_id: claim:bc25cbdb3c7aa2ea8427
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
In addition, we detected memory B cells that were annotated based on the expression of CD27 , CLECL1 , and ZBTB32

summary:
In Homo sapiens neuroblastoma, memory B cells are annotated based on expression of CD27, CLECL1, and ZBTB32.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:f304ccdda415a1617b0b
claim_id: claim:f304ccdda415a1617b0b
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal: GC B cells expressed high levels of VDJ recombination genes, including VPREB3 , VPREB1 , and RAG1.
summary:
In Homo sapiens neuroblastoma, germinal center B cells express high levels of VPREB3, VPREB1, and RAG1.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:dce4696edc4def6f2f1d
claim_id: claim:dce4696edc4def6f2f1d
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
Furthermore, this GC cluster exhibited expression of previously described GC-associated genes, such as AICDA , MME , PRPSAP2 , and MARCKSL1

summary:
In Homo sapiens neuroblastoma, the germinal center B cell cluster exhibits expression of AICDA, MME, PRPSAP2, and MARCKSL1.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:ec9e2e5625d5ad16c32e
claim_id: claim:ec9e2e5625d5ad16c32e
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
The NK-active cell cluster was annotated based on the expression of immediate-early genes, such as ZPF36 , NR4A2 , JUNB , FOS , FOSB , and CD69 .

summary:
In Homo sapiens neuroblastoma, the active natural killer cell cluster is annotated based on expression of ZFP36, NR4A2, JUNB, FOS, FOSB, and CD69.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:e2cc78a025e5e7ac6b57
claim_id: claim:e2cc78a025e5e7ac6b57
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal:
In addition, an ILC3 cell cluster was annotated based on their lack of expression of classical NK cell marker genes TBX21 and EOMES and the high expression of AHR , KIT , IL7R , and RORC

summary:
In Homo sapiens neuroblastoma, the innate lymphoid cell type 3 cluster lacks expression of TBX21 and EOMES and has high expression of AHR, KIT, IL7R, and RORC.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:f9d8186db506769ae72c
claim_id: claim:f9d8186db506769ae72c
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
summary: In Homo sapiens neuroblastoma, T helper 17 cells express RORC, CCL20, CCR6, and IL17A.
span_literal:
Single-cell transcriptomics and immunohistochemistry both showed the presence of Th17 cells ( RORC , CCL20 , CCR6 , and, less prominently, IL17A ).


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:98f6b3a94e0969994f72
claim_id: claim:98f6b3a94e0969994f72
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal: Tregs were identified based on FOXP3 and IL2RA expression, two key Treg marker genes
summary:
In Homo sapiens neuroblastoma, regulatory T cells are identified based on FOXP3 and IL2RA expression.


claim_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98:claim:0da41a352f5f01f955cc
claim_id: claim:0da41a352f5f01f955cc
paper_key: hca:0479_10.1016_j.xcrm.2022.100657_bf09154d98
span_literal: CTL-4 expressed high levels of TNF , CD69 , and IFNG .
summary:
In Homo sapiens neuroblastoma, cytotoxic T lymphocyte 4 expresses high levels of TNF, CD69, and IFNG.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:de9cdc79adb4ccd8ae17
claim_id: claim:de9cdc79adb4ccd8ae17
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CM3 was closest to CD1C + DCs (reference clusters DC2 and DC3) or CLEC9A + DCs (reference cluster DC1), in accordance with the expression of the canonical DC markers CD1C and FLT3

summary:
In Homo sapiens, conventional dendritic cells (cluster CM3) express the canonical dendritic cell markers CD1C and FLT3.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:e32211668253621954f7
claim_id: claim:e32211668253621954f7
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CM3 was closest to CD1C + DCs (reference clusters DC2 and DC3) or CLEC9A + DCs (reference cluster DC1), in accordance with the expression of the canonical DC markers CD1C and FLT3 ( Supplementary Fig. 3a ), and the lack of expression of monocyte markers CD14 and CD16 .

summary:
In Homo sapiens, conventional dendritic cells (cluster CM3) lack expression of the monocyte markers CD14 and CD16.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:e81b677ffc699bd6fa67
claim_id: claim:e81b677ffc699bd6fa67
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CM0 cells were most similar to CD16 + patrolling monocytes (reference clusters Mono2 and DC4), with very high expression of CD16 ( FCGR3A ) and CX3CR1 and low expression of CD14 and CCR2 .

summary:
In Homo sapiens, CD16-positive patrolling monocytes (cluster CM0) express very high levels of FCGR3A and CX3CR1 and low levels of CD14 and CCR2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:188d39a1d37ca257a310
claim_id: claim:188d39a1d37ca257a310
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CM1 expressed upregulated levels of phagocytic receptors CD36 ( SCARB3 ), SCARB2, CD68, CD163, NR1H3 ( LXR ) and GPNMB

summary:
In Homo sapiens, phagocytic monocyte/macrophage cells (cluster CM1) express upregulated levels of CD36, SCARB2, CD68, CD163, NR1H3, and GPNMB.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:af10d775fba0ec05fd46
claim_id: claim:af10d775fba0ec05fd46
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal: cluster CM4 expressed VSIG4, MSR1, CD163, MERTK, STAB1 and CD209 .
summary:
In Homo sapiens, alternatively activated macrophages (cluster CM4) express VSIG4, MSR1, CD163, MERTK, STAB1, and CD209.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:4b67f8790f0e94d4e181
claim_id: claim:4b67f8790f0e94d4e181
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CM0 had the highest level of expression of inflammatory genes including TNF, S100A8, S100A9, NFKB1 and the WNT pathway activator TCF7L2 .

summary:
In Homo sapiens, CD16-positive patrolling monocytes (cluster CM0) express the highest levels of the inflammatory genes TNF, S100A8, S100A9, NFKB1, and TCF7L2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:512715b4906bb8807477
claim_id: claim:512715b4906bb8807477
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
CM4 expressed many genes associated with alternatively activated macrophages, including CD163 and SLC40A1 (ferroportin), which control iron homeostasis 16 ; IGF1 and DAB2 , both drivers of the alternatively activated phenotype 17 , 18 ; and folate receptor beta ( FOLR2 ), a receptor expressed on alternatively activated CD14 + macrophages that are found in inflammatory and malignant tissues 19 .

summary:
In Homo sapiens, alternatively activated macrophages (cluster CM4) express CD163, SLC40A1, IGF1, DAB2, and FOLR2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:ac62f29be99a85c071bf
claim_id: claim:ac62f29be99a85c071bf
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
This cluster demonstrated low expression of CD14, CD16, CX3CR1 and CCR2 , and no clear similarity to the published reference clusters of peripheral myeloid subsets ( Fig. 3b , c ).

summary:
In Homo sapiens, kidney resident macrophages (cluster CM2) demonstrate low expression of CD14, CD16, CX3CR1, and CCR2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:2c32d08b0e710bca458c
claim_id: claim:2c32d08b0e710bca458c
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
In comparison to the other macrophage subsets, CM2 upregulated several genes associated with tissue remodeling including MMP2, ADAMTS10 and HTRA1 .

summary:
In Homo sapiens, kidney resident macrophages (cluster CM2) upregulate MMP2, ADAMTS10, and HTRA1 compared with other macrophage subsets.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:7658cbc3b5f357b0c82e
claim_id: claim:7658cbc3b5f357b0c82e
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
These cells also upregulated BHLHE41 , a gene expressed in microglia and lung resident macrophage populations 20 , consistent with CM2 representing resident cells.

summary:
In Homo sapiens, kidney resident macrophages (cluster CM2) upregulate BHLHE41, consistent with a resident macrophage identity.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:e35977266c5a2abde417
claim_id: claim:e35977266c5a2abde417
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CT1 contained NK cells, which could be identified by the lack of CD3E and CD3D combined with expression of CD56 ( NCAM1 ) and DAP12 ( TYROBP ), as well as high expression of cytotoxic genes including PRF1 , GZMB , and GNLY .

summary:
In Homo sapiens, natural killer cells (cluster CT1) are identified by lack of CD3E and CD3D and expression of NCAM1, TYROBP, PRF1, GZMB, and GNLY.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:8dd723e4e4938e37c93b
claim_id: claim:8dd723e4e4938e37c93b
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
A second population of CD8 + T cells, demonstrating high levels of the granzyme GZMK 24 rather than GZMB and GNLY , populated cluster CT4.

summary:
In Homo sapiens, CD8-positive T cells (cluster CT4) express high levels of GZMK rather than GZMB and GNLY.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:65eb0a1859cb4c8cda3b
claim_id: claim:65eb0a1859cb4c8cda3b
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
These cells expressed relatively low levels of PRF1 compared with cluster CT2 and also showed high expression of HLA-DR/DP/DQ molecules and CCR5 , consistent with an earlier report 25 .

summary:
In Homo sapiens, CD8-positive T cells (cluster CT4) express relatively low levels of PRF1 and high expression of HLA-DR/DP/DQ and CCR5 compared with cytotoxic T lymphocytes (cluster CT2).


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:d4ab3e561f9b9ed331e7
claim_id: claim:d4ab3e561f9b9ed331e7
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
The cells in cluster CT5a had features of resident memory cells, including expression of ZNF683 ( HOBIT ), ITGAE , ITGA1 and XCL1 , and lack of KLF2 26 , 27 , and accordingly were relatively abundant in normal kidney biopsies ( Supplementary Table 3 ).

summary:
In Homo sapiens, resident memory CD8-positive T cells (cluster CT5a) express ZNF683, ITGAE, ITGA1, and XCL1, and lack KLF2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:fca314462edd41f61b3a
claim_id: claim:fca314462edd41f61b3a
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CT5b cells expressed TYROBP and CD56 , suggesting an NK cell identity, but differed from CT1 NK cells by higher expression of KIT , TCF7 , IL7R , and RUNX2 , and lower expression of PRF1 , GZMB , FCGR3A , TBX21 , and S1PR5 , consistent with the identification of these cells as tissue-resident CD56 bright CD16 − NK cells, in contrast to the CD56 dim CD16 + NK cell features observed in CT1 28 .

summary:
In Homo sapiens, tissue-resident CD56-bright CD16-negative natural killer cells (cluster CT5b) express TYROBP, NCAM1, KIT, TCF7, IL7R, and RUNX2, and have lower expression of PRF1, GZMB, FCGR3A, TBX21, and S1PR5 compared with CD56-dim CD16-positive natural killer cells (cluster CT1).


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:ea1f961d4937fade9480
claim_id: claim:ea1f961d4937fade9480
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
summary: In Homo sapiens, T regulatory cells (cluster CT3a) express FOXP3 and IKZF2.
span_literal:
CT3 could be divided into two subclusters, with one (CT3a) containing cells expressing genes associated with T regulatory (T reg ) cells, including FOXP3 and IKZF2 ( HELIOS )


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:d93ccb90340aa23bc04a
claim_id: claim:d93ccb90340aa23bc04a
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
the other (CT3b) consisting of cells with low FOXP3 and features consistent with TFH cells, including the expression of CXCL13, CXCR5, PDCD1, MAF, and CD200

summary:
In Homo sapiens, T follicular helper-like cells (cluster CT3b) express CXCL13, CXCR5, PDCD1, MAF, and CD200, and have low FOXP3.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:8b21bad5dd4c224b767a
claim_id: claim:8b21bad5dd4c224b767a
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
the first containing primarily effector memory CD4 + T cells (CT0a), with more frequent expression of PRDM1, CCL5 and CXCR6

summary:
In Homo sapiens, effector memory CD4-positive T cells (cluster CT0a) express PRDM1, CCL5, and CXCR6.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:11cf430c600d6086eacb
claim_id: claim:11cf430c600d6086eacb
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
summary: In Homo sapiens, central memory CD4-positive T cells (cluster CT0b) express CCR7, SELL, and TCF7.
span_literal:
the second consisting of mostly CCR7 + SELL + TCF7 + central memory T cells (CT0b; Fig 4d and Supplementary Fig. 4h ).


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:eb8ba640b24fd27390e2
claim_id: claim:eb8ba640b24fd27390e2
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
summary: In Homo sapiens, early central memory T cells (cluster CT0b) express TCF7, KLF2, and LEF1.
span_literal:
Expression of TCF7 , KLF2 and LEF1 may indicate an early central memory T-cell (Tcm) phenotype of CT0b cells, in contrast to the late effector phenotype of CT0a cells 32 .


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:e9fe9901c5f48162a83f
claim_id: claim:e9fe9901c5f48162a83f
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
cluster CT6 contained CD4 + T cells demonstrating exceptionally higher levels of ISGs, including ISG15, MX1, RSAD2, OAS3, IFIT1 and IFIT2 , compared with other T cells

summary:
In Homo sapiens, interferon-stimulated gene-high CD4-positive T cells (cluster CT6) express exceptionally high levels of ISG15, MX1, RSAD2, OAS3, IFIT1, and IFIT2 compared with other T cells.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:dfa7d4ed0d59408c3ba3
claim_id: claim:dfa7d4ed0d59408c3ba3
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
summary: In Homo sapiens, plasmablasts/plasma cells (cluster CB1) express high levels of XBP1 and MZB1.
span_literal:
Cluster CB1 contained plasmablasts/plasma cells, expressing high levels of XBP1 and MZB1 , as well as immunoglobulin genes.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:aef28026d4c95fceddc0
claim_id: claim:aef28026d4c95fceddc0
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
The cells in cluster CB3 demonstrated high levels of several ISGs, including IFIT1, IFIT2, IFIT3, ISG15, OAS3 and RSAD2 .

summary:
In Homo sapiens, interferon-stimulated gene-high B cells (cluster CB3) express high levels of IFIT1, IFIT2, IFIT3, ISG15, OAS3, and RSAD2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:60b0400a04550abb8369
claim_id: claim:60b0400a04550abb8369
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
Cluster CB0 cells had upregulated expression of activation markers such as CD27, CD86, IGJ and IGHG1 , and low levels of IGHD and IGHM , suggesting an activated B-cell identity.

summary:
In Homo sapiens, activated B cells (cluster CB0) express upregulated CD27, CD86, IGJ, and IGHG1, and low levels of IGHD and IGHM.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:3cf35d281fa9e5fe9a0d
claim_id: claim:3cf35d281fa9e5fe9a0d
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
the first of these (CB2a), expressing the B cell markers CD19 and CD20 ( MS4A1 ), demonstrated upregulation of genes typical of naive B cells, including high levels of IGHD, IGHM, TCL1A and IL4R , and had nearly undetectable expression of CD27

summary:
In Homo sapiens, naive B cells (cluster CB2a) express CD19, MS4A1, IGHD, IGHM, TCL1A, and IL4R, and have nearly undetectable CD27.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:dc56a57830525e3d5225
claim_id: claim:dc56a57830525e3d5225
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
the other cluster (CB2b) expressed genes known to be upregulated in plasmacytoid DCs (pDCs) ( Fig. 5c and Supplementary Fig. 5c ), including PTPRS, GZMB, CLEC4C, CD123 ( IL3RA ) and CD317 ( BST2 ).

summary:
In Homo sapiens, plasmacytoid dendritic cells (cluster CB2b) express PTPRS, GZMB, CLEC4C, IL3RA, and BST2.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:bad9eae330e17d55732d
claim_id: claim:bad9eae330e17d55732d
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
We found that a single chemokine receptor, CXCR4 , was expressed in the majority of infiltrating cells in nearly all clusters

summary:
In Homo sapiens, CXCR4 is expressed in the majority of infiltrating leukocytes across nearly all kidney cell clusters.


claim_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388:claim:8e5af528cd6068358a80
claim_id: claim:8e5af528cd6068358a80
paper_key: hca:0480_10.1038_s41590-019-0398-x_7e5ee33388
span_literal:
A second chemokine receptor, CX3CR1 , was expressed in most myeloid cells, as well as CD56 dim CD16 + NK cells (cluster CT1) and CTLs (CT2)

summary:
In Homo sapiens, CX3CR1 is expressed in most myeloid cells, CD56-dim CD16-positive natural killer cells (cluster CT1), and cytotoxic T lymphocytes (cluster CT2).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:9864b7d32993fc38104d
claim_id: claim:9864b7d32993fc38104d
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, epithelial cells are marked by EPCAM, KRT8, and KRT18.
span_literal:
Epithelial ( EPCAM , KRT8 , and KRT18 ), Stromal ( CDH5 , COL1A1 , COL1A2 , COL6A2 , and VWF ), and Immune ( CD45/PTPRC , CD3D , CD3G , CD3E , CD79A , CD79B , CD14 , CD16 , CD68 , CD83 , CSF1R , FCER1G ).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:8170b73f8932663b9df1
claim_id: claim:8170b73f8932663b9df1
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
span_literal:
Epithelial ( EPCAM , KRT8 , and KRT18 ), Stromal ( CDH5 , COL1A1 , COL1A2 , COL6A2 , and VWF ), and Immune ( CD45/PTPRC , CD3D , CD3G , CD3E , CD79A , CD79B , CD14 , CD16 , CD68 , CD83 , CSF1R , FCER1G ).

summary:
In Homo sapiens, immune cells are marked by PTPRC, CD3D, CD3G, CD3E, CD79A, CD79B, CD14, CD16, CD68, CD83, CSF1R, and FCER1G.


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:ea1509704e95d1da2f3c
claim_id: claim:ea1509704e95d1da2f3c
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, enterocytes are marked by RBP2, ANPEP, and FABP2.
span_literal:
Epithelial cells were clustered into Enterocytes ( RBP2 , ANPEP , FABP2 ), Stem cells ( LGR5 , ASCL2 , SMOC2 , RGMB , OLFM4 ), Goblets ( CLCA1 , SPDEF , FCGBP , ZG16 , MUC2 ), Paneth cells ( DEFA5 , DEFA6 , REG3A ), Tuft cells ( LRMP, SH2D 6), Enteroendocrine cells ( CHGA, CHGB, NEUROD1 ) and Cycling cells ( UBE2C, TOP2A, MKI67, HMGB2 ).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:deb27e9257959977f5dd
claim_id: claim:deb27e9257959977f5dd
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, fibroblasts are marked by ADAMDEC1, PDGFRA, and BMP4.
span_literal:
Stromal cells were clustered into Fibroblasts ( ADAMDEC1, PDGFRA, BMP4 ), Myofibroblasts ( TAGLN, ACTG2 ), Lymphatics ( CCL21, TFF3 ), Endothelial cells ( CD36, DARC/ACKR1 69 ), Pericytes ( NOTCH3, MCAM/CD146, RGS5 ) and Glial cells ( FOXD3, MPZ, CDH19, PLP1, SOX10, S100B , ERBB3 ).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:03cd1cc15b12a8b7c831
claim_id: claim:03cd1cc15b12a8b7c831
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, T cells are marked by CD3D, CD3G, and CD3E.
span_literal:
Immune cells were first clustered into T cells ( CD3D, CD3G, CD3E ), B cells ( CD79A, MS4A1/CD20, CD19 ), and Myeloid cells ( CD14, CD16, HLA-DR ).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:4f2625103457e9d2545e
claim_id: claim:4f2625103457e9d2545e
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, CD8 T cells are marked by CD8A and CD8B.
span_literal:
T cells were further sub-clustered into CD8 T cells ( CD8A, CD8B ), CD4 T cells ( CD4 ), ILCs ( RORC , IL1R1, IL23R, KIT , TNFSF4, PCDH9 ), NK cells ( EOMES , PRF1, NKG7 ).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:c8593669930e2c0e2e74
claim_id: claim:c8593669930e2c0e2e74
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, plasma cells are marked by SDC1, MZB1, SSR4, and XBP1.
span_literal:
B cells were sub-clustered into Plasma cells ( SDC1, MZB1, SSR4, XBP1 ), B cells ( BANK, MS4A1/CD30, ADAM28, VPREB3 ) and Germinal Center (GC) B cells ( LRMP, GPT2, PAG1 )


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:d11309e3752760fadc6b
claim_id: claim:d11309e3752760fadc6b
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, mast cells are marked by GATA2, CPA3, and HPGDS.
span_literal:
Myeloid cells were sub-clustered into Mast cells ( GATA2, CPA3, HPGDS ), classical Macrophages ( CD163, C1QB, C1QC ), classical Monocytes ( FCN1, S100A4, S100A6 ), DC1 ( CLEC9A, XCR1 ) and DC2 ( CLEC10A, FCER1A ).


