# claims

claim_key: hca:0096_10.1126_sciadv.abo2467_05989af98e:claim:a4b3c4e85b9c877b29e7
claim_id: claim:a4b3c4e85b9c877b29e7
paper_key: hca:0096_10.1126_sciadv.abo2467_05989af98e
span_literal:
Subclustering of neuronal populations allowed the annotation of dopaminergic neurons (DopaNs; TH and SLC6A3 ) as a distinct cluster from GABAergic neurons (GabaNs; GAD1 and GAD2 )

summary:
In Homo sapiens substantia nigra, dopaminergic neurons are marked by TH and SLC6A3, distinguishing them from GABAergic neurons.


claim_key: hca:0096_10.1126_sciadv.abo2467_05989af98e:claim:859ee1467080c458edb8
claim_id: claim:859ee1467080c458edb8
paper_key: hca:0096_10.1126_sciadv.abo2467_05989af98e
span_literal:
Subclustering of neuronal populations allowed the annotation of dopaminergic neurons (DopaNs; TH and SLC6A3 ) as a distinct cluster from GABAergic neurons (GabaNs; GAD1 and GAD2 )

summary:
In Homo sapiens substantia nigra, GABAergic neurons are marked by GAD1 and GAD2, distinguishing them from dopaminergic neurons.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:6da9d87c71c4af80b5d6
claim_id: claim:6da9d87c71c4af80b5d6
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal: We then used the DG marker PROX1 to subclassify the ExN as DG ExN or non-DG ExN.
summary:
In Homo sapiens, PROX1 is a marker of dentate gyrus excitatory neurons used to distinguish them from non-dentate gyrus excitatory neurons in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:fce44f217f96f5f8cd7f
claim_id: claim:fce44f217f96f5f8cd7f
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
The InN were further subclassified as being derived from the medial or caudal ganglionic eminence (MGE or CGE) on the basis of LHX6 and NR2F2 expression (Fig. 1a–d ).

summary:
In Homo sapiens, inhibitory neurons derived from the medial ganglionic eminence are marked by LHX6 expression in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:5a4cb27d3f94c2beaf2d
claim_id: claim:5a4cb27d3f94c2beaf2d
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
The InN were further subclassified as being derived from the medial or caudal ganglionic eminence (MGE or CGE) on the basis of LHX6 and NR2F2 expression (Fig. 1a–d ).

summary:
In Homo sapiens, inhibitory neurons derived from the caudal ganglionic eminence are marked by NR2F2 expression in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:dacf98d122808cf00ac6
claim_id: claim:dacf98d122808cf00ac6
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
summary: In Homo sapiens, ASCL1 was used as a marker of progenitor cells in the developing hippocampus.
span_literal:
The markers ASCL1, NEUROD2, GAD1, OLIG2, MBP, AQP4, SPARC and PTPRC were used to hippocampal cells as progenitor cells, excitatory neurons, inhibitory neurons, OPCs, oligodendrocytes, astrocytes, endothelial cells and microglia, respectively.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:9c8ec7114bf5421f25f8
claim_id: claim:9c8ec7114bf5421f25f8
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
summary:
In Homo sapiens, OLIG2 was used as a marker of oligodendrocyte progenitor cells in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:156d69773c135c30fb32
claim_id: claim:156d69773c135c30fb32
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
EOMES + , MEIS2 + and NEUROD2 + progenitors were in clusters P3 and P4, indicative of ExN generation (Extended Data Fig. 3a ).

summary:
In Homo sapiens, EOMES, MEIS2, and NEUROD2 mark progenitor cells in clusters P3 and P4 that are indicative of excitatory neuron generation in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:be21629b22833364adfb
claim_id: claim:be21629b22833364adfb
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
AQP4 , OLIG1 / OLIG2 and PDGFRA were highly expressed in clusters P5, P6 and P7, respectively, indicative of astrocyte and oligodendrocyte cell fates.