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:c70a705d9c90eec5fec5
claim_id: claim:c70a705d9c90eec5fec5
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, HHIP-positive NPNT-positive myofibroblasts are enriched in COL18A1 and COL23A1.
span_literal:
This myofibroblast population was enriched in genes involved in extracellular matrix deposition, such as COL18A1 , and COL23A1


claim_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446:claim:e672878ef45ca1c2daad
claim_id: claim:e672878ef45ca1c2daad
paper_key: hca:0481_10.1016_j.immuni.2023.01.002_2da3d3f446
summary: In Homo sapiens, intraepithelial lymphocytes are marked by ID3 and ENTPD1 (CD39).
span_literal:
we identified a population of ID3 + ENTPD1(CD39) + IELs, consistent with previous reports 23 that was only detected in epithelial samples


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:9e35025f015db6ef5a6c
claim_id: claim:9e35025f015db6ef5a6c
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Single-cell analysis showed there were distinct populations of cells expressing transcription factors characteristic of paraxial mesoderm ( MEOX2, PAX3 ), myoblasts ( MYF5, MSC ) and myocytes ( MYOG, MEF2C ; Figures 1E and 1F ).

summary:
In Homo sapiens rhabdomyosarcoma, paraxial mesoderm-like cells are characterized by expression of MEOX2 and PAX3.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:812ba5c3ee7d14053ff3
claim_id: claim:812ba5c3ee7d14053ff3
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Single-cell analysis showed there were distinct populations of cells expressing transcription factors characteristic of paraxial mesoderm ( MEOX2, PAX3 ), myoblasts ( MYF5, MSC ) and myocytes ( MYOG, MEF2C ; Figures 1E and 1F ).

summary:
In Homo sapiens rhabdomyosarcoma, myoblast-like cells are characterized by expression of MYF5 and MSC.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:ef8b706f342a40cb4429
claim_id: claim:ef8b706f342a40cb4429
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Single-cell analysis showed there were distinct populations of cells expressing transcription factors characteristic of paraxial mesoderm ( MEOX2, PAX3 ), myoblasts ( MYF5, MSC ) and myocytes ( MYOG, MEF2C ; Figures 1E and 1F ).

summary:
In Homo sapiens rhabdomyosarcoma, myocyte-like cells are characterized by expression of MYOG and MEF2C.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:cc66bcd59c12347260fb
claim_id: claim:cc66bcd59c12347260fb
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Mesoderm cells also expressed significantly higher levels of the xenobiotic transporter ABCG2 , which has been correlated with multidrug resistance to chemotherapy ( Doyle and Ross, 2003 ).

summary:
In Homo sapiens rhabdomyosarcoma, mesoderm-like cells express significantly higher levels of the xenobiotic transporter ABCG2 compared to other tumor cell populations.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:58580c0986034bdca9c4
claim_id: claim:58580c0986034bdca9c4
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
For example, MEOX2 and NFIX (mesoderm), PAX7 and CREB5 (myoblast) and FOXO1 and SOX6 (myocyte) each have CRC-SEs ( Table S6 ).

summary:
In Homo sapiens rhabdomyosarcoma, mesoderm-like cells have core regulatory circuit super-enhancers at MEOX2 and NFIX.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:2723ef4fa39a85df23f3
claim_id: claim:2723ef4fa39a85df23f3
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
For example, MEOX2 and NFIX (mesoderm), PAX7 and CREB5 (myoblast) and FOXO1 and SOX6 (myocyte) each have CRC-SEs ( Table S6 ).

summary:
In Homo sapiens rhabdomyosarcoma, myoblast-like cells have core regulatory circuit super-enhancers at PAX7 and CREB5.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:ac76aedaa061a597262a
claim_id: claim:ac76aedaa061a597262a
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
For example, MEOX2 and NFIX (mesoderm), PAX7 and CREB5 (myoblast) and FOXO1 and SOX6 (myocyte) each have CRC-SEs ( Table S6 ).

summary:
In Homo sapiens rhabdomyosarcoma, myocyte-like cells have core regulatory circuit super-enhancers at FOXO1 and SOX6.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:1bed1d1a20af625ee034
claim_id: claim:1bed1d1a20af625ee034
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Analysis of all 7 O-PDX tumors showed CRC-SEs that change in their chromatin accessibility in tumor cells with mesoderm ( MEOX2, SMAD3 ), myoblast ( CREB5, PAX7 ), and myocyte ( MYOD1, FOXO1 ) features ( Figure S4 and Table S6 ).

summary:
In Homo sapiens rhabdomyosarcoma, mesoderm-like tumor cells show chromatin accessibility changes at MEOX2 and SMAD3 core regulatory circuit super-enhancers.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:f2d45bde9ee302f2c88e
claim_id: claim:f2d45bde9ee302f2c88e
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Analysis of all 7 O-PDX tumors showed CRC-SEs that change in their chromatin accessibility in tumor cells with mesoderm ( MEOX2, SMAD3 ), myoblast ( CREB5, PAX7 ), and myocyte ( MYOD1, FOXO1 ) features ( Figure S4 and Table S6 ).

summary:
In Homo sapiens rhabdomyosarcoma, myoblast-like tumor cells show chromatin accessibility changes at CREB5 and PAX7 core regulatory circuit super-enhancers.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:5c7ac2878b455c819564
claim_id: claim:5c7ac2878b455c819564
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Analysis of all 7 O-PDX tumors showed CRC-SEs that change in their chromatin accessibility in tumor cells with mesoderm ( MEOX2, SMAD3 ), myoblast ( CREB5, PAX7 ), and myocyte ( MYOD1, FOXO1 ) features ( Figure S4 and Table S6 ).

summary:
In Homo sapiens rhabdomyosarcoma, myocyte-like tumor cells show chromatin accessibility changes at MYOD1 and FOXO1 core regulatory circuit super-enhancers.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:1d0d922f2d03cdf5e6bd
claim_id: claim:1d0d922f2d03cdf5e6bd
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
EGFR was significantly activated in the mesoderm population compared to myoblasts (p=4.4x10 −135 ) and myocytes (p=1.8x10 −174 ) and the network was rewired as cells transition through the developmental hierarchy ( Figure 6B ).

summary:
In Homo sapiens rhabdomyosarcoma, EGFR is significantly activated in the mesoderm-like population compared to myoblast-like cells and myocyte-like cells.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:245a4afde9eac31de419
claim_id: claim:245a4afde9eac31de419
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
There was co-localization of EGFR with MEOX2 in 2-color IHC and EGFR was mutually exclusive with MYOG ( Figures 6E and 6F ).

summary:
In Homo sapiens rhabdomyosarcoma, EGFR co-localizes with MEOX2 in mesoderm-like cells and is mutually exclusive with MYOG expressed in myocyte-like cells.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:5051f42d2152ec76d800
claim_id: claim:5051f42d2152ec76d800
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Finally, we used flow sorting for EGFR-positive and -negative cells from an ERMS O-PDX to demonstrate the EGFR+ cells expressed additional markers of the mesoderm population ( CD44 and MEOX2 ) and scRNA-seq showed EGFR+ sorted cells were highly enriched (>97%) for mesoderm cells ( Figures S5D - H ).

summary:
In Homo sapiens embryonal rhabdomyosarcoma, EGFR-positive mesoderm-like cells express additional markers CD44 and MEOX2.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:10d59211aebf2670ec30
claim_id: claim:10d59211aebf2670ec30
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
Importantly, we did not identify cells expressing earlier mesoderm progenitor markers such as Brachyury ( TBXT ) suggesting that RMS tumors arise after specification of paraxial mesoderm.

summary:
In Homo sapiens rhabdomyosarcoma, paraxial mesoderm-like cells do not express the earlier mesoderm progenitor marker TBXT (Brachyury).


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:31b930df68f2a52d118b
claim_id: claim:31b930df68f2a52d118b
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
span_literal:
In addition, SFRP2 and SFRP4 were significantly (p<1x10 −90 ) enriched in fibroblasts from ARMS (45% and 56% of cells, respectively) relative to ERMS (1% and 3%, respectively; Table S4 ).

summary:
In Homo sapiens alveolar rhabdomyosarcoma, SFRP2 and SFRP4 are significantly enriched in fibroblasts compared to fibroblasts from embryonal rhabdomyosarcoma.


claim_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39:claim:385656e18ef252ac843b
claim_id: claim:385656e18ef252ac843b
paper_key: hca:0482_10.1016_j.devcel.2022.04.003_a4b7ddcf39
summary: In Homo sapiens rhabdomyosarcoma, myoblast group 1 expresses both PAX3 and MYF5.
span_literal:
myoblast group 1 had expression of both PAX3 (a mesodermal marker) and MYF5 (a myoblast marker); likewise, myocyte group 1 had expression of MSC (a myoblast marker) and MYOG (a myocyte marker).


claim_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09:claim:c8ad14eb83885f2e721e
claim_id: claim:c8ad14eb83885f2e721e
paper_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09
span_literal:
CD4 and CD8 T-cells were classified into 27 unique subsets by leveraging the expression profiles of TCF7, the presence of co-inhibitory receptors and the spatial distribution.

summary:
In Homo sapiens lymph node, CD4 and CD8 T cells were classified into subsets using TCF7 expression profiles.


claim_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09:claim:5efdd499013d7f50e368
claim_id: claim:5efdd499013d7f50e368
paper_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09
span_literal:
CD4 and CD8 T-cells were classified into 27 unique subsets by leveraging the expression profiles of TCF7, the presence of co-inhibitory receptors and the spatial distribution.

summary:
In Homo sapiens lymph node, CD8 T cells were classified into subsets using TCF7 expression profiles.


claim_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09:claim:da7c3f3123b10c8499a1
claim_id: claim:da7c3f3123b10c8499a1
paper_key: hca:0483_10.1101_2025.10.19.683341_89f4c4be09
span_literal:
CD27+ mature B-cells occupied previously unrecognized nodal spaces non-overlapping with the cortex and the plasma-cell rich medullary cords.

summary:
In Homo sapiens lymph node, CD27-positive mature B cells occupied previously unrecognized nodal spaces.


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:3be22f213a6d829a854c
claim_id: claim:3be22f213a6d829a854c
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
summary: In Homo sapiens, alpha-smooth muscle actin (ACTA2) is a positive marker for myofibroblasts.
span_literal:
Knockdown of both genes strongly reduced TGFβ1-mediated expression of alpha-smooth muscle actin (αSMA), a marker for myofibroblasts


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:69e5bf7e781e8e4fadf4
claim_id: claim:69e5bf7e781e8e4fadf4
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
span_literal:
AEBP1 and PRSS23 expression also increased in ECs and melanocytes, HTRA 1 in ECs and KC3, and PLAU in DCs.

summary:
In Homo sapiens scar tissue, AEBP1 and PRSS23 expression is increased in endothelial cells and melanocytes, HTRA1 in endothelial cells and keratinocyte cluster 3, and PLAU in dendritic cells. In Homo sapiens scar tissue, HTRA1 expression is increased in endothelial cells.


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:5670fe56d6751cc79fc0
claim_id: claim:5670fe56d6751cc79fc0
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
span_literal:
TGFβ1 drives differentiation of FBs into myofibroblasts, which have a contractile phenotype, are characterized by excessive secretion of ECM-components

summary:
In Homo sapiens, myofibroblasts are characterized by excessive secretion of extracellular matrix components, driven by transforming growth factor beta 1 (TGFB1).


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:f5c2805c7ba6f4bc01df
claim_id: claim:f5c2805c7ba6f4bc01df
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
span_literal:
Genes related to ECM production (e.g., COL1A1/2, COL3A1, COL5A1/2, FN1, BGN, LOX, LUM, OGN, PCOLCE ) were mainly overrepresented in FBs, but notably also in PCs and ECs (Figure S3A-C ).

summary:
In Homo sapiens scar tissue, genes related to extracellular matrix production including COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, FN1, BGN, LOX, LUM, OGN, and PCOLCE are mainly overrepresented in fibroblasts.


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:87e0d3b8f00a458b9c24
claim_id: claim:87e0d3b8f00a458b9c24
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
span_literal:
Although DPP4 -positive FBs have previously been identified as the main source of ECM production in the skin

summary:
In Homo sapiens, dipeptidyl-peptidase 4 (DPP4)-positive fibroblasts have been identified as the main source of extracellular matrix production in the skin.


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:2ff6f406b47591305ca6
claim_id: claim:2ff6f406b47591305ca6
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
span_literal:
Western blot of primary FBs after knockdown of DPP4 or PLAU stimulated with active TGFβ1 for 24 h to differentiate FBs into alpha-smooth muscle actin-expressing (αSMA) myofibroblasts, and western blot quantification

summary:
In Homo sapiens, myofibroblasts express alpha-smooth muscle actin (ACTA2), and knockdown of DPP4 or PLAU reduces TGFβ1-mediated myofibroblast differentiation.


claim_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff:claim:a91b1ac48cf34640259e
claim_id: claim:a91b1ac48cf34640259e
paper_key: hca:0485_10.1038_s41467-021-26495-2_5e641690ff
span_literal:
In human SMC/Pericytes for example, we found a strong upregulation of a group of methallothionins ( MT1G, MT1E, MT2A, MT1A )

summary:
In Homo sapiens scar tissue, smooth muscle cells/pericytes show strong upregulation of metallothioneins MT1G, MT1E, MT2A, and MT1A.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:2ad5879c4bbe4955f732
claim_id: claim:2ad5879c4bbe4955f732
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Endometrial mesenchymal stem cells (eMSC) were a small subset of colony forming cells, characterized as co-expressions of MCAM and PDGFRB , and single expression of SUSD2

summary:
In Homo sapiens, endometrial mesenchymal stem cells are characterized by co-expression of MCAM and PDGFRB, and expression of SUSD2.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:e1e445d35ed5f9709e08
claim_id: claim:e1e445d35ed5f9709e08
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
cluster 1 was enriched with muscle contraction gene KRT19 ( 53 ), stress response gene NUPR1 ( 54 ), and stem cell marker ALDH1A1 ( 55 )

summary:
In Homo sapiens, mature fibroblast cluster 1 of cultured human endometrial stromal cells is enriched with KRT19, NUPR1, and the stem cell marker ALDH1A1.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:b6608bb605e5ab4c637e
claim_id: claim:b6608bb605e5ab4c637e
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 0 was enriched with IGF1 binding protein IGFBP5, basal cell marker KRT17 ( 56 ), and canonical smooth muscle marker ACTG2 ( 34 )

summary:
In Homo sapiens, mature fibroblast cluster 0 of cultured human endometrial stromal cells is enriched with IGFBP5, basal cell marker KRT17, and smooth muscle marker ACTG2.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:3ceb64de2f7978c13000
claim_id: claim:3ceb64de2f7978c13000
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 8 only had six differentiated expressed marker genes, that mainly belong to the AP1 family including FOS, ATF3, and JUN ( 57 )

summary:
In Homo sapiens, mature fibroblast cluster 8 of cultured human endometrial stromal cells is marked by AP1 family genes including FOS, ATF3, and JUN.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:5106a4fba01f37ba78c5
claim_id: claim:5106a4fba01f37ba78c5
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 9 shared the maker IGFBP5 with cluster 0, stem cell marker ALDH1A1 ( 55 ) with cluster 1, while cluster 9 also presented some unique markers related with aging including SRFBP1 and IGFBP2 ( 58 , 59 )

summary:
In Homo sapiens, mature fibroblast cluster 9 of cultured human endometrial stromal cells expresses IGFBP5, stem cell marker ALDH1A1, and aging-related markers SRFBP1 and IGFBP2.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:f0912a9ea92a487870f9
claim_id: claim:f0912a9ea92a487870f9
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
cluster 3 was enriched with myofibroblast transition markers, such as ACTA2, VCAN and CRYAB ( 35 , 60 , 61 )

summary:
In Homo sapiens, active fibroblast cluster 3 of cultured human endometrial stromal cells is enriched with myofibroblast transition markers ACTA2, VCAN, and CRYAB.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:1fd78ae0a651d319ba15
claim_id: claim:1fd78ae0a651d319ba15
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 7 shared some cluster 3 marker genes including VCAN and ACTA2, but cluster 7 also had some unique marker, such as PTX3 that is a key immune mediator ( 62 )

summary:
In Homo sapiens, active fibroblast cluster 7 of cultured human endometrial stromal cells expresses VCAN, ACTA2, and the unique marker PTX3.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:c828e74c283934b71749
claim_id: claim:c828e74c283934b71749
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 6 also had a unique marker gene LRR75A, that labels mesenchymal stromal cells with ossification ability ( 41 )

summary:
In Homo sapiens, active fibroblast cluster 6 of cultured human endometrial stromal cells has the unique marker gene LRRC75A, which labels mesenchymal stromal cells with ossification ability.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:3aceed5b5b7377812bf5
claim_id: claim:3aceed5b5b7377812bf5
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
The mature fibroblasts were characterized as having an abundance of keratins, collagens and cellular matrix proteins, such as KRT17, ACTG2, VCAN.

summary:
In Homo sapiens, mature fibroblasts of cultured human endometrial stromal cells are characterized by abundance of KRT17, ACTG2, and VCAN.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:024749980f93775483a5
claim_id: claim:024749980f93775483a5
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
cluster 3 was enriched with DIO2, that has been associated with recurrent pregnancy loss ( 11 ) and pro-fibrotic factor IGFBP5 ( 28 )

summary:
In Homo sapiens, mature fibroblast cluster 3 of cultured human endometrial stromal cells is enriched with DIO2 and the pro-fibrotic factor IGFBP5.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:5be3c83cb4ee4d8f10a1
claim_id: claim:5be3c83cb4ee4d8f10a1
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 0 showed highly expressed retinoid synthesis related genes, such as Aldehyde Dehydrogenase ALDH1A1 and Retinol binding protein RBP1 ( 29 , 30 )

summary:
In Homo sapiens, mature fibroblast cluster 0 of cultured human endometrial stromal cells highly expresses retinoid synthesis related genes ALDH1A1 and RBP1.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:9a94927ddd849234451d
claim_id: claim:9a94927ddd849234451d
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal: Cluster 2 had higher levels of decidual regulators PRRX2 ( 31 ) and PTX2 ( 32 )
summary:
In Homo sapiens, mature fibroblast cluster 2 of cultured human endometrial stromal cells has higher levels of decidual regulators PRRX2 and PTX3.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:a515f5940873d0ac72e2
claim_id: claim:a515f5940873d0ac72e2
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 1 had abundant Keratin KRT17, that was also detected in the cultured human skin fibroblast ( 33 ), and contractile related smooth muscle actin ACTG2 ( 34 )

summary:
In Homo sapiens, mature fibroblast cluster 1 of cultured human endometrial stromal cells has abundant KRT17 and contractile related smooth muscle actin ACTG2.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:3043478692eedde373a4
claim_id: claim:3043478692eedde373a4
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 5 exhibited marker genes, such as extracellular matrix Versican (VCAN) and cell adhesion protein ITGA1, that were critical for the differentiation of the myofibroblast ( 35 , 36 )

summary:
In Homo sapiens, mature fibroblast cluster 5 of cultured human endometrial stromal cells exhibits marker genes VCAN and ITGA1, critical for myofibroblast differentiation.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:554dc54c6f4ba691ac61
claim_id: claim:554dc54c6f4ba691ac61
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal: cluster 4 showed relatively higher expression of mitosis markers CCNB1 and CDC20 ( 37 )
summary:
In Homo sapiens, proliferative fibroblast cluster 4 of cultured human endometrial stromal cells shows relatively higher expression of mitosis markers CCNB1 and CDC20.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:41e7edfd5377dfe19d9b
claim_id: claim:41e7edfd5377dfe19d9b
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal: The top marker genes in cluster 8 were DNA replication regulators CLSPN and FEN1 ( 38 , 39 )
summary:
In Homo sapiens, proliferative fibroblast cluster 8 of cultured human endometrial stromal cells has top marker genes CLSPN and FEN1, which are DNA replication regulators.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:65b333e069a611e3f15a
claim_id: claim:65b333e069a611e3f15a
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Cluster 6 was enriched with TM4SF1, that can facilitate cell migration ( 40 ) and the proliferative marker TOP2A

summary:
In Homo sapiens, proliferative fibroblast cluster 6 of cultured human endometrial stromal cells is enriched with TM4SF1 and the proliferative marker TOP2A.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:e0615bb369ff7de7bce4
claim_id: claim:e0615bb369ff7de7bce4
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal: Cluster 7 had more ASPM and AURKA, that plays critical roles in spindle organization during mitosis
summary:
In Homo sapiens, proliferative fibroblast cluster 7 of cultured human endometrial stromal cells has higher expression of ASPM and AURKA, which play critical roles in spindle organization during mitosis.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:e2b08d6efdf70ec4c644
claim_id: claim:e2b08d6efdf70ec4c644
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal: Cluster 9 was enriched with proliferative markers TOP2A and MKI67
summary:
In Homo sapiens, proliferative fibroblast cluster 9 of cultured human endometrial stromal cells is enriched with proliferative markers TOP2A and MKI67.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:7e43d591c3aa6607bd0d
claim_id: claim:7e43d591c3aa6607bd0d
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal: Cluster 10 had relatively higher expressions of ribosome proteins RPL27A and RPL38A.
summary:
In Homo sapiens, proliferative fibroblast cluster 10 of cultured human endometrial stromal cells has relatively higher expression of ribosome proteins RPL27A and RPL38A.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:e749224ca37fa8f55b51
claim_id: claim:e749224ca37fa8f55b51
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
LRRC75A, that labels mesenchymal stromal cells with ossification ability ( 41 ), and EGR1, that was essential for decidualization ( 42 ), were more enriched in cluster 11

summary:
In Homo sapiens, active fibroblast cluster 11 of cultured human endometrial stromal cells is enriched with LRRC75A, which labels mesenchymal stromal cells with ossification ability, and EGR1, essential for decidualization.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:079c5d0956f452badb4d
claim_id: claim:079c5d0956f452badb4d
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
Chemokine CXCL12 that mediates epithelial proliferation ( 43 ), and fibroblast growth factor FGF5 were expressed at much higher levels in cluster 12.

summary:
In Homo sapiens, active fibroblast cluster 12 of cultured human endometrial stromal cells expresses chemokine CXCL12 and fibroblast growth factor FGF5 at much higher levels.


claim_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917:claim:c70513b465ab6e410d73
claim_id: claim:c70513b465ab6e410d73
paper_key: hca:0486_10.1016_j.xfss.2022.09.001_c256ed6917
span_literal:
eMSC has been successfully isolated using the mesenchymal stem cell marker MCAM/PDGFRB or SUSD2 and cultured in vitro

summary:
In Homo sapiens, endometrial mesenchymal stem cells have been successfully isolated using the mesenchymal stem cell markers MCAM, PDGFRB, or SUSD2.


claim_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233:claim:25685ef049616b4a6e59
claim_id: claim:25685ef049616b4a6e59
paper_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233
summary: In Homo sapiens, mesangial cells and vascular smooth muscle cells both express ITGA8 and PDGFRB.
span_literal:
A total of 512 mesangial cells were identified, which likely represents an admixture of mesangial cells and vascular smooth muscle cells; both of which express ITGA8 and PDGFRB (Human Protein Atlas).


claim_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233:claim:a1bf03cfe085f97dd418
claim_id: claim:a1bf03cfe085f97dd418
paper_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233
span_literal:
Decreased expression of CFH was observed in the cluster of cells defined by CFH , CLDN1 , VCAM1 , and AKAP12 , which likely represent parietal epithelial cells.

summary:
In Homo sapiens, parietal epithelial cells are defined by expression of CFH, CLDN1, VCAM1, and AKAP12.


claim_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233:claim:974526e35fd6b36e15cf
claim_id: claim:974526e35fd6b36e15cf
paper_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233
summary: In Homo sapiens, infiltrating diabetic CD14+ monocytes show increased expression of TNFRSF21.
span_literal:
We saw increased expression of TNFRSF21 (LFC = 1.12, P = 7.6e-58) in the infiltrating diabetic CD14+ monocyte subset ( Fig. 3 A ), which was one of the few KRIS markers that showed a correlation between enhanced urinary excretion and end-stage renal disease ( 15 ).


claim_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233:claim:d55312deedfb04d1b274
claim_id: claim:d55312deedfb04d1b274
paper_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233
span_literal:
Infiltrating monocytes expressed markers downstream of IFN gamma signaling ( IFNGR1 and IFNGR2 ), HLA class II histocompatibility antigens ( HLA-DRB1 , HLA-DRB5 , HLA-DQA1 ), and TNFRSF1B , which has been implicated as a biomarker for diabetic nephropathy ( 43 ).

summary:
In Homo sapiens, infiltrating monocytes express IFNGR1, IFNGR2, HLA-DRB1, HLA-DRB5, HLA-DQA1, and TNFRSF1B.


claim_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233:claim:0f4fd3b068cf5ec394a2
claim_id: claim:0f4fd3b068cf5ec394a2
paper_key: hca:0488_10.1073_pnas.1908706116_5dfd6c0233
summary: In Homo sapiens, infiltrating CD14+ monocytes have increased expression of TNFRSF21.
span_literal:
Comparison of our dataset to publicly available peripheral blood mononuclear datasets showed that infiltrating CD14+ monocytes have increased TNFRSF21 , which is a urinary marker of diabetic nephropathy progression ( 15 ).


claim_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0:claim:79851b66614998724480
claim_id: claim:79851b66614998724480
paper_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0
span_literal:
our analysis revealed that apoptotic gene signatures in pDCs, including BRCA2 , CASP3 , CASP8 , BID , BAK1 , and XBP1 , were positively associated with disease status and severity

summary:
In Homo sapiens, apoptotic gene signatures in plasmacytoid dendritic cells, including BRCA2, CASP3, CASP8, BID, BAK1, and XBP1, were positively associated with COVID-19 disease status and severity.


claim_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0:claim:9708415afd6d4a1234f5
claim_id: claim:9708415afd6d4a1234f5
paper_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0
span_literal:
as were oxidative stress-induced senescence genes such as FOS , HIST1H2AC , PHC3 , MDM4 , CBX6 , and CDKN2D

summary:
In Homo sapiens, oxidative stress-induced senescence genes such as FOS, HIST1H2AC, PHC3, MDM4, CBX6, and CDKN2D were positively associated with COVID-19 disease status and severity in plasmacytoid dendritic cells.


claim_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0:claim:e3c0ba812026f8cd6e47
claim_id: claim:e3c0ba812026f8cd6e47
paper_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0
span_literal:
the NF-κB and inflammation signatures, such as RELA , NFKB1B , STAT1 , and IL8 , although they also contained additional genes such as XCL1 and XCL2 , which are chemokines that can be produced and secreted early after NK cell activation following an infection

summary:
In Homo sapiens, CD56 dim CD16 hi natural killer cells express nuclear factor kappa B and inflammation signature genes such as RELA, NFKB1B, STAT1, IL8, XCL1, and XCL2, which are negatively associated with disease severity.


claim_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0:claim:f0d8306ab30b459c1e29
claim_id: claim:f0d8306ab30b459c1e29
paper_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0
span_literal:
the FA signature was negatively correlated with inflammation related processes, including the nuclear factor κB (NF-κB) ( Figures 4 E and 4G; Pearson r = −0.55, p = 0.004) and IL-1 response signatures (see below) ( Figures 4 F and 4G; Table S4 A), as well as with the mTORC1 signature (HALLMARK_mTORC1_signaling) (Pearson r = −0.63; p = 0.0008) and the IFNG transcript (Pearson r = −0.46; p = 0.02)

summary:
In Homo sapiens, the fatty acid metabolism signature in CD56 dim CD16 hi natural killer cells was negatively correlated with the IFNG transcript, indicating attenuated interferon gamma expression in cells with elevated fatty acid metabolism.


claim_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0:claim:ef5cac29d22e18206c38
claim_id: claim:ef5cac29d22e18206c38
paper_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0
span_literal:
ICOS hi PD1 hi clusters were further gated by using DSB value cutoffs of 4 and 0 for ICOS and PD1, respectively. The gated population exhibited higher expression of ICOS, MAF and SH2D1A (encoding SAP protein) mRNA

summary:
In Homo sapiens, circulating T follicular helper cells exhibit higher expression of ICOS, MAF, and SH2D1A (encoding SAP protein).


claim_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0:claim:736ba5d950ef6efd627e
claim_id: claim:736ba5d950ef6efd627e
paper_key: hca:0489_10.1016_j.cell.2021.02.018_b0761e6af0
span_literal: Plasmablasts were gated as CD19 + CD20 - CD38 hi
summary:
In Homo sapiens, plasmablasts are defined by expression of CD19, absence of CD20, and high expression of CD38.


claim_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9:claim:270e0987fd0d33a042bf
claim_id: claim:270e0987fd0d33a042bf
paper_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9
summary: In Homo sapiens, trophectoderm cells show high expression of CDX2 in late blastocysts.
span_literal:
high expression of CDX2 in TE; high expression of SOX2 , NANOG and KLF4 in EPI; and low expression of SOX2 , NANOG and KLF4 , but high expression of FGFR4 and CLDN3 , in PE.


claim_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9:claim:acfd9246cf556a7114ac
claim_id: claim:acfd9246cf556a7114ac
paper_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9
span_literal:
high expression of CDX2 in TE; high expression of SOX2 , NANOG and KLF4 in EPI; and low expression of SOX2 , NANOG and KLF4 , but high expression of FGFR4 and CLDN3 , in PE.

summary:
In Homo sapiens, primitive endoderm cells show low expression of SOX2, NANOG, and KLF4 but high expression of FGFR4 and CLDN3 in late blastocysts.


claim_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9:claim:ffb9db1e82cea492dd9e
claim_id: claim:ffb9db1e82cea492dd9e
paper_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9
span_literal:
The mural TE cells physically isolated by syringe needle showed high expression of CDX2 , KRT18 , GATA2 , GATA3 and CLDN10 , as previously reported 7 , 11 .

summary:
In Homo sapiens, mural trophectoderm cells show high expression of CDX2, KRT18, GATA2, GATA3, and CLDN10.


claim_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9:claim:9e3aaf11169491fbdb76
claim_id: claim:9e3aaf11169491fbdb76
paper_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9
span_literal:
Further, they contained an EPI population with high expression of SOX2 , NANOG , KLF4 , GDF3 , FOXD3 , ESRRB and PRDM14 (partially shown in Supplementary Fig. 3d ) 11 , 55 , and a PE population with low expression of SOX2 , NANOG , KLF4 , GDF3 , FOXD3 , ESRRB and PRDM14 but high expression of FGFR4 and CLDN3 .

summary:
In Homo sapiens, the epiblast population shows high expression of SOX2, NANOG, KLF4, GDF3, FOXD3, ESRRB, and PRDM14 in late blastocysts.


claim_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9:claim:97f4798740d49536f71e
claim_id: claim:97f4798740d49536f71e
paper_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9
span_literal:
Further, they contained an EPI population with high expression of SOX2 , NANOG , KLF4 , GDF3 , FOXD3 , ESRRB and PRDM14 (partially shown in Supplementary Fig. 3d ) 11 , 55 , and a PE population with low expression of SOX2 , NANOG , KLF4 , GDF3 , FOXD3 , ESRRB and PRDM14 but high expression of FGFR4 and CLDN3 .

summary:
In Homo sapiens, the primitive endoderm population shows low expression of SOX2, NANOG, KLF4, GDF3, FOXD3, ESRRB, and PRDM14 but high expression of FGFR4 and CLDN3 in late blastocysts.


claim_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9:claim:219890f8f0a2ccef278c
claim_id: claim:219890f8f0a2ccef278c
paper_key: hca:0490_10.1038_nsmb.2660_4e6a41d8b9
span_literal:
we found a clear upregulation of the alpha 1 ( ATP1A1 ) and beta3 ( ATP1B3 ) subunits of the Na + /K + transporting ATPase in TE cells compared with EPI and PE cells ( Fig. 6b ).

summary:
In Homo sapiens, trophectoderm cells show upregulation of ATP1A1 and ATP1B3 compared with epiblast and primitive endoderm cells.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:6f0c2356349b8786c405
claim_id: claim:6f0c2356349b8786c405
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
We named the two cell populations expressing the highest levels of KRT5 and KRT14 ( Table S2 ) ‘ basal1 ’ and ‘ basal2 ,’ respectively, in accordance with their predicted position in the epidermis.

summary:
In Homo sapiens, basal keratinocytes (basal1 and basal2) are marked by high expression of KRT5 and KRT14 in the epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:f7a4ba6b13ce793f481b
claim_id: claim:f7a4ba6b13ce793f481b
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
We named the two cell populations expressing the highest levels of KRT5 and KRT14 ( Table S2 ) ‘ basal1 ’ and ‘ basal2 ,’ respectively, in accordance with their predicted position in the epidermis.

summary:
In Homo sapiens, basal keratinocytes (basal2) are marked by high expression of KRT5 and KRT14 in the epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:e31a3c56878126726957
claim_id: claim:e31a3c56878126726957
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
KRT1 - and KRT10 -expressing cells also displayed high DSG1 and DSP levels and were termed ‘ spinous

summary:
In Homo sapiens, spinous keratinocytes are marked by high expression of KRT1, KRT10, DSG1, and DSP in the epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:e66574b79317ebddb6c2
claim_id: claim:e66574b79317ebddb6c2
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
A cluster of cells (‘ granular ’) expressing a suite of late differentiation markers, including LOR , FLG , and SPINK5 , was also identified, although at consistently low cell numbers.

summary:
In Homo sapiens, granular keratinocytes are marked by expression of LOR, FLG, and SPINK5 in the epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:f0425ae30993346bef14
claim_id: claim:f0425ae30993346bef14
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
summary: In Homo sapiens, mitotic keratinocytes are marked by elevated expression of PCNA and KI67.
span_literal:
One showed coordinate elevation of more than a dozen well-recognized DNA synthesis and cell division transcripts, such as PCNA and KI67 .


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:88de734007409dce47f7
claim_id: claim:88de734007409dce47f7
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Another showed high levels of transcripts whose gene products are secreted and antagonize WNT signaling, including SFRP1 , FRZB , DKK3 ( Cruciat and Niehrs, 2013 ), and WIF1 ( Malinauskas et al., 2011 ).

summary:
In Homo sapiens, WNT-inhibitory keratinocytes are marked by high expression of SFRP1, FRZB, DKK3, and WIF1.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:bee47f2bf691e3d0ba03
claim_id: claim:bee47f2bf691e3d0ba03
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
The third was elevated for transcripts known to be expressed in human follicular root sheaths ( S100A2 ; Mitoma et al., 2014 ), sebaceous gland and root sheath hair follicles (mouse, APOE ; Grehan et al., 2001 ; human, KRT17 ; Troyanovsky et al., 1989 ), and mouse sebaceous glands ( MGST1 ; Joost et al., 2016 ; APOC1 ; Jong et al., 1998 ).

summary:
In Homo sapiens, follicular keratinocytes are marked by expression of S100A2 in follicular root sheaths and KRT17 in sebaceous gland and root sheath hair follicles.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:2cb87d4cd383330a24af
claim_id: claim:2cb87d4cd383330a24af
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Finally, a fourth cluster was distinguished by coordinate upregulation of ion channel and cell-cell communication transcripts, including GJB2 , GJB6 , ATP1B3 , ATP1A1 , ATP1B1 , ATP5B , and FXYD3 , and also mitochondrial channel proteins such as VDAC2 and SLC25A5 .

summary:
In Homo sapiens, channel keratinocytes are marked by upregulation of GJB2, GJB6, ATP1B3, ATP1A1, ATP1B1, ATP5B, FXYD3, VDAC2, and SLC25A5.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:f8808cee2a2fedb236ee
claim_id: claim:f8808cee2a2fedb236ee
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Two clusters (‘ mel1 ’ and ‘ mel2 ’) showed markedly higher expression of the PMEL , TYRP1 , and MLANA components of the melanocyte pigment synthesis pathway ( Hoashi et al., 2005 ), identifying them as melanocytes.

summary:
In Homo sapiens, melanocytes (mel1 and mel2) are marked by high expression of PMEL, TYRP1, and MLANA.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:0376fa1e880fc6008cce
claim_id: claim:0376fa1e880fc6008cce
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Limma-based differential gene expression analysis ( Ritchie et al., 2015 ) between these three clusters shows that basal1 is particularly enriched for CXCL14 and DMKN , whereas basal2 is enriched for CCL2 and IL1R2 , suggesting immunosecretory distinctions among basal keratinocytes.

summary:
In Homo sapiens, basal keratinocyte basal1 is enriched for CXCL14 and DMKN, whereas basal keratinocyte basal2 is enriched for CCL2 and IL1R2.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:7501f4e0dc6b3ad67cc8
claim_id: claim:7501f4e0dc6b3ad67cc8
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Limma-based differential gene expression analysis ( Ritchie et al., 2015 ) between these three clusters shows that basal1 is particularly enriched for CXCL14 and DMKN , whereas basal2 is enriched for CCL2 and IL1R2 , suggesting immunosecretory distinctions among basal keratinocytes.

summary:
In Homo sapiens, basal keratinocyte basal2 is enriched for CCL2 and IL1R2, whereas basal keratinocyte basal1 is enriched for CXCL14 and DMKN.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:b345f73444943a154600
claim_id: claim:b345f73444943a154600
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
In contrast, basal3 is highly enriched for amphiregulin ( AREG ), an epidermal growth factor receptor (EGFR) ligand that promotes keratinocyte proliferation ( Stoll et al., 2016 ; Table S2 ).

summary:
In Homo sapiens, basal keratinocyte basal3 is highly enriched for amphiregulin (AREG), an epidermal growth factor receptor ligand.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:b91f4ff12ec198594125
claim_id: claim:b91f4ff12ec198594125
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
SFRP1 , FRZB , and DKK3 ) again localized to a discrete cellular population in this scalp-specific analysis (named high-resolution WNTI , or ‘ HR-WNTI

summary:
In Homo sapiens, high-resolution WNT-inhibitory keratinocytes (HR-WNTI) are marked by expression of SFRP1, FRZB, and DKK3 in scalp epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:57a5724f3e553594fe98
claim_id: claim:57a5724f3e553594fe98
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
MGST1 and APOE transcripts of the follicular cluster were also identified in a scalp subpopulation we named ‘ sebaceous

summary:
In Homo sapiens, sebaceous keratinocytes in the scalp are marked by elevated MGST1 and APOE expression.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:8716b98380697b33085d
claim_id: claim:8716b98380697b33085d
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
We further partitioned the immune cell epidermal subpopulation from our normal and psoriatic samples into 5 clusters ( Supplemental Experimental Procedures ) and identified CD3 + αβT cells as well as three clusters representing major histocompatibility complex (MHC) class II + antigen-presenting cells of the myeloid lineage: CD207 + CD1A + Langerhans cells, CD1C + CD301A + myeloid dendritic cells (DCs), and CD14 + CCL3 hi IL1β hi monocyte-derived macrophages ( Figure 6 ).

summary:
In Homo sapiens, CD3-positive alpha-beta T cells, CD207-positive CD1A-positive Langerhans cells, CD1C-positive CD301A-positive myeloid dendritic cells, and CD14-positive CCL3-high IL1B-high monocyte-derived macrophages were identified in the epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:6c4efb417e1ce6443fe7
claim_id: claim:6c4efb417e1ce6443fe7
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
summary:
In Homo sapiens, monocyte-derived macrophages are marked by CD14 expression and high levels of CCL3 and IL1B in the epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:37d9e60a9a799d612118
claim_id: claim:37d9e60a9a799d612118
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
The HR-WNTI cluster retains elevated levels of SFRP1 , DKK3 , KRT15 , WIF1 , PHLDA1 , DIO2 , DPYSL2 , DCN , and DCT , all previously identified as selectively upregulated in the human hair bulge ( Lim et al., 2016 ; Ohyama et al., 2006 ).

summary:
In Homo sapiens, high-resolution WNT-inhibitory keratinocytes retain elevated levels of SFRP1, DKK3, KRT15, WIF1, PHLDA1, DIO2, DPYSL2, DCN, and DCT, which are selectively upregulated in the hair bulge.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:c52ccf53b49e0c89935b
claim_id: claim:c52ccf53b49e0c89935b
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Psoriatic epidermis is enriched for channel cells ( Figure 2B ), which show elevated levels of the psoriasis-associated keratins KRT6A and KRT16 .

summary:
In Homo sapiens, channel keratinocytes show elevated levels of KRT6A and KRT16 in psoriatic epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:d5c82caf5d014db43c0c
claim_id: claim:d5c82caf5d014db43c0c
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Gene expression of the established psoriasis risk gene GJB6 (connexin 30.3) is also increased ( Sun et al., 2010 ).

summary:
In Homo sapiens, channel keratinocytes show increased expression of GJB6 (connexin 30.3) in psoriatic epidermis.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:ee731a755530bd719077
claim_id: claim:ee731a755530bd719077
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Peak expression of DEFB1 in this cluster, and the known association between KRT16 and innate immunity ( Lessard et al., 2013 ), support an inherent inflammatory nature of these cells.

summary:
In Homo sapiens, channel keratinocytes show peak expression of DEFB1, supporting their inflammatory nature.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:4703b05c644badfd6213
claim_id: claim:4703b05c644badfd6213
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Although the T cell lineage markers CD4 , CD8 , and FOXP3 were not detectable within the CD3 + αβ T cell cluster, specific genes suggested a heterogeneous population of activated, antigen-experienced T cells ( IL2RG , CD69 , and CD44 ), cytotoxic T cells ( GZMA and GZMB ), and regulatory T cells ( IL2RG and TNFRSF18 ).

summary:
In Homo sapiens, CD3-positive alpha-beta T cells include activated antigen-experienced T cells marked by IL2RG, CD69, and CD44, cytotoxic T cells marked by GZMA and GZMB, and regulatory T cells marked by IL2RG and TNFRSF18.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:95c06628cc1b04d1184b
claim_id: claim:95c06628cc1b04d1184b
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Although the T cell lineage markers CD4 , CD8 , and FOXP3 were not detectable within the CD3 + αβ T cell cluster, specific genes suggested a heterogeneous population of activated, antigen-experienced T cells ( IL2RG , CD69 , and CD44 ), cytotoxic T cells ( GZMA and GZMB ), and regulatory T cells ( IL2RG and TNFRSF18 ).

summary:
In Homo sapiens, cytotoxic T cells within the epidermal CD3-positive alpha-beta T cell cluster are marked by GZMA and GZMB expression.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:7929ddccade5a41f3e2b
claim_id: claim:7929ddccade5a41f3e2b
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
span_literal:
Although the T cell lineage markers CD4 , CD8 , and FOXP3 were not detectable within the CD3 + αβ T cell cluster, specific genes suggested a heterogeneous population of activated, antigen-experienced T cells ( IL2RG , CD69 , and CD44 ), cytotoxic T cells ( GZMA and GZMB ), and regulatory T cells ( IL2RG and TNFRSF18 ).

summary:
In Homo sapiens, regulatory T cells within the epidermal CD3-positive alpha-beta T cell cluster are marked by IL2RG and TNFRSF18 expression.


claim_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa:claim:fc0909e080068a2c6b72
claim_id: claim:fc0909e080068a2c6b72
paper_key: hca:0491_10.1016_j.celrep.2018.09.006_befb59b9fa
summary: In Homo sapiens, CD4 T helper cells in the epidermis express GATA3 at low positive levels.
span_literal:
Notably, the only CD4 T helper cell lineage-defining transcription factor identified was GATA3 (low positive).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:3db830f1e39d4e0ac5ec
claim_id: claim:3db830f1e39d4e0ac5ec
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Secretory1 subset includes cells characterized by expression of Secretoglobin Family Member 1A1 ( SCGB1A1) and various Serpin family members.

summary:
In Homo sapiens, the Secretory1 subset of airway epithelial cells is characterized by expression of Secretoglobin Family Member 1A1 (SCGB1A1).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:98cf518cd03d6586aff9
claim_id: claim:98cf518cd03d6586aff9
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Secretory2 subset is composed of cells expressing mucins MUC5B and MUC5AC , anterior gradient 2 ( AGR2 ) and SAM-pointed domain–containing Ets-like factor ( SPDEF ), suggesting that they are goblet cells 6 .

summary:
In Homo sapiens, the Secretory2 subset (goblet cells) of airway epithelial cells expresses MUC5B, MUC5AC, anterior gradient 2 (AGR2), and SAM-pointed domain-containing Ets-like factor (SPDEF).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:4fc88e01f9a40e8fc5e1
claim_id: claim:4fc88e01f9a40e8fc5e1
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
Cells in the Secretory3 subset can be distinguished by their expression of Dynein Axonemal Heavy Chain proteins ( DNAHs ), Ankyrin Repeat Domain proteins ( ANKRDs ), and the mucins MUC16 and MUC4 , suggesting that they act as progenitors for ciliated cell differentiation.

summary:
In Homo sapiens, the Secretory3 subset of airway epithelial cells is distinguished by expression of Dynein Axonemal Heavy Chain proteins (DNAHs), Ankyrin Repeat Domain proteins (ANKRDs), MUC16, and MUC4.