summary:
In Homo sapiens, AQP4 is highly expressed in progenitor cluster P5 indicative of astrocyte fate, while OLIG1, OLIG2, and PDGFRA are highly expressed in progenitor clusters P6 and P7 indicative of oligodendrocyte fate in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:3b994dc7cc9118a2c537
claim_id: claim:3b994dc7cc9118a2c537
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
Cluster P8 contained a small number of progenitors that highly expressed DLX1 and DLX2 , indicating that these cells may differentiate as InN (Extended Data Fig. 3a–f ).

summary:
In Homo sapiens, progenitor cluster P8 highly expresses DLX1 and DLX2, indicating these progenitor cells may differentiate as inhibitory neurons in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:40bd94a5673dbeeb3113
claim_id: claim:40bd94a5673dbeeb3113
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
SEMA5A and PID1 were selected as marker genes for DG and CA1, respectively, while SULF2 and NRIP3 were considered as CA3 markers (Fig. 3c , Extended Data Fig. 6b ).

summary:
In Homo sapiens, SEMA5A is a marker gene for dentate gyrus excitatory neurons in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:7ded163d2ffb0a10174d
claim_id: claim:7ded163d2ffb0a10174d
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
SEMA5A and PID1 were selected as marker genes for DG and CA1, respectively, while SULF2 and NRIP3 were considered as CA3 markers (Fig. 3c , Extended Data Fig. 6b ).

summary:
In Homo sapiens, PID1 is a marker gene for cornu ammonis 1 excitatory neurons in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:f70789ae164a3b64695a
claim_id: claim:f70789ae164a3b64695a
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
SEMA5A and PID1 were selected as marker genes for DG and CA1, respectively, while SULF2 and NRIP3 were considered as CA3 markers (Fig. 3c , Extended Data Fig. 6b ).

summary:
In Homo sapiens, SULF2 and NRIP3 are marker genes for cornu ammonis 3 excitatory neurons in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:3f9c6d80f0bcfdd5f13a
claim_id: claim:3f9c6d80f0bcfdd5f13a
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
Notably, monocle analysis suggested that the majority of MGE-derived InN ( LHX6 + ) and CGE-derived InN ( NR2F1/2 + ) were separated (Fig. 3k , Extended Data Fig. 7a–c ).

summary:
In Homo sapiens, medial ganglionic eminence-derived inhibitory neurons are marked by LHX6 expression in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:dfb60869b76a2e235a36
claim_id: claim:dfb60869b76a2e235a36
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
Notably, monocle analysis suggested that the majority of MGE-derived InN ( LHX6 + ) and CGE-derived InN ( NR2F1/2 + ) were separated (Fig. 3k , Extended Data Fig. 7a–c ).

summary:
In Homo sapiens, caudal ganglionic eminence-derived inhibitory neurons are marked by NR2F1/NR2F2 expression in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:f2903a1bf088e0a065ed
claim_id: claim:f2903a1bf088e0a065ed
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
The pseudo-time analysis demonstrated that InN expressing CCK , CALB2 and VIP accumulated in the CGE differentiation path, and the majority of SATB1 + and SST + neurons were in the MGE path (Fig. 3l , Extended Data Fig. 7b, c ).

summary:
In Homo sapiens, inhibitory neurons expressing CCK, CALB2, and VIP accumulate in the caudal ganglionic eminence differentiation path in the developing hippocampus.


claim_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353:claim:5d774201b8ee09cf5040
claim_id: claim:5d774201b8ee09cf5040
paper_key: hca:0097_10.1038_s41586-019-1917-5_7f634d5353
span_literal:
The pseudo-time analysis demonstrated that InN expressing CCK , CALB2 and VIP accumulated in the CGE differentiation path, and the majority of SATB1 + and SST + neurons were in the MGE path (Fig. 3l , Extended Data Fig. 7b, c ).