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:dc1a055da771648ca907
claim_id: claim:dc1a055da771648ca907
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Secretory4 subset is defined by expression of MUC5B and Trefoil Factor family domain peptides ( TFF1 and TFF3 ) and represents mucous-like cells that are distinct from goblet cells 7 .

summary:
In Homo sapiens, the Secretory4 subset (mucous-like cells) of airway epithelial cells is defined by expression of MUC5B, TFF1, and TFF3, and is distinct from goblet cells.


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:327f97d50e004959103a
claim_id: claim:327f97d50e004959103a
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Secretory5 subset contains a serous-like signature 7 , expressing Lysozyme ( LYZ ), Proline-Rich Proteins ( PRBs, and PRRs ), and Lactoferrin ( LTF ), and represent glandular cell types of submucosal glands (SMGs) ( Supp Table 2 ).

summary:
In Homo sapiens, the Secretory5 subset (serous-like glandular cells) of submucosal glands expresses Lysozyme (LYZ), Proline-Rich Proteins (PRBs and PRRs), and Lactoferrin (LTF).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:c87126e8e21625b2b5a6
claim_id: claim:c87126e8e21625b2b5a6
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The three ciliated subsets (Ciliated1-3) ( Fig 1e ) all share expression of markers and regulator of ciliogenesis including Forkhead box protein J1 ( FOXJ1 ) 8 .

summary:
In Homo sapiens, the ciliated cell subsets (Ciliated1-3) of the proximal airway epithelium share expression of Forkhead box protein J1 (FOXJ1).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:4de30d7fe90687594e59
claim_id: claim:4de30d7fe90687594e59
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Ciliated1 subset expressed markers of cilia pre-assembly 9 , including Sperm Associated Antigen 1 ( SPAG1 ), Leucin Rich Repeat Containing 6 ( LRRC6 ) and Dynein Axonemal Assembly Factor 1 ( DNAAF1 ) most highly, whereas cells within the Ciliated2 subset show the highest expression of markers of mature ciliated cells including TUBA1A and TUBB4B .

summary:
In Homo sapiens, the Ciliated1 subset expresses Sperm Associated Antigen 1 (SPAG1), Leucine Rich Repeat Containing 6 (LRRC6), and Dynein Axonemal Assembly Factor 1 (DNAAF1), while the Ciliated2 subset shows the highest expression of TUBA1A and TUBB4B.


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:6d136f33b5f36700ec7b
claim_id: claim:6d136f33b5f36700ec7b
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Ciliated1 subset expressed markers of cilia pre-assembly 9 , including Sperm Associated Antigen 1 ( SPAG1 ), Leucin Rich Repeat Containing 6 ( LRRC6 ) and Dynein Axonemal Assembly Factor 1 ( DNAAF1 ) most highly, whereas cells within the Ciliated2 subset show the highest expression of markers of mature ciliated cells including TUBA1A and TUBB4B .

summary:
In Homo sapiens, the Ciliated2 subset of airway epithelial cells shows the highest expression of mature ciliated cell markers TUBA1A and TUBB4B.


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:3bad73696029c84abde9
claim_id: claim:3bad73696029c84abde9
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Ciliated3 subset is characterized by Serum Amyloid A proteins ( SAA1 and SAA2 ), reflective of a pro-inflammatory state 10 , suggesting that this subset of ciliated cells is either responding to or regulating immune responses.

summary:
In Homo sapiens, the Ciliated3 subset of airway epithelial cells is characterized by expression of Serum Amyloid A proteins SAA1 and SAA2.


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:dff48de7782ac1f2319a
claim_id: claim:dff48de7782ac1f2319a
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
The Basal 1 subset is characterized by high expression of canonical basal cell markers including tumor protein P63 ( TP63 ) and the cytokeratins 5 and 15 ( KRT5 and KRT15 ) ( Fig 1e , Supp Table2 ) 11 .

summary:
In Homo sapiens, the Basal1 subset of airway basal cells is characterized by high expression of tumor protein P63 (TP63), keratin 5 (KRT5), and keratin 15 (KRT15).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:250093a34006dff6ef6d
claim_id: claim:250093a34006dff6ef6d
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
Cells of the Basal2 subset show enrichment for transcripts such as DNA Topoisomerase II Alpha ( TOP2A) and the Marker of Proliferation Ki-67 ( MKI67 ) suggesting that they represent proliferating basal cells ( Fig 1e , Supp Table2 ).

summary:
In Homo sapiens, the Basal2 subset (proliferating basal cells) of airway epithelial cells is enriched for DNA Topoisomerase II Alpha (TOP2A) and Marker of Proliferation Ki-67 (MKI67).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:3e54dc2c6e0ba9ae6464
claim_id: claim:3e54dc2c6e0ba9ae6464
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal: the Basal5 subset uniquely expresses high levels of β-catenin ( CTNNB1 ) ( Fig 1e , Supp Table2 ).
summary:
In Homo sapiens, the Basal5 subset of airway basal cells uniquely expresses high levels of beta-catenin (CTNNB1).


claim_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b:claim:ab0472ae45d008090748
claim_id: claim:ab0472ae45d008090748
paper_key: hca:0492_10.1038_s41591-021-01332-7_1dacee7a8b
span_literal:
ALI Basal3 identified cells with high KRT14 expression that lacked a counterpart basal cell subset in the fresh tissue data sets ( Fig 1e , g ).

summary:
In Homo sapiens, the ALI Basal3 subset of airway basal cells is identified by high keratin 14 (KRT14) expression.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:cb94c753cb566def5b1a
claim_id: claim:cb94c753cb566def5b1a
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, atrial cardiomyocytes are marked by NPPA, MYL7, and MYH6 in the human heart.
span_literal:
Cluster 3 displayed canonical markers of the atrium, including NPPA (AUC 3 =0.91), MYL7 (AUC 3 =0.93) and MYH6 (AUC 3 =0.96)


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:650e7eae49fd65a97e46
claim_id: claim:650e7eae49fd65a97e46
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, mature cardiomyocytes are marked by TTN and MYH7 in the human heart.
span_literal:
Clusters 4, 6, and 15 displayed obvious markers of mature cardiomyocytes such as TTN (AUC 4 =0.85, AUC 6 =0.86, AUC 15 =0.79) and MYH7 (AUC 4 =0.87, AUC 15 =0.79)


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:4af4a5c551b8d9a7b5c6
claim_id: claim:4af4a5c551b8d9a7b5c6
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
CM-S4 correlates strongly to cluster 15 in the global map and displays increased expression of ANKRD1 (AUC CM-S4 =0.82), which is thought to have a role in cardiomyopathy associated remodeling

summary:
In Homo sapiens, cardiomyocyte subcluster 4 is marked by increased expression of ANKRD1 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:e5aef40669eb3973b424
claim_id: claim:e5aef40669eb3973b424
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
These cells display common markers of fibroblast lineages, with enriched expression of known fibroblast genes such as DCN (AUC 1 =0.85, AUC 2 =0.83), which encodes the proteoglycan decorin which regulates collagen fibrillogenesis, and ( ELN (AUC 1 =0.71, AUC 2 =0.86), which produces elastin, a major component of the extracellular matrix

summary:
In Homo sapiens, cardiac fibroblasts are marked by enriched expression of DCN and ELN in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:ffebe183aadced7defcd
claim_id: claim:ffebe183aadced7defcd
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
members of the ATP binding cassette subfamily of transmembrane transporters, including ABCA6 , −8 and −9 , were also preferentially expressed in one or more of these clusters ( ABCA6 : AUC 1 =0.80, AUC 2 =0.77; ABCA8 : AUC 1 =0.79, AUC 2 =0.79, ABCA9 : AUC 1 =0.75, AUC 2 =0.74)

summary:
In Homo sapiens, cardiac fibroblasts preferentially express ABCA6, ABCA8, and ABCA9 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:35c65cff12c97653ba62
claim_id: claim:35c65cff12c97653ba62
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
Cluster FB-S3 displays enriched expression of fibrosis associated genes NOX4 (AUC FB-S3 =0.70) and IGF1 (AUC FB-S3 =0.69)

summary:
In Homo sapiens, fibroblast subcluster 3 displays enriched expression of NOX4 and IGF1 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:ccb73a3a63c58f568100
claim_id: claim:ccb73a3a63c58f568100
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
cluster FB-S4, which corresponds to cluster 14 in the main map, exhibits clear upregulation of pro-fibrotic markers, including ADAMTS4 (AUC FB-S4 =0.69), which encodes a pro-fibrotic metalloprotease, VCAN (AUC FB-S4 =0.69), which encodes the proteoglycan versican [ 16 ], and AXL (AUC FB-S4 =0.69), which encodes a receptor tyrosine kinase associated with pathologic remodeling

summary:
In Homo sapiens, fibroblast subcluster 4 exhibits upregulation of pro-fibrotic markers ADAMTS4, VCAN, and AXL in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:a9e376e935a679771a65
claim_id: claim:a9e376e935a679771a65
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
We observed a relative enrichment of pericyte-specific PDGFRB in cluster 7 (AUC 7 =0.75) and the expression of smooth muscle actin ( MYH11 ) in cluster 13 (AUC 13 =0.89)

summary:
In Homo sapiens, pericytes are marked by PDGFRB and vascular smooth muscle cells are marked by MYH11 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:7e095a27c7f8ed67b986
claim_id: claim:7e095a27c7f8ed67b986
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
The first, cluster 8, represent cardiac resident macrophages and can be characterized by expression of the scavenger receptors CD163 (AUC 8 =0.84) and COLEC12 (AUC 8 =0.72), the mannose receptor MRC1 (AUC 8 =0.85), the E3 ubiquitin ligase MARCH1 (AUC 8 =0.72) and natural resistance-associated macrophage protein 1 ( NRAMP1 or SLC11A1) (AUC 8 =0.74)

summary:
In Homo sapiens, cardiac resident macrophages are characterized by expression of CD163, COLEC12, MRC1, MARCH1, and SLC11A1 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:544f28ae04d416093205
claim_id: claim:544f28ae04d416093205
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
Subclustering further revealed two populations that both express M2-polarization associated genes, including RBPJ and F13A1 in M-S1 (AUC M-S1 =0.85 and 0.84, respectively) and the transmembrane collagen COL23A1 in M-S2 (AUC M-S2 =0.65)

summary:
In Homo sapiens, macrophage subcluster 1 expresses RBPJ and F13A1, while macrophage subcluster 2 expresses COL23A1 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:162567c6ab7467c99c19
claim_id: claim:162567c6ab7467c99c19
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
This includes the T cell surface antigen CD2 (PPV50 17 =0.99), the early T cell activation antigen CD69 (PPV50 17 =0.99), the T cell receptor associated transmembrane adaptor 1 ( TRAT1 ) (PPV50 17 =0.98)

summary:
In Homo sapiens, lymphocytes selectively express the T cell surface antigen CD2, the early T cell activation antigen CD69, and the T cell receptor associated transmembrane adaptor 1 TRAT1 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:8437a2c7f1e12db5a0b6
claim_id: claim:8437a2c7f1e12db5a0b6
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
In addition, PTPRC/CD45 (AUC 17 =0.77), an essential regulator of T- and B-cell antigen receptor signaling, the T cell immune adaptor SKAP1 (AUC 17 =0.77), and the thymocyte selection marker CD53 (PPV50 17 =0.91) show selectivity to this cluster

summary:
In Homo sapiens, lymphocytes show selective expression of PTPRC, SKAP1, and CD53 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:689780c1ade72c98d126
claim_id: claim:689780c1ade72c98d126
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
Given the expression of tryptases ( TPSB2 , TPSAB1 ) and the FcεR1 subunit MS4A2 , LC-S2 exhibit canonical signatures of mast cells.

summary:
In Homo sapiens, mast cells (lymphocyte subcluster 2) exhibit canonical signatures including expression of TPSB2, TPSAB1, and MS4A2 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:fa8b3b8b8bdfc7eedc44
claim_id: claim:fa8b3b8b8bdfc7eedc44
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, endothelial cells express canonical markers VWF and PECAM1 in the human heart.
span_literal:
From global clustering, we identified two major endothelial cell clusters (clusters 9 and 10), which express canonical markers such as VWF (AUC 9 =0.88, AUC 10 =0.77) and PECAM-1 (AUC 9 =0.71, AUC 10 =0.81)


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:a5a58f4c0322832ea32e
claim_id: claim:a5a58f4c0322832ea32e
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
in subcluster 4 (L-EC), we observed enrichment for cells expressing lymphatic endothelial cell markers including PROX1 , FLT4 and PDPN (PPV50 L-EC of 0.95, 0.91, and 0.94, respectively)

summary:
In Homo sapiens, lymphatic endothelial cells are marked by PROX1, FLT4, and PDPN in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:262f5ad529e2e6292cb6
claim_id: claim:262f5ad529e2e6292cb6
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
span_literal:
A subset of cells in EC-S2 express BMX (AUC EC-S2 =0.65), an artery specific endothelial cell marker as well as NPR3 (AUC EC-S2 =0.65).

summary:
In Homo sapiens, endothelial subcluster 2 expresses BMX, an artery-specific endothelial cell marker, and NPR3 in the human heart.


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:407e8295c968dcd9d500
claim_id: claim:407e8295c968dcd9d500
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, epicardial adipocytes are characterized by CIDEC and PLIN5 in the human heart.
span_literal:
These cells were characterized by genes whose expression ultimately regulate the size and stability of lipid droplets, such as CIDEC (AUC 11 =0.72) and PLIN5 (AUC 11 =0.78).


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:6fac4880f037a585d2f3
claim_id: claim:6fac4880f037a585d2f3
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, epicardial adipocytes are marked by ADIPOQ in the human heart.
span_literal:
ADIPOQ , which modulates fatty acid transport and increases intracellular calcium is present in nearly 65% of adipocyte nuclei but only 0.3% of other cell types (AUC 11 =0.82).


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:de9afca999e4f7de02de
claim_id: claim:de9afca999e4f7de02de
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, epicardial adipocytes are enriched for CD96 in the human heart.
span_literal:
Surprisingly these cells are also enriched for CD96 , a marker most often identified with Natural Killer (NK) and T-cells (AUC 11 =0.73)


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:138980ed070c4ffa1c92
claim_id: claim:138980ed070c4ffa1c92
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, neuronal cells are defined by NRXN1, NRXN3, and NCAM2 in the human heart.
span_literal:
We identified a subset of neuronal cells in cluster 16, largely defined by neuronal cell adhesion genes such as the neurexins ( NRXN1, AUC 16 =0.91 and NRXN3, AUC 16 =0.87), and NCAM2 (AUC 16 =0.73)


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:38af1c5d0de7c967a7b3
claim_id: claim:38af1c5d0de7c967a7b3
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, neuronal cells are marked by the ion channel gene SCN7A in the human heart.
span_literal:
The only ion channel gene identified as a marker in this cluster is SCN7A (AUC 16 =0.74), initially described in glia, but since understood to reside in other cell types of the nervous system


claim_key: hca:0493_10.1161_circulationaha.119.045401_814f085618:claim:84d1c6dba70b1130c584
claim_id: claim:84d1c6dba70b1130c584
paper_key: hca:0493_10.1161_circulationaha.119.045401_814f085618
summary: In Homo sapiens, neuronal cells robustly express ADGRB3 and SHISA9 in the human heart.
span_literal:
For signaling genes, the receptor genes ADGRB3 (AUC 16 =0.72), which acts to promote angiogenesis, and SHISA9 (AUC 16 =0.72), which modulates AMPA-type glutamate receptors, were robustly expressed within this cluster


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:2ae5d54ade9b994ea963
claim_id: claim:2ae5d54ade9b994ea963
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
span_literal:
Co-expression of established MY markers encoding for transcription factor p63 ( TP63 ), keratin 17 ( KRT17 ), metallopeptidase CD10 ( MME ), together with contractility genes encoding for alpha-smooth muscle actin ( ACTA2 ), transgelin ( TAGLN ), myosin light chain kinase ( MYLK ) and tropomyosin ( TPM2 ) demarked a single cluster as containing MY cells.

summary:
In Homo sapiens, myoepithelial cells are marked by positive expression of TP63, KRT17, MME, ACTA2, TAGLN, MYLK, and TPM2.


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:f6dcad05d4077deaa466
claim_id: claim:f6dcad05d4077deaa466
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
summary: In Homo sapiens, luminal cells express the markers KRT18 and EPCAM.
span_literal:
The two remaining NMC clusters expressed key luminal markers encoding for keratin 18 ( KRT18 ) and EPCAM ( EPCAM ).


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:da50753011774d0a59f3
claim_id: claim:da50753011774d0a59f3
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
summary: In Homo sapiens, hormone-responsive luminal cells express ESR1, PGR, and PRLR.
span_literal:
Upon closer examination, one cluster resembled the HR cluster previously described 12 , 13 which expressed genes encoding for hormone receptors for oestrogen, progesterone and prolactin ( ESR1 , PGR , PRLR ; Fig. 2a, b and Supplementary Fig. 6d ).


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:89f629bba2a40830184b
claim_id: claim:89f629bba2a40830184b
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
summary: In Homo sapiens, luminal progenitor cells co-express ELF5, ALDH1A3, KIT, SLPI, and KRT23.
span_literal:
The last LC resembled the previously annotated “hormone insensitive” 13 or “secretory L1” 12 clusters that co-expressed transcription factor ELF5 as well as ALDH1A3 , KIT , SLPI and KRT23 .


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:046250cd3246b3c9b8e1
claim_id: claim:046250cd3246b3c9b8e1
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
span_literal:
both of these clusters co-expressed luminal markers ( KRT18 and EPCAM ), major human milk protein genes ( LALBA , CSN2 and CSN3 18 ) and other secretory genes integral to milk fat secretion such as xanthine hydrogenase ( XDH ), CD36 ( CD36 ) and mucin-1 ( MUC1 ) 19

summary:
In Homo sapiens, secretory luminal cluster 1 cells co-express luminal markers KRT18 and EPCAM, milk protein genes LALBA, CSN2, and CSN3, and secretory genes XDH, CD36, and MUC1.


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:a28254af80deb9aef66c
claim_id: claim:a28254af80deb9aef66c
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
span_literal:
both of these clusters co-expressed luminal markers ( KRT18 and EPCAM ), major human milk protein genes ( LALBA , CSN2 and CSN3 18 ) and other secretory genes integral to milk fat secretion such as xanthine hydrogenase ( XDH ), CD36 ( CD36 ) and mucin-1 ( MUC1 ) 19

summary:
In Homo sapiens, secretory luminal cluster 2 cells co-express luminal markers KRT18 and EPCAM, milk protein genes LALBA, CSN2, and CSN3, and secretory genes XDH, CD36, and MUC1.


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:7c6a6a376083485abe5a
claim_id: claim:7c6a6a376083485abe5a
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
summary: In Homo sapiens, FOLR1 is significantly upregulated in secretory luminal cluster 2 cells.
span_literal:
FOLR1 , which encodes the alpha chain of the folate receptor (FR), was significantly upregulated in LC2 cells (Fig. 2b and Supplementary Dataset 1 ).


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:30992fe9aefb3127358e
claim_id: claim:30992fe9aefb3127358e
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
span_literal:
we identified GJPA4 + (encoding gap junction protein alpha 4) vascular accessory (VA) cells, PECAM1 + (encoding CD31) endothelial (EN) cells and DCN + / LUM + / COL1A1 + fibroblasts (FB) within all NMC samples (Fig. 3a, b ).

summary:
In Homo sapiens, vascular accessory cells are marked by GJPA4, endothelial cells are marked by PECAM1, and fibroblasts are marked by DCN, LUM, and COL1A1.


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:1aa7c95de0988b619b3d
claim_id: claim:1aa7c95de0988b619b3d
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
summary: In Homo sapiens, myeloid cells are marked by CD68 and FCER1G.
span_literal:
One CD68 + / FCER1G + myeloid, three ITGAX + / CD33 + monocyte/neutrophil and two CD163 + / MSR1 + / C1QB + macrophage subclusters were identified consisting of LMC and NMC samples (Fig. 3b and Supplementary Fig. 13 ).


claim_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf:claim:6e1829e8369c6e5daaa0
claim_id: claim:6e1829e8369c6e5daaa0
paper_key: hca:0494_10.1038_s41467-021-27895-0_bbe3158fbf
summary: In Homo sapiens, T cells are marked by CD4 and IL7R.
span_literal:
Four clusters consisted of ( CD4 + , IL7R + ) T cells or B cells ( CD79A + / MS4A1 + ), with a small subset of JCHAIN + plasma B cells consisting of both NMC and LMC samples (Fig. 3c and Supplementary Fig. 13 ).


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:871519fcfef710c8273d
claim_id: claim:871519fcfef710c8273d
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
The orientation of each sample was confirmed by delineating the border between layer 6 (L6) and the adjacent white matter (WM) and identifying layer (L5) using marker genes for gray matter/neurons ( SNAP25 ), WM/oligodendrocytes ( MOBP ), and L5 ( PCP4 ) in each tissue section

summary:
In Homo sapiens dorsolateral prefrontal cortex, SNAP25 is a marker gene for neurons in gray matter, MOBP is a marker gene for oligodendrocytes in white matter, and PCP4 is a marker gene for layer 5.


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:7e94beb27a192bdc69b8
claim_id: claim:7e94beb27a192bdc69b8
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
The orientation of each sample was confirmed by delineating the border between layer 6 (L6) and the adjacent white matter (WM) and identifying layer (L5) using marker genes for gray matter/neurons ( SNAP25 ), WM/oligodendrocytes ( MOBP ), and L5 ( PCP4 ) in each tissue section

summary:
In Homo sapiens dorsolateral prefrontal cortex, MOBP is a marker gene for oligodendrocytes in white matter.


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:b0d587bdb3785a86492e
claim_id: claim:b0d587bdb3785a86492e
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
we identified several SVGs that were non-laminar, including HBB, IGKC , and NPY , which likely relate to blood cells, immune cells, and inhibitory interneuron classes

summary:
In Homo sapiens dorsolateral prefrontal cortex, HBB is a spatially variable gene related to blood cells.


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:37ba23f2bde2bc171e0a
claim_id: claim:37ba23f2bde2bc171e0a
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
we identified several SVGs that were non-laminar, including HBB, IGKC , and NPY , which likely relate to blood cells, immune cells, and inhibitory interneuron classes

summary:
In Homo sapiens dorsolateral prefrontal cortex, IGKC is a spatially variable gene related to immune cells.


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:46b076ecff5545ae4c70
claim_id: claim:46b076ecff5545ae4c70
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
we identified several SVGs that were non-laminar, including HBB, IGKC , and NPY , which likely relate to blood cells, immune cells, and inhibitory interneuron classes

summary:
In Homo sapiens dorsolateral prefrontal cortex, NPY is a spatially variable gene related to inhibitory interneurons.


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:a1b41f9b0c81ca95ee38
claim_id: claim:a1b41f9b0c81ca95ee38
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
1) NPY , which encodes a neuropeptide highly expressed in a subpopulation of inhibitory interneurons, 2) HBB , which encodes a subunit of hemoglobin found in red blood cells, and 3) IGKC , which encodes the constant region of immunoglobulin light chains found in antibodies

summary:
In Homo sapiens, NPY encodes a neuropeptide highly expressed in a subpopulation of inhibitory interneurons.


claim_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662:claim:65ea0ce33644dd5b4c3e
claim_id: claim:65ea0ce33644dd5b4c3e
paper_key: hca:0496_10.1038_s41593-020-00787-0_59956d4662
span_literal:
We also confirmed laminar enrichment of several genes identified as cell type markers in specific cortical layers by Hodge et al. ( LAMP5, AQP4, FREM3 ), suggesting conservation between laminar markers in middle temporal gyrus and DLPFC

summary:
In Homo sapiens dorsolateral prefrontal cortex, LAMP5, AQP4, and FREM3 are confirmed as cell type markers with laminar enrichment in specific cortical layers.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:8b6dac2c63733fe9f739
claim_id: claim:8b6dac2c63733fe9f739
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
The separation of cells along principal component 1 (PC1) corresponded to the TE and ICM segregation since the genes with the strongest loadings on PC1 were well-known TE lineage markers ( GATA2 and GATA3 ) as well as known ICM markers ( SOX2 and PDGFRA ).

summary:
In Homo sapiens preimplantation embryos, GATA2 and GATA3 are markers of trophectoderm, while SOX2 and PDGFRA are markers of inner cell mass.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:58703ea3b6d4ce42187c
claim_id: claim:58703ea3b6d4ce42187c
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
summary: In Homo sapiens preimplantation embryos, SOX2, TDGF1, DPPA5, GDF3, and PRDM14 are epiblast markers.
span_literal:
Among the genes with the highest PC loadings were pluripotency-related genes and known EPI markers ( SOX2 , TDGF1 , DPPA5 , GDF3 , and PRDM14 ), and among the genes with the most negative PC loadings were genes implicated in endoderm specification ( PDGFRA , FGFR2 , LAMA4 , and HNF1B ).


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:f1d2b757b388824fa542
claim_id: claim:f1d2b757b388824fa542
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
Among the genes with the highest PC loadings were pluripotency-related genes and known EPI markers ( SOX2 , TDGF1 , DPPA5 , GDF3 , and PRDM14 ), and among the genes with the most negative PC loadings were genes implicated in endoderm specification ( PDGFRA , FGFR2 , LAMA4 , and HNF1B ).

summary:
In Homo sapiens preimplantation embryos, PDGFRA, FGFR2, LAMA4, and HNF1B are markers of primitive endoderm.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:501e00d7f3547e0e942c
claim_id: claim:501e00d7f3547e0e942c
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
summary: In Homo sapiens preimplantation embryos, GATA3, DAB2, and GATA2 are known trophectoderm markers.
span_literal:
Several known TE markers, such as GATA3 , DAB2 , and GATA2 were among the top-ranked genes (rank 2, 25, and 58, respectively).


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:36691deda27cd92fc80a
claim_id: claim:36691deda27cd92fc80a
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
Interestingly, CDX2 was differentially expressed, but only ranked 209 th , and EOMES was not expressed at all.

summary:
In Homo sapiens preimplantation embryos, CDX2 is a differentially expressed trophectoderm marker but lowly ranked, and EOMES is not expressed at all in trophectoderm.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:be099bdde1cd55e2c8ad
claim_id: claim:be099bdde1cd55e2c8ad
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
In addition to known markers, several less-described markers were identified, such as PTGES , EMP2 , TGFBR3 , and PDGFA (rank 1, 4, 23, and 33).

summary:
In Homo sapiens preimplantation embryos, PTGES, EMP2, TGFBR3, and PDGFA are identified as trophectoderm-specific markers.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:4a76c54cf922f7399dab
claim_id: claim:4a76c54cf922f7399dab
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
Among top-ranked EPI-specific genes were factors implicated in embryonic preimplantation development in mouse or human, such as PRDM14 , GDF3 , TDGF1 , NODAL , SOX2 , and NANOG (rank 1, 3, 9, 10, 12, and 22) and a few less-established markers, including DPPA5 , ESRG , KLF17 , ARGFX , and DPPA2 (rank 2, 4, 5, 7, 19).

summary:
In Homo sapiens preimplantation embryos, PRDM14, GDF3, TDGF1, NODAL, SOX2, NANOG, DPPA5, ESRG, KLF17, ARGFX, and DPPA2 are epiblast-specific genes.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:1ddaf3c503bf587fac9b
claim_id: claim:1ddaf3c503bf587fac9b
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
PE-specific genes included known factors such as COL4A1 , HNF1B , PDGFRA , GATA4 and FN1 (rank 3, 4, 7, 13, and 15) and among highly ranked genes were also LINC00261 , FRZB , AMOTL1 , and DPP4 (rank 1, 5, 6, and 14).

summary:
In Homo sapiens preimplantation embryos, COL4A1, HNF1B, PDGFRA, GATA4, FN1, LINC00261, FRZB, AMOTL1, and DPP4 are primitive endoderm-specific genes.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:ad2f8d3dcf087c3578f3
claim_id: claim:ad2f8d3dcf087c3578f3
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
We identified several genes that have been previously associated with trophoblast differentiation ( Figure 3 F), including CCR7 (rank 1) ( Drake et al., 2004 ), CYP19A1 (rank 4) ( Kumar et al., 2013 ), DLX5 (rank 5) ( Marchand et al., 2011 ), ERVFRD-1 (rank 6) ( Mi et al., 2000 ), GCM1 (rank 7) ( Marchand et al., 2011 ), GREM2 (rank 8) ( Sudheer et al., 2012 ), MUC15 (rank 13) ( Marchand et al., 2011 ), and OVOL1 (rank 16) ( Renaud et al., 2015 ).

summary:
In Homo sapiens preimplantation embryos, CCR7, CYP19A1, DLX5, ERVFRD-1, GCM1, GREM2, MUC15, and OVOL1 are associated with polar trophectoderm differentiation.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:d3e90566f823fd964a4f
claim_id: claim:d3e90566f823fd964a4f
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
summary: In Homo sapiens preimplantation embryos, CLDN4, CLDN10, GATA2, and SLC2A1 are trophectoderm genes.
span_literal:
Top genes included DNMT3L (E3 versus E4), TE genes such as CLDN4 , CLDN10 , GATA2 , and SLC2A1 (E4 versus E5.pre-lineage) and CGA and PGF , which were strongly upregulated in all three lineages from E5 to E7 ( Table S5 ).


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:375b5d0c7ef2e8612e82
claim_id: claim:375b5d0c7ef2e8612e82
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
In the late E4 compacting morula cells, a transcriptional TE program is initiated, including increased expression of GATA3 , PTGES , and PDGFA .

summary:
In Homo sapiens preimplantation embryos, GATA3, PTGES, and PDGFA are part of the trophectoderm transcriptional program.


claim_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04:claim:5392d9e1001c44176394
claim_id: claim:5392d9e1001c44176394
paper_key: hca:0497_10.1016_j.cell.2016.03.023_1e72ea1d04
span_literal:
LINC00261 , the top ranked gene enriched in PE, was recently identified as a definitive endoderm-specific lncRNA driving FOXA2 expression through recruitment of SMAD2/3 to its promoter ( Jiang et al., 2015 ).

summary:
In Homo sapiens preimplantation embryos, LINC00261 is the top ranked gene enriched in primitive endoderm.


claim_key: hca:0498_10.1038_s41598-017-11044-z_4cb11e808c:claim:0f5afc08bb805a923ee0
claim_id: claim:0f5afc08bb805a923ee0
paper_key: hca:0498_10.1038_s41598-017-11044-z_4cb11e808c
span_literal:
Analysis of XIST expression in single cells from dataset-2 shows that at the 8-cell and blastocyst stages XIST expression in female was significantly higher than in pre-EGA or male embryos

summary:
In Homo sapiens, XIST expression in female preimplantation embryos is significantly higher than in pre-embryonic genome activation or male embryos at the 8-cell and blastocyst stages, serving as a positive marker of female embryonic cells.


claim_key: hca:0498_10.1038_s41598-017-11044-z_4cb11e808c:claim:34c752ee61f3cadbdded
claim_id: claim:34c752ee61f3cadbdded
paper_key: hca:0498_10.1038_s41598-017-11044-z_4cb11e808c
span_literal:
Embryos were sexed based on expression of Y-linked genes, using oocytes and male human embryonic stem cells at passage 0 (hESp0) as female and male controls, respectively.

summary:
In Homo sapiens, Y-linked genes are used as positive markers to sex embryos, distinguishing male from female preimplantation embryos.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:b4e5e930d8f52d14cfd0
claim_id: claim:b4e5e930d8f52d14cfd0
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
They were, however, distinguishable by selective expression of multiple genes, including ACTN2 and SLC4A8, enriched in C0, and LRRC7 and DCC, enriched in C2

summary:
In Homo sapiens, oligodendrocyte cluster C0 is distinguished from oligodendrocyte cluster C2 by enriched expression of ACTN2 and SLC4A8.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:56c80211b92263052c6d
claim_id: claim:56c80211b92263052c6d
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
They were, however, distinguishable by selective expression of multiple genes, including ACTN2 and SLC4A8, enriched in C0, and LRRC7 and DCC, enriched in C2

summary:
In Homo sapiens, oligodendrocyte cluster C2 is distinguished from oligodendrocyte cluster C0 by enriched expression of LRRC7 and DCC.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:62de108bebd05a366ece
claim_id: claim:62de108bebd05a366ece
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
summary: In Homo sapiens, oligodendrocyte precursor cells express OLIG1 and OLIG2 as marker genes.
span_literal:
Cells in the other two clusters (C13 and C33) expressed known markers of oligodendrocyte precursor cells (OPCs) such as OLIG1 and OLIG2


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:9071928ec5378619128e
claim_id: claim:9071928ec5378619128e
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C33 was distinguishable from C13 by higher expression of several genes, including GPR17 , ENPP6 , and PLP1 , which have been shown to be expressed by premyelinating oligodendrocytes

summary:
In Homo sapiens, premyelinating oligodendrocytes (cluster C33) are distinguished from oligodendrocyte precursor cells (cluster C13) by higher expression of GPR17, ENPP6, and PLP1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:9bdeb571eb9d9f4de61b
claim_id: claim:9bdeb571eb9d9f4de61b
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C35 but not C15 expressed high levels of PRX, MBP, and MPZ which encode myelin proteins expressed by Schwann cells but not oligodendrocytes

summary:
In Homo sapiens, myelinating Schwann cells (cluster C35) express high levels of PRX, MBP, and MPZ, which are not expressed by nonmyelinating Schwann cells (cluster C15).


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:2f3b267ab3f539bc1b8d
claim_id: claim:2f3b267ab3f539bc1b8d
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal: In contrast, C15 is rich in SCN7A , NCAM1 , L1CAM , and NGFR
summary:
In Homo sapiens, nonmyelinating Schwann cells (cluster C15) are enriched in SCN7A, NCAM1, L1CAM, and NGFR.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:ad6737b6a0665f501c67
claim_id: claim:ad6737b6a0665f501c67
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
summary: In Homo sapiens, astrocytes express known markers including GFAP and ALDH1L1.
span_literal:
Five clusters (C1, 6, 8, 11, and 12) were close transcriptomic relatives and expressed known astrocyte markers including GFAP and ALDH1L1


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:7638fd30f3462db80764
claim_id: claim:7638fd30f3462db80764
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal: C1 selectively expressed SLC14A1 and SOX9 , whereas C12 expressed higher levels of GAP43 and CHI3L1
summary:
In Homo sapiens, astrocyte cluster C1 selectively expresses SLC14A1 and SOX9, whereas astrocyte cluster C12 expresses higher levels of GAP43 and CHI3L1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:60386cac2dd1d5c55f96
claim_id: claim:60386cac2dd1d5c55f96
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal: C1 selectively expressed SLC14A1 and SOX9 , whereas C12 expressed higher levels of GAP43 and CHI3L1
summary:
In Homo sapiens, astrocyte cluster C12 expresses higher levels of GAP43 and CHI3L1 compared to astrocyte cluster C1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:93418a92cd7c02126061
claim_id: claim:93418a92cd7c02126061
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal: For example, DACH1 was expressed at the highest levels in C11, LINC01727 in C8, and FGF10 in C6
summary:
In Homo sapiens, astrocyte cluster C11 expresses DACH1 at the highest levels, astrocyte cluster C8 expresses LINC01727, and astrocyte cluster C6 expresses FGF10.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:6a294bee606559ee7812
claim_id: claim:6a294bee606559ee7812
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
Eight transcriptomically related clusters (C5, 10, 17, 22, 28, 29, 31, and 32) were classified as fibroblasts, based on their expression of known markers such as COL1A1 and DCN

summary:
In Homo sapiens, fibroblasts are classified based on their expression of known markers such as COL1A1 and DCN.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:298310171e678a519bbf
claim_id: claim:298310171e678a519bbf
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
summary: In Homo sapiens, fibroblast cluster C5 differentially expresses HS6ST3 and SMOC2.
span_literal:
Differentially expressed genes included HS6ST3 and SMOC2 by C5; TRDN by C10; SLC47A1 and GADL1 by C17; TRPM3 and SLC6A13 by C22; KCNQ3 and LGR5 by C28; ANO3 and TNN by C29; SLC22A3 and EBF2 by C31; and PTGIS and COL12A1 by C32


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:93382165819ad5f27ef5
claim_id: claim:93382165819ad5f27ef5
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
Six clusters (C16, 18, 20, 21, 23, and 27) were identified as vascular endothelial cells based on the expression of markers such as PECAM1 and FLT1

summary:
In Homo sapiens, vascular endothelial cells are identified based on the expression of markers such as PECAM1 and FLT1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:efc1e2f2d10e59bb1420
claim_id: claim:efc1e2f2d10e59bb1420
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal: C16 cells expressed markers of venules including ADGRG6 , MMRN1 , and POSTN
summary:
In Homo sapiens, vascular endothelial cell cluster C16 (venule) expresses markers including ADGRG6, MMRN1, and POSTN.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:6d2cd9e2a90c6092966c
claim_id: claim:6d2cd9e2a90c6092966c
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C20 and C27 cells were enriched in the expression of artery/arteriole markers such as SEMA3G , HEY1, and BMX

summary:
In Homo sapiens, vascular endothelial cell cluster C20 is enriched in artery/arteriole markers such as SEMA3G, HEY1, and BMX.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:ca229df07b1adc445c06
claim_id: claim:ca229df07b1adc445c06
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C20 and C27 cells were enriched in the expression of artery/arteriole markers such as SEMA3G , HEY1, and BMX

summary:
In Homo sapiens, vascular endothelial cell cluster C27 is enriched in artery/arteriole markers such as SEMA3G, HEY1, and BMX.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:6e58af7eb561fa9c89d8
claim_id: claim:6e58af7eb561fa9c89d8
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C18 and C21 were enriched in the expression of genes previously shown to be associated with fenestrated capillaries, including PLVAP and CA4 in C18, and postcapillary venules including PKHD1L1 and MMRN1 in C21

summary:
In Homo sapiens, vascular endothelial cell cluster C18 (fenestrated capillary) is enriched in PLVAP and CA4.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:48ab41d89956bf3344f7
claim_id: claim:48ab41d89956bf3344f7
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C18 and C21 were enriched in the expression of genes previously shown to be associated with fenestrated capillaries, including PLVAP and CA4 in C18, and postcapillary venules including PKHD1L1 and MMRN1 in C21

summary:
In Homo sapiens, vascular endothelial cell cluster C21 (postcapillary venule) is enriched in PKHD1L1 and MMRN1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:b6142f96bf9dfc87b620
claim_id: claim:b6142f96bf9dfc87b620
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C19, 26, and 34 were identified as mural cells based on their expression of known markers such as TAGLN and ACTA2

summary:
In Homo sapiens, mural cells are identified based on their expression of known markers such as TAGLN and ACTA2.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:b107cfe0e0da3187a68d
claim_id: claim:b107cfe0e0da3187a68d
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
The three mural cell types were further distinguishable by selective expression of multiple genes including UNC13C, RGS6 , and CASQ2 in C19, TRPC4 , RGS5 , and LAMA2 in C26, and FGF7 , SLC7A2 , and CLSTN2 in C34

summary:
In Homo sapiens, mural cell cluster C19 (vascular smooth muscle cell) selectively expresses UNC13C, RGS6, and CASQ2.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:ce61d1f2687266a4ddf2
claim_id: claim:ce61d1f2687266a4ddf2
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
The three mural cell types were further distinguishable by selective expression of multiple genes including UNC13C, RGS6 , and CASQ2 in C19, TRPC4 , RGS5 , and LAMA2 in C26, and FGF7 , SLC7A2 , and CLSTN2 in C34

summary:
In Homo sapiens, mural cell cluster C34 (vascular smooth muscle cell) selectively expresses FGF7, SLC7A2, and CLSTN2.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:e0aed7c57cd6d6361550
claim_id: claim:e0aed7c57cd6d6361550
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C4 and C24 expressed markers of macrophages (e.g., MRC1 and CD163 ) but could be differentiated from each other by selective expression of IL1R2 , and VCAN in C24, and CD163L1 , and LYVE1 in C4

summary:
In Homo sapiens, macrophages (clusters C4 and C24) express markers MRC1 and CD163. Macrophage cluster C24 selectively expresses IL1R2 and VCAN, while macrophage cluster C4 selectively expresses CD163L1 and LYVE1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:b24eeaf9ed26d704cf17
claim_id: claim:b24eeaf9ed26d704cf17
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C4 and C24 expressed markers of macrophages (e.g., MRC1 and CD163 ) but could be differentiated from each other by selective expression of IL1R2 , and VCAN in C24, and CD163L1 , and LYVE1 in C4

summary:
In Homo sapiens, macrophage cluster C24 selectively expresses IL1R2 and VCAN, distinguishing it from macrophage cluster C4.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:4be2e9a83cbd830e9a0a
claim_id: claim:4be2e9a83cbd830e9a0a
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
C4 and C24 expressed markers of macrophages (e.g., MRC1 and CD163 ) but could be differentiated from each other by selective expression of IL1R2 , and VCAN in C24, and CD163L1 , and LYVE1 in C4

summary:
In Homo sapiens, macrophage cluster C4 selectively expresses CD163L1 and LYVE1, distinguishing it from macrophage cluster C24.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:96028e0b8768f4d42fa1
claim_id: claim:96028e0b8768f4d42fa1
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
summary: In Homo sapiens, T lymphocytes (cluster C7) express CD2 and THEMIS.
span_literal:
We identified C7 as T lymphocytes (e.g., CD2 + and THEMIS +), C25 as Natural Killer (NK) cells (e.g., KLRD1 + and KLRF1 +), and C30 as B lymphocytes (e.g., EBF1 + and BCL11A +)


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:65b16dbf1c56de7f8bce
claim_id: claim:65b16dbf1c56de7f8bce
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal: Two cell types, C3 and C14, expressed genes characteristic of pigmented cells such as TYR and MLANA
summary:
In Homo sapiens, pigmented cells (clusters C3 and C14) express genes characteristic of pigmented cells such as TYR and MLANA.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:10d7920b8c9e24f1b3b5
claim_id: claim:10d7920b8c9e24f1b3b5
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
They could, however, be distinguished from each other by the expression of genes including PMEL and PAX3 in C3 and PAX6 and CCBE1 in C14

summary:
In Homo sapiens, melanocyte cluster C3 is distinguished from pigmented cell cluster C14 by expression of PMEL and PAX3.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:8359f300ff720d4076ab
claim_id: claim:8359f300ff720d4076ab
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
They could, however, be distinguished from each other by the expression of genes including PMEL and PAX3 in C3 and PAX6 and CCBE1 in C14

summary:
In Homo sapiens, pigmented cell cluster C14 is distinguished from melanocyte cluster C3 by expression of PAX6 and CCBE1.


claim_key: hca:0500_10.1073_pnas.2306153120_5c49b25904:claim:1f5da06d026d3aa803b0
claim_id: claim:1f5da06d026d3aa803b0
paper_key: hca:0500_10.1073_pnas.2306153120_5c49b25904
span_literal:
Additional markers that distinguished astrocytes from other cell classes included PAX8 and the noncoding RNAs AC092957.1 , LINC00299, and JAKMIP2-AS1

summary:
In Homo sapiens, astrocytes are distinguished from other cell classes by expression of PAX8, AC092957.1, LINC00299, and JAKMIP2-AS1.


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:a0912e867ce2ad8ea516
claim_id: claim:a0912e867ce2ad8ea516
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
span_literal:
blood were naïve CD4 (CD4 naïve blood) and naïve CD8 (CD8 naïve blood) that were defined by expression of genes including CCR7 , SELL , and LEF1

summary:
In Homo sapiens, naive CD4 T cells and naive CD8 T cells in the blood are defined by expression of CCR7, SELL, and LEF1.


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:abcec6f080ddbbfac58c
claim_id: claim:abcec6f080ddbbfac58c
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
summary: In Homo sapiens, naive CD8 T cells in the blood are defined by expression of CCR7, SELL, and LEF1.
span_literal:
blood) and naïve CD8 (CD8 naïve blood) that were defined by expression of genes including CCR7 , SELL , and LEF1


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:f1d85343146c6ce0e3c7
claim_id: claim:f1d85343146c6ce0e3c7
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
summary: In Homo sapiens, CD4 memory blood T cells are marked by expression of S100A4, GATA3, and KLRB1.
span_literal:
The blood also contained a cluster of CD4 T cells (CD4 memory blood) marked by expression of molecules associated with memory T cells ( S100A4 ) and markers of various T cell subsets including the T H 2 transcription factor GATA3 and the T H 17 marker KLRB1 (CD161)


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:83275790093ea7da6389
claim_id: claim:83275790093ea7da6389
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
span_literal:
The CD4 memory CSF.1 cluster was marked by expression of the subunits of the alpha 4 ( ITGA4 ) beta 1 ( ITGB1 ) integrin, which has been shown to be important for T cell entry into the CNS ( 1 ), KLRB1 , and S1PR1 that promotes T cell egress from tissues

summary:
In Homo sapiens, CD4 memory cerebrospinal fluid 1 T cells are marked by expression of ITGA4, ITGB1, KLRB1, and S1PR1.


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:8f339206581591fb2aef
claim_id: claim:8f339206581591fb2aef
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
span_literal:
CSF (CD4 memory CSF.2 and CD4 memory CSF.3) have phenotypes similar to each other characterized by the chemokine receptor CXCR3 associated with T H 1 cells and CSF T cell trafficking ( 2 , 32 ) and markers that have been found in tissue-resident T cells and T cells residing within nonlymphoid tissues, including CCL5 ( 24 , 33 , 34 ), LGALS1 ( 24 , 25 , 34 ), PTGER2 ( 35 ), and CD69

summary:
In Homo sapiens, CD4 memory cerebrospinal fluid 2 and CD4 memory cerebrospinal fluid 3 T cells are characterized by expression of CXCR3, CCL5, LGALS1, PTGER2, and CD69.


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:ce3dce183d1c87a619e9
claim_id: claim:ce3dce183d1c87a619e9
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
span_literal:
CSF.2 and CD4 memory CSF.3) have phenotypes similar to each other characterized by the chemokine receptor CXCR3 associated with T H 1 cells and CSF T cell trafficking ( 2 , 32 ) and markers that have been found in tissue-resident T cells and T cells residing within nonlymphoid tissues, including CCL5 ( 24 , 33 , 34 ), LGALS1 ( 24 , 25 , 34 ), PTGER2 ( 35 ), and CD69

summary:
In Homo sapiens, CD4 memory cerebrospinal fluid 3 T cells are characterized by expression of CXCR3, CCL5, LGALS1, PTGER2, and CD69.


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:a228fbc38ab25a62cb82
claim_id: claim:a228fbc38ab25a62cb82
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
span_literal:
However, CD4 memory CSF.3 was also defined by the cytotoxicity-related genes GZMA , GZMK , GZMM , and CST7 ( 37 ), whereas CD4 memory CSF.2 was not.

summary:
In Homo sapiens, CD4 memory cerebrospinal fluid 3 T cells are defined by expression of the cytotoxicity-related genes GZMA, GZMK, GZMM, and CST7.


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:17179285966726fbe9c7
claim_id: claim:17179285966726fbe9c7
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
summary: In Homo sapiens, CD8 memory cerebrospinal fluid T cells express KLRG1 and EOMES.
span_literal:
CD8 memory CSF also expressed KLRG1 and EOMES , which suggests that these may represent a less differentiated tissue T cell population than canonical tissue-resident CD8 T cells, for example, similar to recently described tissue-resident effector cells


claim_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd:claim:b1838cc82e312ed9e449
claim_id: claim:b1838cc82e312ed9e449
paper_key: hca:0501_10.1126_sciimmunol.abb8786_1f1edec8bd
span_literal:
we found that clonally expanded CD8 T cells expressed higher levels of CD8 effector function–related molecules including NKG7 , CCL5 , and CCL4 and express lower levels of SELL or L-selectin that is associated with a naïve phenotype compared with unexpanded cells

summary:
In Homo sapiens, clonally expanded CD8 T cells in the cerebrospinal fluid express higher levels of NKG7, CCL5, and CCL4 and lower levels of SELL compared with unexpanded CD8 T cells.


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:9e8e2c1dcb8cf3bde09e
claim_id: claim:9e8e2c1dcb8cf3bde09e
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
span_literal:
EECs expressed several genes that allowed their distinction from VECs, including LEPR , NPR3 , and PCDH15 , whereas VECs expressed GRB10 , PREX2 , and VWF

summary:
In Homo sapiens, endocardial endothelial cells are distinguished from vascular endothelial cells by expression of LEPR, NPR3, and PCDH15.


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:bf6542278184d08665ed
claim_id: claim:bf6542278184d08665ed
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
span_literal:
EECs expressed several genes that allowed their distinction from VECs, including LEPR , NPR3 , and PCDH15 , whereas VECs expressed GRB10 , PREX2 , and VWF

summary:
In Homo sapiens, vascular endothelial cells are distinguished from endocardial endothelial cells by expression of GRB10, PREX2, and VWF.


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:42f2838097cb2b0881ec
claim_id: claim:42f2838097cb2b0881ec
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
summary: In Homo sapiens, CHRM2 is a marker gene for cardiomyocytes in right atrial tissue.
span_literal:
establishing specific marker genes for different cell types, such as CHRM2 for CMs, PCDH7 for EECs, ABCA6 for FBs, PRG4 for epicardial MESOs, and MPZ for Schwann cells


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:62e31ae8f01453cfeecb
claim_id: claim:62e31ae8f01453cfeecb
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
summary: In Homo sapiens, coronary artery endothelial cells are marked by DKK2, GJA5, and EFNA5.
span_literal:
UMAP embeddings showing vascular marker gene expression for CA ( DKK2 , GJA5 , and EFNA5 ), ART ( PCSK5 , FUT8 , and EFNB2 ), ACAP ( VEGFC , PIK3R3 , and BTNL9 ), CAP ( CCDC85A , ABLIM3 , and PKD1L1 ), TIP ( ARHGAP18 , FMNL2 , and TMEM163 ), VCAP ( SLCO2A1 , PLVAP , and NRP2 ), VEN ( GPM6A , PKHD1L1 , and POSTN ), PER ( RGS5 , PDE1C , and ABCC9 ), and SMC ( MYH11 , RGS6 , and DGKG ).


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:c9bc3652b28c864f8c3b
claim_id: claim:c9bc3652b28c864f8c3b
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
span_literal:
the MP marker gene, CD163 , co-localized with infla-MP marker gene, LYVE1 , with increased expression in IHF compared to control

summary:
In Homo sapiens, CD163 is a marker gene for macrophages and LYVE1 is a marker gene for inflammatory macrophages in right atrial tissue.


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:5ed65a02da67ba53566b
claim_id: claim:5ed65a02da67ba53566b
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
span_literal:
We confirmed the colocalization of an established LAM marker TREM2 59 with lipid droplets in IHF sections and observed increased signal in IHF compared to IHD

summary:
In Homo sapiens, TREM2 is an established marker for lipid-associated macrophages in right atrial tissue.


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:8bccea0a21856b440be3
claim_id: claim:8bccea0a21856b440be3
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
span_literal:
In spatial images (Visium), CXCL10 , a marker gene for the IFN-MP population, was detected in IHF, clustering in the myocardium but not in the control sections

summary:
In Homo sapiens, CXCL10 is a marker gene for the interferon-responsive macrophage population in right atrial tissue.


claim_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11:claim:cd53cd24ec7a33e83512
claim_id: claim:cd53cd24ec7a33e83512
paper_key: hca:0502_10.1016_j.xcrm.2024.101556_a84a219a11
summary: In Homo sapiens, endocardial endothelial cells are marked by LEPR, NPR3, and PCDH15.
span_literal:
snRNA-seq data highlight the expression of the marker genes for EEC ( LEPR , NPR3 , and PCDH15 ), VEC ( GRB10 , PREX2 , and VWF ), MESO ( SLC4A4 , EZR , and PRG4 ), and PER ( DACH1 , ABCC9 , and SEMA5A ).


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:3ccc3f3f98193bf2af87
claim_id: claim:3ccc3f3f98193bf2af87
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
span_literal:
LAIR1, a collagen receptor ( 32 , 33 ) and a type 1 Ig containing two immunoreceptor tyrosine-based inhibitory motifs ( 34 ), was most differentially up-regulated in myeloid cell types of critical COVID-19 + cases compared to healthy controls (cM, ncM, and cDC: log 2 FC = 0.51 to 0.97, P adjusted = 4.8 × 10 −3 to 3.9 × 10 −5 )

summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is up-regulated on classical monocytes from patients with critical COVID-19 compared to healthy controls.


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:12e9338ab8d88e8dd7d5
claim_id: claim:12e9338ab8d88e8dd7d5
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
span_literal:
LAIR1, a collagen receptor ( 32 , 33 ) and a type 1 Ig containing two immunoreceptor tyrosine-based inhibitory motifs ( 34 ), was most differentially up-regulated in myeloid cell types of critical COVID-19 + cases compared to healthy controls (cM, ncM, and cDC: log 2 FC = 0.51 to 0.97, P adjusted = 4.8 × 10 −3 to 3.9 × 10 −5 )

summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is up-regulated on nonclassical monocytes from patients with critical COVID-19 compared to healthy controls.


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:ed93acb125b1e3ebcb9d
claim_id: claim:ed93acb125b1e3ebcb9d
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
span_literal:
LAIR1, a collagen receptor ( 32 , 33 ) and a type 1 Ig containing two immunoreceptor tyrosine-based inhibitory motifs ( 34 ), was most differentially up-regulated in myeloid cell types of critical COVID-19 + cases compared to healthy controls (cM, ncM, and cDC: log 2 FC = 0.51 to 0.97, P adjusted = 4.8 × 10 −3 to 3.9 × 10 −5 )

summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is up-regulated on conventional dendritic cells from patients with critical COVID-19 compared to healthy controls.


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:221b8b130a6ec60572bd
claim_id: claim:221b8b130a6ec60572bd
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
span_literal:
LAIR1 transcripts were also differentially expressed by cM, ncM, cDC, and NK cells in COVID-19 + cases when compared to healthy controls (log 2 FC = 0.65 to 1.06, FDR = 5.0 × 10 −6 to 3.0 × 10 −3 ; other cell types: log 2 FC = −1.2 × 10 −2 to 1.6 × 10 −2 , FDR = 0.64 to 0.93)

summary:
In Homo sapiens, LAIR1 transcripts are differentially up-regulated in natural killer cells from patients with COVID-19 compared to healthy controls.


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:e1930abf443bc9157dae
claim_id: claim:e1930abf443bc9157dae
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
span_literal:
Of the five proteins differentially expressed in cMs, four [transferrin receptor (TFRC), sialic acid binding Ig-like lectin 1 (SIGLEC1), Fc fragment of IgG receptor 1a (FCGR1A), and leukocyte-associated Ig-like receptor 1 (LAIR1)] were higher expressed in COVID-19 + cases.

summary:
In Homo sapiens, transferrin receptor (TFRC), sialic acid binding immunoglobulin-like lectin 1 (SIGLEC1), Fc fragment of IgG receptor 1a (FCGR1A), and leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) are higher expressed on classical monocytes from patients with COVID-19.


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:ff01fc69959f69cf0eeb
claim_id: claim:ff01fc69959f69cf0eeb
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
span_literal:
SIGLEC1 is a known up-regulated ISG ( 31 ) whose pattern of surface expression is consistent with the expression of ISG-I present in moderate and severe cases

summary:
In Homo sapiens, SIGLEC1 is a known up-regulated interferon-stimulated gene expressed on classical monocytes.


claim_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7:claim:ba540161722c96bd5cc5
claim_id: claim:ba540161722c96bd5cc5
paper_key: hca:0505_10.1126_scitranslmed.abh2624_475f0b05e7
summary: In Homo sapiens, LAIR1 is an inhibitory surface protein expressed in lymphocytes.
span_literal:
LAIR1 is an inhibitory surface protein first described to be expressed in lymphocytes and involved in inhibiting NK-mediated cell lysis and effector T cell cytotoxicity upon FcR-mediated cross-linking ( 34 , 40 , 41 ).


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:7d757ae24c5a16429db7
claim_id: claim:7d757ae24c5a16429db7
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal: CD2 and CD7 ), innate lymphoid cells ( CD2 , CD7 and no CD3D
summary:
In Homo sapiens, innate lymphoid cells are identified by expression of CD2 and CD7 and negative expression of CD3D.


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:94e191f361af9f8ab5d4
claim_id: claim:94e191f361af9f8ab5d4
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
summary: In Homo sapiens, B cells are marked by CD19, MS4A1, BANK1, and HLA-DRA.
span_literal:
Twenty clusters of B cells ( CD19 , MS4A1 , BANK1 and HLA-DRA ) and PCs ( SDC1 , XBP1 , TNFRSF17 , PRDM1 , MZB1 and SEC11C ) with variable cell numbers (276–3,778 cells; Supplementary Table 2 ), and unique molecular inhibitor (UMI) counts per cell were identified


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:0c5183e214ce02c6ae36
claim_id: claim:0c5183e214ce02c6ae36
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
summary: In Homo sapiens, naive B cells are identified by expression of IGHD, FCER2, and CD72.
span_literal:
we identified naive ( IGHD , FCER2 and CD72 ; clusters 8 and 12) and memory ( CD27 , TNFRSF13B and no expression of IGHD ; clusters 2, 7 and 13) B cells


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:d2a10c6a4ea1d9cddac8
claim_id: claim:d2a10c6a4ea1d9cddac8
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal:
we identified naive ( IGHD , FCER2 and CD72 ; clusters 8 and 12) and memory ( CD27 , TNFRSF13B and no expression of IGHD ; clusters 2, 7 and 13) B cells

summary:
In Homo sapiens, memory B cells are identified by expression of CD27 and TNFRSF13B and negative expression of IGHD.


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:6f8b5eb168d76ae0a776
claim_id: claim:6f8b5eb168d76ae0a776
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal:
Cluster 16 was annotated as germinal center (GC)-like B cells based on the expression of well-established GC B cell genes, such as AICDA , BCL6 , CD38 , FAS and MME (CD10)

summary:
In Homo sapiens, germinal center-like B cells are identified by expression of AICDA, BCL6, CD38, FAS, and MME.


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:0c31dd8df59276479ce4
claim_id: claim:0c31dd8df59276479ce4
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal:
Colonic CXCL13 + T cells expressed genes such as PDCD1 (PD-1), CD200 , BCL6 , TIGIT , ICOS and BATF but no CXCR5 transcripts

summary:
In Homo sapiens, colonic CXCL13-positive T peripheral helper cells express PDCD1, CD200, BCL6, TIGIT, ICOS, and BATF but do not express CXCR5.


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:7e029ac3548fb7f4cbe9
claim_id: claim:7e029ac3548fb7f4cbe9
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal:
colonic TPH cells expressed several genes in common with regulatory T (Treg) cells, such as TIGIT , CTLA4 , TNFRSF4 and MAF , whereas key Treg-defining genes, such as FOXP3 and IKZF2 , were not detected

summary:
In Homo sapiens, colonic T peripheral helper cells express TIGIT, CTLA4, TNFRSF4, and MAF but do not express the regulatory T cell-defining genes FOXP3 and IKZF2.


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:7fa85fa46e043b9a13dc
claim_id: claim:7fa85fa46e043b9a13dc
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
summary: In Homo sapiens, T peripheral helper cells uniquely express NMB, FABP5, and PGM2L1.
span_literal:
TPH cells, in turn, uniquely expressed the TFH program as well as previously unreported genes, such as NMB , FABP5 and PGM2L1


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:5bca5adafe74ee39a48f
claim_id: claim:5bca5adafe74ee39a48f
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
summary: In Homo sapiens, T peripheral helper cells are marked by expression of CXCL13.
span_literal:
Although CXCL13 expression was restricted to TPH cells, Treg cells expressed the immunoregulatory cytokine IL-10


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:8b4afe0f7799efc72e2e
claim_id: claim:8b4afe0f7799efc72e2e
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal:
we identified ‘resident-like’ macrophages in both healthy and inflamed UC colons expressing tissue macrophage-associated genes, including C1qc , DNASE1L13 , MRC1 (CD206), MAFB and CSF1R

summary:
In Homo sapiens, resident-like macrophages express tissue macrophage-associated genes including C1QC, DNASE1L3, MRC1, MAFB, and CSF1R.


claim_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86:claim:aad38df0af9e6cdad7bf
claim_id: claim:aad38df0af9e6cdad7bf
paper_key: hca:0506_10.1038_s41591-022-01680-y_160aaf8b86
span_literal:
T cell clusters 4 and 13 expressed high levels of Treg-associated genes, including FOXP3 , IL2RA (CD25) and CTLA4 , together with genes whose high expression was consistently associated with Tregs by recent scRNA-seq 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:0507_10.1101_2021.12.22.473889_9350d13595:claim:84312cd749263d1504b8
claim_id: claim:84312cd749263d1504b8
paper_key: hca:0507_10.1101_2021.12.22.473889_9350d13595
span_literal:
The SHH -expressing basal cells supported organoid generation in vitro and accurately predicted the differentiation trajectory from basal stem cells to terminally differentiated umbrella cells.

summary:
In Homo sapiens ureter, basal cells express SHH (Sonic Hedgehog), supporting organoid generation and predicting differentiation trajectory from basal stem cells to umbrella cells.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:c81829f17d07f275103f
claim_id: claim:c81829f17d07f275103f
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
we identified one cluster each for mast cells (cluster 13: KIT, TPSAB1 ), NK cells (cluster 3: KLRD1, CD247 ), and B cells (cluster 6: CD79A, JCHAIN )

summary:
In Homo sapiens ureter, mast cells are marked by KIT and TPSAB1, natural killer cells are marked by KLRD1 and CD247, and B cells are marked by CD79A and JCHAIN.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:a3e9b3de4af0f1096a85
claim_id: claim:a3e9b3de4af0f1096a85
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Higher levels of CD14 were observed in dendritic cells (cluster 7: HLA-DRA, HLA-DRB1 ) and macrophages (cluster 8: CD14, C1QA )

summary:
In Homo sapiens ureter, dendritic cells express higher levels of CD14 and are marked by HLA-DRA and HLA-DRB1.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:ed5d701b13c7c55e0770
claim_id: claim:ed5d701b13c7c55e0770
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Three CD14/CD68 -expressing monocyte clusters with high expression of ficolin 1 ( FCN1 ) were also identified, and they were further divided into classical (clusters 0 & 10: S100A8 , S100A9 ) and non-classical (cluster 12: MS4A7 , LILRB2 , SELPLG ) monocytes

summary:
In Homo sapiens ureter, classical monocytes are marked by FCN1, S100A8, and S100A9, while non-classical monocytes are marked by FCN1, MS4A7, LILRB2, and SELPLG.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:82bf0b39ae2683dd6010
claim_id: claim:82bf0b39ae2683dd6010
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Also amongst the T cell clusters were regulatory T (Treg) cells (cluster 11: FOXP3, CTLA4 ), central memory T (Tcm) cells (cluster 4: CCR7 ), and two clusters of tissue resident memory T (Trm) cells (clusters 2 & 14: ZNF683, CD69, ITGA1 ).

summary:
In Homo sapiens ureter, regulatory T cells are marked by FOXP3 and CTLA4, central memory T cells are marked by CCR7, and tissue resident memory T cells are marked by ZNF683, CD69, and ITGA1.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:f7b8def366bbd0498419
claim_id: claim:f7b8def366bbd0498419
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Expression of cytokines IFNG and TNF in cluster 14 Trm cells suggests that this cluster may have been recently activated.

summary:
In Homo sapiens ureter, a recently activated subset of tissue resident memory T cells expresses IFNG and TNF.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:94b72da899d9ab700de4
claim_id: claim:94b72da899d9ab700de4
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
We also identified two clusters of CD8 effector T cells, the GZMK + cluster 5 and the GZMH + cluster 9.

summary:
In Homo sapiens ureter, CD8 effector T cells include a GZMK-positive cluster and a GZMH-positive cluster.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:cca38ad737dc32e0889b
claim_id: claim:cca38ad737dc32e0889b
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Finally, we resolved a cluster of mucosal-associated invariant T (MAIT) cells (cluster 15: KLRB1, IL23R, IL18R1 ), which are innate-like T cells that play an important role in the antibacterial response

summary:
In Homo sapiens ureter, mucosal-associated invariant T cells are marked by KLRB1, IL23R, and IL18R1.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:f9d62940b16748382e15
claim_id: claim:f9d62940b16748382e15
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
we identified two PECAM1 + endothelial cell clusters, which could be separated into venous endothelial cells (cluster 1: NRP1, NRP2 ), and arterial endothelial cells (cluster 6: GJA5, BMX )

summary:
In Homo sapiens ureter, venous endothelial cells are marked by PECAM1, NRP1, and NRP2, and arterial endothelial cells are marked by PECAM1, GJA5, and BMX.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:591a0140450c2b2d0af8
claim_id: claim:591a0140450c2b2d0af8
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
summary: In Homo sapiens ureter, smooth muscle cells are marked by ACTA2 and MYH11.
span_literal:
We also identified one smooth muscle cell cluster (cluster 2: ACTA2, MYH11 ) and four distinct fibroblast clusters (clusters 0, 3, 4, and 5).


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:077fd71080efe4435e71
claim_id: claim:077fd71080efe4435e71
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 5 fibroblasts expressed the highest levels of COL1A1 and was the most distinct from the other fibroblasts based on its position on the UMAP.

summary:
In Homo sapiens ureter, periurothelial fibroblasts express the highest levels of COL1A1 among fibroblast subtypes.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:1a0d85a3b260ad25ca88
claim_id: claim:1a0d85a3b260ad25ca88
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
The major interstitial fibroblasts were identified by being LIF1 + /COL15A1 − and the periurothelial fibroblasts by LIF1 − /COL15A1 +

summary:
In Homo sapiens ureter, major interstitial fibroblasts are LIF1-positive and COL15A1-negative, while periurothelial fibroblasts are LIF1-negative and COL15A1-positive.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:ad022a1320b340bdc237
claim_id: claim:ad022a1320b340bdc237
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
The major interstitial fibroblasts were identified by being LIF1 + /COL15A1 − and the periurothelial fibroblasts by LIF1 − /COL15A1 +

summary:
In Homo sapiens ureter, periurothelial fibroblasts are LIF1-negative and COL15A1-positive, distinguished from major interstitial fibroblasts.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:16fd5d02126673ba0f05
claim_id: claim:16fd5d02126673ba0f05
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
summary: In Homo sapiens ureter, periurothelial fibroblasts are FOXF1-positive.
span_literal:
The periurothelial fibroblasts could also be visualized as FOXF1 + cells, which localized just below the urothelium, consistent with the spatial gene expression data


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:479083ff2c2493d7ebf9
claim_id: claim:479083ff2c2493d7ebf9
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
summary: In Homo sapiens ureter, intradetrusor fibroblasts express APOE and GPC3.
span_literal:
Finally, cluster 3 fibroblasts, which express APOE and GPC3 ( Figures 3B and S3E ), clearly stained for APOE and could be seen interspersed between the ACTA2 + smooth muscle bundles


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:c7257ac376c530d56f48
claim_id: claim:c7257ac376c530d56f48
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 4 umbrella cells were defined by high expression of UPK genes ( UPK1A, UPK2, UPK3A ) and labeled as UPK hi

summary:
In Homo sapiens ureter, UPK-high umbrella cells are defined by high expression of UPK1A, UPK2, and UPK3A.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:51b5b5fd49b450855639
claim_id: claim:51b5b5fd49b450855639
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
summary: In Homo sapiens ureter, FTL-high umbrella cells express KRT20 and low levels of uroplakin genes.
span_literal:
Conversely, cluster 7 cells expressed low levels of UPK genes but showed KRT20 , which is often used as a terminal differentiation marker


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:4c0bbdd950119417e5a3
claim_id: claim:4c0bbdd950119417e5a3
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Interestingly, cluster 7 umbrella cells expressed high levels of ferritin light ( FTL ) and heavy ( FTH1 ) chain genes.

summary:
In Homo sapiens ureter, FTL-high umbrella cells express high levels of ferritin light chain (FTL) and ferritin heavy chain 1 (FTH1).


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:65211258acc7c57e8bbd
claim_id: claim:65211258acc7c57e8bbd
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 0, which is the largest and most diffuse cluster, had very few distinguishing genes with the exception of cadherin-related family member 5 ( CDHR5 ).

summary:
In Homo sapiens ureter, CDHR5-positive intermediate cells are marked by cadherin-related family member 5 (CDHR5).


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:274ee1ec693bde44afb5
claim_id: claim:274ee1ec693bde44afb5
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 1 was defined by high expression of cellular retinoic acid-binding protein 2 ( CRABP2 ) and LY6/PLAUR domain containing 3 ( LYPD3 ).

summary:
In Homo sapiens ureter, CRABP2-high intermediate cells are defined by high expression of cellular retinoic acid-binding protein 2 (CRABP2) and LY6/PLAUR domain containing 3 (LYPD3).


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:a9fae9f66e38ce29bf80
claim_id: claim:a9fae9f66e38ce29bf80
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 5 showed high expression of FOXA1 transcription factor, which is involved in bladder differentiation ( DeGraff et al., 2012 ), and grainyhead like transcription factor 3 ( GRHL3 ), which drives terminal differentiation and barrier formation in the urothelium

summary:
In Homo sapiens ureter, FOXA1-high intermediate cells show high expression of FOXA1 and grainyhead like transcription factor 3 (GRHL3).


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:2c2c81277ec3db4893f5
claim_id: claim:2c2c81277ec3db4893f5
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 2 ( SHH hi ) had the highest proportion of sonic hedgehog signaling molecule ( SHH ) expressing cells

summary:
In Homo sapiens ureter, SHH-high basal cells have the highest proportion of sonic hedgehog signaling molecule (SHH)-expressing cells.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:1c06e0c103441a53ef68
claim_id: claim:1c06e0c103441a53ef68
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 3 ( JUN/FOS hi ) also contained a small number of SHH -expressing cells but was saliently marked by robust expression of JUN and FOS transcription factors.

summary:
In Homo sapiens ureter, JUN/FOS-high basal cells are marked by robust expression of JUN and FOS transcription factors.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:da0a2cd0ddfb522a6fcc
claim_id: claim:da0a2cd0ddfb522a6fcc
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
Cluster 6, the smallest of the KRT5 + basal cells, expressed high levels of proliferative genes including MKI67, PCLAF, TYMS, TK1, BIRC5 , and RRM2

summary:
In Homo sapiens ureter, MKI67-high basal cells express high levels of MKI67, PCLAF, TYMS, TK1, BIRC5, and RRM2.


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:46436d6d4a97e43195ea
claim_id: claim:46436d6d4a97e43195ea
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
span_literal:
the top marker gene for this cluster, growth arrest specific-1 ( GAS1 ), is an anti-mitogenic factor that mediates growth arrest of fibroblasts.

summary:
In Homo sapiens ureter, minor interstitial fibroblasts are marked by growth arrest specific-1 (GAS1).


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:faa569a2e7cd877314a8
claim_id: claim:faa569a2e7cd877314a8
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
summary: In Homo sapiens ureter, major interstitial fibroblasts are marked by Hyaluronan synthase 1 (HAS1).
span_literal:
the top cluster marker, Hyaluronan synthase 1 ( HAS1 ), is responsible for the production of hyaluronan, which is a key constituent of the extracellular matrix and is involved in cell migration, wound healing, and tissue repair


claim_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf:claim:3b47aecdf9de6327ee4a
claim_id: claim:3b47aecdf9de6327ee4a
paper_key: hca:0508_10.1016_j.devcel.2022.07.004_cfe769c9cf
summary: In Homo sapiens ureter, classical monocytes co-express intermediate markers BCL6 and STAT3.
span_literal:
Interestingly, cluster 0 classical monocytes appeared to co-express intermediate markers, including BCL6 and STAT3


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:ac923040f3ec21dff857
claim_id: claim:ac923040f3ec21dff857
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
we observed a cluster of nuclei enriched in α-cell-specific genes, namely cluster 1; a nuclear cluster enriched in SST and PPY genes, namely cluster 2; and a high INS and MAF bZIP transcription factor A ( MAFA) -expressing nuclear cluster (natural log of counts ≥ 5), namely cluster 3

summary:
In Homo sapiens, alpha cells in transplanted pancreatic islets are enriched in alpha-cell-specific genes in cluster 1, while beta cells express high levels of INS and MAFA.


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:700ff0c38b135e2f793d
claim_id: claim:700ff0c38b135e2f793d
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
we observed a cluster of nuclei enriched in α-cell-specific genes, namely cluster 1; a nuclear cluster enriched in SST and PPY genes, namely cluster 2; and a high INS and MAF bZIP transcription factor A ( MAFA) -expressing nuclear cluster (natural log of counts ≥ 5), namely cluster 3

summary:
In Homo sapiens, pancreatic islet delta cells and PP cells are enriched in SST and PPY genes, respectively, in cluster 2.


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:345e43f5d6aa0b82852c
claim_id: claim:345e43f5d6aa0b82852c
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
other β-cell marker genes, including ATP binding cassette subfamily C member 8 ( ABCC8 ) and solute carrier family 30 member 8 ( SLC30A8 ), were also expressed in cluster 0, which displayed low levels of INS expression

summary:
In Homo sapiens, beta cell marker genes include ATP binding cassette subfamily C member 8 (ABCC8) and solute carrier family 30 member 8 (SLC30A8).


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:762ab9acd555ae66ff9b
claim_id: claim:762ab9acd555ae66ff9b
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
cluster 0 was enriched in endocrine cell-specific genes, such as paired box 6 ( PAX6 ), suggesting that such clusters likely included β-cells in a different maturity state

summary:
In Homo sapiens, endocrine cells in pancreatic islets express paired box 6 (PAX6) as an endocrine cell-specific gene.


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:3c93fded3e3e27ae208e
claim_id: claim:3c93fded3e3e27ae208e
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
a cluster of nuclei enriched in ductal cell genes—including CF transmembrane conductance regulator ( CFTR) , SRY-box transcription factor 9 ( SOX9 ), and keratin 19 ( KRT19 ), was identified in cluster 4

summary:
In Homo sapiens, ductal cells in pancreatic islets are enriched in CF transmembrane conductance regulator (CFTR), SRY-box transcription factor 9 (SOX9), and keratin 19 (KRT19).


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:428a8cc8c77ac7f94135
claim_id: claim:428a8cc8c77ac7f94135
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
Cells and nuclei expressing high levels of INS gene (natural log of counts > 3) were distributed in clusters #3, while GCG -enriched cells/nuclei were distributed in clusters #1

summary:
In Homo sapiens, pancreatic islet beta cells express high levels of INS, while alpha cells are enriched in GCG.


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:d0c14a6459cf446ab33b
claim_id: claim:d0c14a6459cf446ab33b
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
Violin plots representing the expression levels of endocrine cell gene markers, including insulin ( INS ), glucagon ( GCG ), pancreatic polypeptide ( PPY ), or somatostatin ( SST ) in each nuclear cluster.

summary:
In Homo sapiens, endocrine cell gene markers in pancreatic islets include insulin (INS), glucagon (GCG), pancreatic polypeptide (PPY), and somatostatin (SST).


claim_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5:claim:a1cab3eb60376cb7a302
claim_id: claim:a1cab3eb60376cb7a302
paper_key: hca:0509_10.1186_s13073-021-00941-8_26def488c5
span_literal:
Violin plots representing the expression levels of β-cell gene markers, such as ABCC8 , SLC30A8 , MAFA , and endocrine markers, such as PAX6 within the nuclear clusters.

summary:
In Homo sapiens, beta cell gene markers include ABCC8, SLC30A8, and MAFA, while PAX6 is an endocrine cell marker in pancreatic islets.


claim_key: hca:0510_10.1101_2021.08.19.457030_7771c9367f:claim:af3ac2114d384be5ddc3
claim_id: claim:af3ac2114d384be5ddc3
paper_key: hca:0510_10.1101_2021.08.19.457030_7771c9367f
span_literal:
Markers representative of the three groups defining the pseudotime: pluripotency (POU5F1), Neural Ectoderm (LIX1) and Epidermal Ectoderm (PTN).

summary:
In Homo sapiens human induced pluripotent stem cells, POU5F1 is a marker of pluripotent cells, LIX1 is a marker of neural ectoderm cells, and PTN is a marker of epidermal ectoderm cells.


claim_key: hca:0510_10.1101_2021.08.19.457030_7771c9367f:claim:b9e4362a8d85c41d6c7a
claim_id: claim:b9e4362a8d85c41d6c7a
paper_key: hca:0510_10.1101_2021.08.19.457030_7771c9367f
span_literal: stem cell markers such as MYC, NANOG, SOX2 and POU5F1
summary:
In Homo sapiens, MYC, NANOG, SOX2, and POU5F1 are common stem cell markers of human induced pluripotent stem cells.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:861ca5747d247020f491
claim_id: claim:861ca5747d247020f491
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
BNC2 ( P = .0102), PBX3 ( P = .0021), RBFOX1 ( P = .0016), and TBX2 ( P = .0162) are largely restricted to CHAT+ neurons

summary:
In Homo sapiens, BNC2 is a positive marker of cholinergic neurons (CHAT-positive) in the colon myenteric plexus.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:7179c3546557aa6e6b3e
claim_id: claim:7179c3546557aa6e6b3e
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
PBX3 ( P = .0021), RBFOX1 ( P = .0016), and TBX2 ( P = .0162) are largely restricted to CHAT+ neurons

summary:
In Homo sapiens, PBX3 is a positive marker of cholinergic neurons (CHAT-positive) in the colon myenteric plexus.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:3c7907684a94dc42d971
claim_id: claim:3c7907684a94dc42d971
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal: RBFOX1 ( P = .0016), and TBX2 ( P = .0162) are largely restricted to CHAT+ neurons
summary:
In Homo sapiens, RBFOX1 is a positive marker of cholinergic neurons (CHAT-positive) in the colon myenteric plexus.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:082dc754784d9f267050
claim_id: claim:082dc754784d9f267050
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal: TBX2 ( P = .0089, n = 3) are primarily in CHAT+ neurons
summary:
In Homo sapiens, TBX2 is a positive marker of cholinergic neurons (CHAT-positive) in the colon myenteric plexus.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:2ea3d242f8fab9982c87
claim_id: claim:2ea3d242f8fab9982c87
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal: TBX3 impacts NOS1+ neurons
summary:
In Homo sapiens, TBX3 is a positive marker of nitrergic neurons (NOS1-positive) in the colon myenteric plexus. In Homo sapiens, TBX3 is primarily expressed in NOS1-positive nitrergic neurons in the adult enteric nervous system.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:07f6b2e14edf7ea5add3
claim_id: claim:07f6b2e14edf7ea5add3
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
Consistent with mouse data, ETV1 was most abundant in NOS1+ neurons, while RBFOX1 and BNC2 were enriched in NOS1 – neurons

summary:
In Homo sapiens, ETV1 is a positive marker of NOS1-positive nitrergic myenteric neurons in the colon.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:84d3e125172bc83460cb
claim_id: claim:84d3e125172bc83460cb
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
Consistent with mouse data, ETV1 was most abundant in NOS1+ neurons, while RBFOX1 and BNC2 were enriched in NOS1 – neurons

summary:
In Homo sapiens, RBFOX1 is a positive marker of NOS1-negative myenteric neurons in the colon. In Homo sapiens, BNC2 is a positive marker of NOS1-negative myenteric neurons in the colon.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:d59ad5c91dbbae247a83
claim_id: claim:d59ad5c91dbbae247a83
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
No POU3F3 staining was detectable in human small intestine submucosal plexus, whereas ( AD–AF , AP–AR ) clear nuclear POU3F3 staining could be seen in human colon submucosal neurons.

summary:
In Homo sapiens, POU3F3 is a positive marker of submucosal neurons in the colon, but is negative in small intestine submucosal plexus neurons.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:9d336c79b02b55d8b2a7
claim_id: claim:9d336c79b02b55d8b2a7
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
Quantification of ( Z ) CHAT+ and ( AA ) NOS1+ reveals that BNC2 ( P = .0102), PBX3 ( P = .0021), RBFOX1 ( P = .0016), and TBX2 ( P = .0162) are largely restricted to CHAT+ neurons in adult human ENS ( P values compare Transcription factor+EGFP+/Transcription factor+ vs EGFP+/Total neuron ratios).

summary:
In Homo sapiens, BNC2, PBX3, RBFOX1, and TBX2 are largely restricted to cholinergic (CHAT-positive) neurons in the adult enteric nervous system.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:30dad0812900d15be1cb
claim_id: claim:30dad0812900d15be1cb
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
summary: In Homo sapiens, POU3F3 is a negative marker of small bowel submucosal neurons.
span_literal:
Human small bowel submucosal neurons lacked POU3F3, but some small bowel myenteric neurons had cytoplasmic POU3F3 immunoreactivity of uncertain significance


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:ce8c1b1682e09c197c2a
claim_id: claim:ce8c1b1682e09c197c2a
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
summary: In Homo sapiens, TBX3, PBX3, and TBX2 are positive markers of subsets of enteric neurons.
span_literal:
Immunohistochemistry confirmed that TBX3, PBX3, and TBX2 are also present in subsets of human enteric neurons as predicted by mouse data.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:7957109074166fd70b27
claim_id: claim:7957109074166fd70b27
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
Guided by RNA-seq, we found that ETV1 was more abundant in human nitrergic neurons, while RBFOX1 and BNC2 were enriched in non-nitrergic neurons, suggesting that subtype-specific genes may be conserved between humans and mice.

summary:
In Homo sapiens, ETV1 is a positive marker of nitrergic neurons, while RBFOX1 and BNC2 are enriched in non-nitrergic neurons.


claim_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7:claim:82ecc6dd68fa7b3d0c10
claim_id: claim:82ecc6dd68fa7b3d0c10
paper_key: hca:0511_10.1016_j.jcmgh.2020.12.014_7220e03ee7
span_literal:
Guided by RNA-seq, we found that ETV1 was more abundant in human nitrergic neurons, while RBFOX1 and BNC2 were enriched in non-nitrergic neurons, suggesting that subtype-specific genes may be conserved between humans and mice.

summary:
In Homo sapiens, RBFOX1 is a positive marker of non-nitrergic neurons compared with nitrergic neurons. In Homo sapiens, BNC2 is a positive marker of non-nitrergic neurons compared with nitrergic neurons.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:3a42e09e7d70dc712f9a
claim_id: claim:3a42e09e7d70dc712f9a
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: PαC clusters express PDGFRA (G), KCNN3 (H), and P2YR1 (I).
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells express PDGFRA, KCNN3, and P2RY1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:c681a0e8ea8fdcde99fa
claim_id: claim:c681a0e8ea8fdcde99fa
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: PαCs were identified based on PDGFRA expression.
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells are identified based on PDGFRA expression.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:df5a346969e3f3a9cc1f
claim_id: claim:df5a346969e3f3a9cc1f
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
Cell identity was confirmed using canonical markers for SMC ( MYH11 , ACTG2 , ACTA2 ), ICC ( KIT , ANO1 ), and PαC ( KCNN3, PDGFRA ).

summary:
In Homo sapiens, smooth muscle cell identity was confirmed using canonical markers MYH11, ACTG2, and ACTA2.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:01b20dc3465a168ac99b
claim_id: claim:01b20dc3465a168ac99b
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
Cell identity was confirmed using canonical markers for SMC ( MYH11 , ACTG2 , ACTA2 ), ICC ( KIT , ANO1 ), and PαC ( KCNN3, PDGFRA ).

summary:
In Homo sapiens, interstitial cell of Cajal identity was confirmed using canonical markers KIT and ANO1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:c4e67cf1904316ae686b
claim_id: claim:c4e67cf1904316ae686b
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
Cell identity was confirmed using canonical markers for SMC ( MYH11 , ACTG2 , ACTA2 ), ICC ( KIT , ANO1 ), and PαC ( KCNN3, PDGFRA ).

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cell identity was confirmed using canonical markers KCNN3 and PDGFRA.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:fc9975a2aa72a5171edd
claim_id: claim:fc9975a2aa72a5171edd
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
Genes most abundantly and differentially expressed in SMC are canonical smooth muscle genes ( ACTG2, MYH11, TAGLN, ACTA2, MYL9, TPM2, CNN1 ) of the contractile apparatus.

summary:
In Homo sapiens, smooth muscle cells most abundantly and differentially express canonical smooth muscle genes ACTG2, MYH11, TAGLN, ACTA2, MYL9, TPM2, and CNN1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:b6cb512ff9846053406a
claim_id: claim:b6cb512ff9846053406a
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
Several ion channels ( CACNA1C, KCNMA1, RYR2, CACNB2, KCNAB1 ) and cholinergic G protein–coupled receptors ( CHRM2, CHRM3 ) are much more abundant in SMC compared with all other cell types

summary:
In Homo sapiens, smooth muscle cells express CACNA1C, KCNMA1, RYR2, CACNB2, KCNAB1, CHRM2, and CHRM3 at much higher levels compared with all other cell types.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:89fc9819ea4c6cab5fe1
claim_id: claim:89fc9819ea4c6cab5fe1
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
ICC express relatively high levels of ion channels ( KCNIP4 , ANO1 , KCND2 , CACNB2 , CACNA2D3 , TRPC4 ) and cholinergic muscarinic receptor CHRM3

summary:
In Homo sapiens, interstitial cells of Cajal express relatively high levels of ion channels KCNIP4, ANO1, KCND2, CACNB2, CACNA2D3, TRPC4, and cholinergic muscarinic receptor CHRM3.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:e4344453abac04702411
claim_id: claim:e4344453abac04702411
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: Combined PαC cluster prominently expresses ion channels ( KCNN3 , SCN7A , PIEZO2 , and GRIA4 ).
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells prominently express ion channels KCNN3, SCN7A, PIEZO2, and GRIA4.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:032ea2ffc69622c6d81e
claim_id: claim:032ea2ffc69622c6d81e
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
PαC highly differentially express neurotransmitter receptor VIPR2 (Fold change 4.32), not previously reported, and express relatively high levels of GUCY1A3 (Fold change 5.23), which is activated by nitric oxide

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells highly differentially express neurotransmitter receptor VIPR2 and express relatively high levels of GUCY1A3.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:911bf7df7c450c57720a
claim_id: claim:911bf7df7c450c57720a
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
well-known PαC marker KCNN3 is the fourth-most differentially expressed gene in PαCs compared with all other cells.

summary:
In Homo sapiens, KCNN3 is a well-known marker of platelet-derived growth factor receptor alpha cells and is the fourth-most differentially expressed gene compared with all other cells.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:5d25f69a3841d0307916
claim_id: claim:5d25f69a3841d0307916
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
PαC clusters express high levels of many genes encoding ECM components or ECM remodeling proteins (16 of the top 50 most differentially expressed genes; Figure 3 C, Figure A4 C). These include MGP , DPT , FBLN1 , SVEP1 , DCN , GPC6 , LUM , KAZN , COL6A3 , COL5A2 , COL3A1 , SULF1 , TNXB , MMP16 , LAMA2 , and LAMB1 .

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells express high levels of extracellular matrix component and remodeling genes including MGP, DPT, FBLN1, SVEP1, DCN, GPC6, LUM, KAZN, COL6A3, COL5A2, COL3A1, SULF1, TNXB, MMP16, LAMA2, and LAMB1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:71849e81f7e52c63ff4a
claim_id: claim:71849e81f7e52c63ff4a
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
ICC and PαC differentially express relatively high levels of mechanosensitive channels ( PIEZO2 in ICC and PαC, and TMEM150C in ICC; Figure A6 B and C).

summary:
In Homo sapiens, interstitial cells of Cajal differentially express relatively high levels of mechanosensitive channels PIEZO2 and TMEM150C.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:a7e8d15eda5c8b8b80ed
claim_id: claim:a7e8d15eda5c8b8b80ed
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
ICC and PαC differentially express relatively high levels of mechanosensitive channels ( PIEZO2 in ICC and PαC, and TMEM150C in ICC; Figure A6 B and C).

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells differentially express relatively high levels of mechanosensitive channel PIEZO2.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:7ff49ea161a0c0687c0a
claim_id: claim:7ff49ea161a0c0687c0a
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: This shared subset includes FOS , MEIS1 , MEIS2 , PBX1 , SCMH1 , and ZBTB16 .
summary:
In Homo sapiens, smooth muscle cells, interstitial cells of Cajal, and platelet-derived growth factor receptor alpha cells share expression of transcriptional regulators FOS, MEIS1, MEIS2, PBX1, SCMH1, and ZBTB16.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:c676c20f6480b87bfd79
claim_id: claim:c676c20f6480b87bfd79
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: This shared subset includes FOS , MEIS1 , MEIS2 , PBX1 , SCMH1 , and ZBTB16 .
summary:
In Homo sapiens, interstitial cells of Cajal share expression of transcriptional regulators FOS, MEIS1, MEIS2, PBX1, SCMH1, and ZBTB16 with other SIP syncytium cells.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:dd6edb0712cb445f3b0c
claim_id: claim:dd6edb0712cb445f3b0c
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: This shared subset includes FOS , MEIS1 , MEIS2 , PBX1 , SCMH1 , and ZBTB16 .
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells share expression of transcriptional regulators FOS, MEIS1, MEIS2, PBX1, SCMH1, and ZBTB16 with other SIP syncytium cells.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:c784ee0638b6377ee11c
claim_id: claim:c784ee0638b6377ee11c
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
These include tyrosine kinase growth factor receptors FGFR2 and IGF1R preferentially expressed in SMCs, and FGFR1 , NTRK2 , and KIT preferentially expressed in ICCs.

summary:
In Homo sapiens, smooth muscle cells preferentially express tyrosine kinase growth factor receptors FGFR2 and IGF1R.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:a0b5997f35e0186c0fd6
claim_id: claim:a0b5997f35e0186c0fd6
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: PαCs preferentially express PDGFRA (by definition) and FGFR1 , GHR , and CNTFR .
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells preferentially express PDGFRA, FGFR1, GHR, and CNTFR.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:ea9993174b64e8aae382
claim_id: claim:ea9993174b64e8aae382
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
In particular, vasoactive intestinal peptide receptor VIPR2 , calcitonin receptor CALCRL , and adrenergic receptor ADRA1A are preferentially expressed in PαCs, whereas acetylcholine receptors CHRM2 and CHRM3 and calcitonin gene–related peptide (CGRP) receptor RAMP1 are preferentially expressed in SMCs.

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells preferentially express vasoactive intestinal peptide receptor VIPR2, calcitonin receptor-like CALCRL, and adrenergic receptor ADRA1A.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:c9b72cc07145751b03d6
claim_id: claim:c9b72cc07145751b03d6
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
In particular, vasoactive intestinal peptide receptor VIPR2 , calcitonin receptor CALCRL , and adrenergic receptor ADRA1A are preferentially expressed in PαCs, whereas acetylcholine receptors CHRM2 and CHRM3 and calcitonin gene–related peptide (CGRP) receptor RAMP1 are preferentially expressed in SMCs.

summary:
In Homo sapiens, smooth muscle cells preferentially express acetylcholine receptors CHRM2 and CHRM3 and calcitonin gene-related peptide receptor RAMP1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:12bd008f77c79f0cec90
claim_id: claim:12bd008f77c79f0cec90
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: Interestingly, PαCs express KITLG , a trophic factor that activates KIT to support ICCs survival.
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells express KITLG, a trophic factor that activates KIT to support interstitial cells of Cajal survival.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:59057afb2c56c361d53f
claim_id: claim:59057afb2c56c361d53f
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
we compared PαC clusters against the fibroblasts (identified by MEOX2 , COL1A2 , COL1A1 , FM O 1 , LSP1, and VIM ) in our data set.

summary:
In Homo sapiens, fibroblasts are identified by expression of MEOX2, COL1A2, COL1A1, FMO1, LSP1, and VIM.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:e5b7387b7baa21fd4339
claim_id: claim:e5b7387b7baa21fd4339
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
Our data also show for the first time high expression of vasoactive intestinal peptide receptor 2 ( VIPR2 ) in PαC

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells show high expression of vasoactive intestinal peptide receptor 2 (VIPR2) for the first time.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:0ea0358d14fd21048f42
claim_id: claim:0ea0358d14fd21048f42
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
In addition, we detected relatively high levels of CGRP co-receptors CALCRL in PαCs and RAMP1 in SMCs.

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells express relatively high levels of calcitonin gene-related peptide co-receptor CALCRL, and smooth muscle cells express relatively high levels of RAMP1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:b798ef52e218390728df
claim_id: claim:b798ef52e218390728df
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
In addition, we detected relatively high levels of CGRP co-receptors CALCRL in PαCs and RAMP1 in SMCs.

summary:
In Homo sapiens, smooth muscle cells express relatively high levels of calcitonin gene-related peptide co-receptor RAMP1.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:5eb2922d72b882968eb5
claim_id: claim:5eb2922d72b882968eb5
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal: our human data show THBS4 at relatively high levels in PαC (3.16-fold higher than all other cells)
summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells express THBS4 at relatively high levels, 3.16-fold higher than all other cells.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:5aa62ca13a5629fa1c98
claim_id: claim:5aa62ca13a5629fa1c98
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
all SIP syncytium cells express high levels of 6 transcriptional regulators relative to other cells ( MEIS1 , MEIS2, PBX1, FOS, ZBTB16, and SCMH1 ; Figure 4 E and F).

summary:
In Homo sapiens, smooth muscle cells express high levels of transcriptional regulators MEIS1, MEIS2, PBX1, FOS, ZBTB16, and SCMH1 relative to other cells.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:37410bc7db7161bb2039
claim_id: claim:37410bc7db7161bb2039
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
all SIP syncytium cells express high levels of 6 transcriptional regulators relative to other cells ( MEIS1 , MEIS2, PBX1, FOS, ZBTB16, and SCMH1 ; Figure 4 E and F).

summary:
In Homo sapiens, interstitial cells of Cajal express high levels of transcriptional regulators MEIS1, MEIS2, PBX1, FOS, ZBTB16, and SCMH1 relative to other cells.


claim_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db:claim:96558575e1b574a6bfda
claim_id: claim:96558575e1b574a6bfda
paper_key: hca:0512_10.1016_j.gastha.2022.12.004_3866b352db
span_literal:
all SIP syncytium cells express high levels of 6 transcriptional regulators relative to other cells ( MEIS1 , MEIS2, PBX1, FOS, ZBTB16, and SCMH1 ; Figure 4 E and F).

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha cells express high levels of transcriptional regulators MEIS1, MEIS2, PBX1, FOS, ZBTB16, and SCMH1 relative to other cells.


claim_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5:claim:470b821bcf419199d2c1
claim_id: claim:470b821bcf419199d2c1
paper_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5
span_literal:
Dividing B cells potentially undergoing affinity maturation were annotated by the expression of AICDA and detected with a frequency of 0.5% (437 cells).

summary:
In Homo sapiens spleen, dividing B cells potentially undergoing affinity maturation are marked by expression of AICDA.


claim_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5:claim:79a529136169e048aebc
claim_id: claim:79a529136169e048aebc
paper_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5
span_literal:
This results in the differential expression of the marker AGER and surfactant-protein encoding genes SFTPB, SFTPA1, and SFTPA2.

summary:
In Homo sapiens lung, pulmonary alveolar cells are marked by expression of AGER, SFTPB, SFTPA1, and SFTPA2.


claim_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5:claim:31a7ef544bf03b151070
claim_id: claim:31a7ef544bf03b151070
paper_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5
summary: In Homo sapiens lung, blood vessel endothelial cells are marked by expression of VWF and PECAM1.
span_literal:
Other genes with high fold changes between bulk and sc-pseudo-bulk lung are blood vessel endothelial markers VWF and PECAM1.


claim_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5:claim:f69b238b45d4234f108f
claim_id: claim:f69b238b45d4234f108f
paper_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5
span_literal:
In the esophagus, stromal-specific genes FLNA and MYH11 and both KRT4 and KRT5, expressed in the majority of keratinocytes, are higher in bulk vs sc-pseudo-bulk.

summary:
In Homo sapiens esophagus, stromal cells are marked by expression of FLNA and MYH11, and keratinocytes are marked by expression of KRT4 and KRT5.


claim_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5:claim:9e21da9e747a87404955
claim_id: claim:9e21da9e747a87404955
paper_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5
span_literal:
In the spleen, the list of top genes includes APOE, CD5L, VCAM1, HMOX1, C1QA, and C1QC, which are strongly expressed in macrophages.

summary:
In Homo sapiens spleen, macrophages are marked by strong expression of APOE, CD5L, VCAM1, HMOX1, C1QA, and C1QC.


claim_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5:claim:aa11f2ad9ec7c8cadfb4
claim_id: claim:aa11f2ad9ec7c8cadfb4
paper_key: hca:0513_10.1186_s13059-019-1906-x_0a4cb34cd5
summary: In Homo sapiens spleen, plasma cells are marked by expression of JCHAIN, IGHA1, and IGLC3.
span_literal:
For example, in the spleen, the plasma cell-specific genes such as JCHAIN, IGHA1, and IGLC3 are high in ambient RNA (Additional file 1 : Figure S19) and are also overrepresented in the cold storage signature.


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:1b7e881bc2e0ea2f1be9
claim_id: claim:1b7e881bc2e0ea2f1be9
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
span_literal:
ZO-1 was weak but detectable on Fib surfaces and neatly lined tight junctions in likely iRPE and iPSC.RPE cell junctions. S100A4 labeled Fib, and before bulk passage a distinct layer of S100A4+ Fib underlay the BEST1: :EGFP+ RPE65+ iRPE colonies that had neat ZO-1 junctions

summary:
In Homo sapiens, S100A4 is a positive marker of fibroblasts, while ZO-1 (TJP1) lines tight junctions in retinal pigment epithelium-like cells.


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:aadbc4a18508470de52e
claim_id: claim:aadbc4a18508470de52e
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
span_literal: Fib-specific marker S100A4
summary:
In Homo sapiens, S100A4 is a fibroblast-specific marker, while RPE65 is a retinal pigment epithelium-specific marker.


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:1dbd9db62c002de25a0b
claim_id: claim:1dbd9db62c002de25a0b
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
span_literal:
we could generate high numbers of cells resembling RPE with important markers such as RPE65, LHX2, TYRP1, and ZO-1 in tight junctions with gross similarity to model RPE cells

summary:
In Homo sapiens, retinal pigment epithelium cells express important markers RPE65, LHX2, TYRP1, and ZO-1 (TJP1).


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:d223db214111dae74ac4
claim_id: claim:d223db214111dae74ac4
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
span_literal:
We compared iRPE to iRPENC and found that a distinct iRPENC subpopulation was the most enriched for BEST1:: EGFP counts and important RPE features ( CRX, TYR, MERTK, LHX2 )

summary:
In Homo sapiens, retinal pigment epithelium cells are characterized by important features including CRX, TYR, MERTK, and LHX2.


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:684c15308e3619e92e51
claim_id: claim:684c15308e3619e92e51
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
span_literal:
we checked expression for RPE markers ( CRX, TYR, RLBP1, RPE65, BEST1, RAX ) and found relatively comparable expression between the RPE models and iRPENC.HQ

summary:
In Homo sapiens, retinal pigment epithelium cells express markers CRX, TYR, RLBP1, RPE65, BEST1, and RAX.


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:8d46868a343a005e50e3
claim_id: claim:8d46868a343a005e50e3
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
span_literal:
Interestingly, the HQ1 and HQ2 fraction of cells predominately expressed SERPINF1 (PEDF) and VEGFA (VEGF)

summary:
In Homo sapiens, high-quality induced retinal pigment epithelium-like cells predominantly express SERPINF1 (pigment epithelium-derived factor) and VEGFA (vascular endothelial growth factor A).


claim_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f:claim:bc88867846004c3a3396
claim_id: claim:bc88867846004c3a3396
paper_key: hca:0514_10.1016_j.stemcr.2021.12.008_8ef526797f
summary: In Homo sapiens, BSG is an apical marker of retinal pigment epithelium cells.
span_literal:
We found that the apical RPE marker BSG ( Deora et al., 2004 ) had labeled the apical face of the RPE cell layer opposite the basal choroid


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:0926b99c560dc7590473
claim_id: claim:0926b99c560dc7590473
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
All three subsets displayed gene expression profiles typical for type 1 immune cells (lymphotoxin β, IFN-γ, and STAT4), regulatory T (T reg) cells (TGF-β, STAT5, and CCR4), and regulators of hematopoietic stem/progenitor cell self-renewal (TGF-β; Fig. 1 H ).

summary:
In Homo sapiens, fetal skin T cell subsets including double-positive αβγδ T cells display gene expression of lymphotoxin beta, interferon gamma, and STAT4 typical for type 1 immune cells, and TGF-beta, STAT5, and CCR4 typical for regulatory T cells.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:dda70338b536352fba35
claim_id: claim:dda70338b536352fba35
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
All three subsets displayed gene expression profiles typical for type 1 immune cells (lymphotoxin β, IFN-γ, and STAT4), regulatory T (T reg) cells (TGF-β, STAT5, and CCR4), and regulators of hematopoietic stem/progenitor cell self-renewal (TGF-β; Fig. 1 H ).

summary:
In Homo sapiens, fetal skin T cell subsets display gene expression of TGF-beta, STAT5, and CCR4 typical for regulatory T cells.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:811cb2cb2dd2234a1e6b
claim_id: claim:811cb2cb2dd2234a1e6b
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
In line with this, some genes are exclusively expressed in SP (IL-7, CCR8, and TGF-α) and DP T cells (IL-18 and TWIST1; Fig. 1 I ).

summary:
In Homo sapiens, single-positive T cells exclusively express IL-7, CCR8, and TGF-alpha compared to double-positive αβγδ T cells in fetal skin.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:468921506daed30540bf
claim_id: claim:468921506daed30540bf
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
In line with this, some genes are exclusively expressed in SP (IL-7, CCR8, and TGF-α) and DP T cells (IL-18 and TWIST1; Fig. 1 I ).

summary:
In Homo sapiens, double-positive αβγδ T cells exclusively express IL-18 and TWIST1 compared to single-positive T cells in fetal skin.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:9cccce0ad444499f30a2
claim_id: claim:9cccce0ad444499f30a2
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
DP αβγδ skin T cells expressed surface markers that are characteristic for naive T cells and recent thymic emigrants (CD45RA and CD31), hematopoietic stem cells (CD34 and CD38), and T cell progenitors (CD62L and CCR7; Fig. 3 L and Fig. S3, A and B ).

summary:
In Homo sapiens, double-positive αβγδ T cells express CD45RA and CD31, which are characteristic for naive T cells and recent thymic emigrants.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:0e3bc46723c202ad5d20
claim_id: claim:0e3bc46723c202ad5d20
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
DP αβγδ skin T cells expressed surface markers that are characteristic for naive T cells and recent thymic emigrants (CD45RA and CD31), hematopoietic stem cells (CD34 and CD38), and T cell progenitors (CD62L and CCR7; Fig. 3 L and Fig. S3, A and B ).

summary:
In Homo sapiens, double-positive αβγδ T cells express CD34 and CD38, which are characteristic for hematopoietic stem cells.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:cc376652d7dea3162238
claim_id: claim:cc376652d7dea3162238
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
DP αβγδ skin T cells expressed surface markers that are characteristic for naive T cells and recent thymic emigrants (CD45RA and CD31), hematopoietic stem cells (CD34 and CD38), and T cell progenitors (CD62L and CCR7; Fig. 3 L and Fig. S3, A and B ).

summary:
In Homo sapiens, double-positive αβγδ T cells express CD62L and CCR7, which are characteristic for T cell progenitors.


claim_key: hca:0515_10.1084_jem.20201189_d8d9a9e257:claim:16f154413edfbecd4d9f
claim_id: claim:16f154413edfbecd4d9f
paper_key: hca:0515_10.1084_jem.20201189_d8d9a9e257
span_literal:
Of note, gene expression of other costimulatory molecules was identified in DP αβγδ T cells (CD40L and CD99), while coinhibitory genes (CTLA-4 and PD1) were hardly ever expressed (data not shown).

summary:
In Homo sapiens, double-positive αβγδ T cells express the costimulatory molecules CD40L and CD99, while the coinhibitory genes CTLA-4 and PD1 are hardly ever expressed.