summary:
In Homo sapiens, the majority of SATB1-positive and SST-positive inhibitory neurons are in the medial ganglionic eminence differentiation path in the developing hippocampus.


claim_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0:claim:c06a09be5064c8c0fca4
claim_id: claim:c06a09be5064c8c0fca4
paper_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0
summary: In Homo sapiens, monocyte-derived alveolar macrophages are characterized by CCL2 expression.
span_literal:
Four clusters of monocyte-derived alveolar macrophages (MoAM) were characterized by CCL2 expression and gradually increasing expression of genes associated with alveolar macrophage maturation.


claim_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0:claim:751481c8700344933b86
claim_id: claim:751481c8700344933b86
paper_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0
span_literal:
In patients with COVID-19, genes distinguishing infected TRAM2 from non-infected TRAM1 included several chemokines and cytokines important for T cell and monocyte recruitment, such as CCL4, CCL20 , CXCL10 and CXCL11.

summary:
In Homo sapiens, tissue-resident alveolar macrophage 2 is distinguished from tissue-resident alveolar macrophage 1 by expression of CCL4, CCL20, CXCL10, and CXCL11.


claim_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0:claim:088687f4d2623a98b5e9
claim_id: claim:088687f4d2623a98b5e9
paper_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0
summary: In Homo sapiens, T cells express interferon gamma (IFNG) in patients with COVID-19.
span_literal:
expression of type II interferon ( IFNG ) was detected in T cells from all 10 patients with COVID-19


claim_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0:claim:e15784b23580f1b49607
claim_id: claim:e15784b23580f1b49607
paper_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0
span_literal:
DC1 – conventional dendritic cells type 1, CLEC9A +; DC2 – conventional dendritic cells type 2, CD1C +; Migratory DC – migratory dendritic cells, CCR7 +; pDC – plasmacytoid dendritic cells, CLEC4C +

summary:
In Homo sapiens, conventional dendritic cell type 1 is marked by CLEC9A, conventional dendritic cell type 2 is marked by CD1C, migratory dendritic cell is marked by CCR7, and plasmacytoid dendritic cell is marked by CLEC4C.


claim_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0:claim:4589c51f2d9150262086
claim_id: claim:4589c51f2d9150262086
paper_key: hca:0098_10.1038_s41586-020-03148-w_f50cb505c0
span_literal:
Cluster 1 also included genes encoding the chemokines CCL7 , CCL8 , and CCL13, which drive recruitment of monocytes and T cells.

summary:
In Homo sapiens, alveolar macrophages from COVID-19 patients upregulate CCL7, CCL8, and CCL13, which drive recruitment of monocytes and T cells.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:fa82b8d707349effef2f
claim_id: claim:fa82b8d707349effef2f
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Among T cells, we identified two CCR7 + , SELL + , KLF2 + ( 21 ), CD3D + populations, one corresponding to central memory cells (Tcm) with elevated CD69 and CD45RO protein epitope expression (CITE-seq data) and one smaller cluster representing a naïve T cell population with high CD45RA protein expression

summary:
In Homo sapiens skin, central memory T cells are marked by positive expression of CCR7, SELL, KLF2, CD3D, CD69, and CD45RO, while naïve T cells are marked by CCR7, SELL, KLF2, CD3D, and CD45RA.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:6cff0c58104b86aa2523
claim_id: claim:6cff0c58104b86aa2523
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Among T cells, we identified two CCR7 + , SELL + , KLF2 + ( 21 ), CD3D + populations, one corresponding to central memory cells (Tcm) with elevated CD69 and CD45RO protein epitope expression (CITE-seq data) and one smaller cluster representing a naïve T cell population with high CD45RA protein expression

summary:
In Homo sapiens skin, naïve T cells are marked by positive expression of CCR7, SELL, KLF2, and CD3D.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:0c2d88f05e2791e403e1
claim_id: claim:0c2d88f05e2791e403e1
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Three CD3D + T cell clusters expressed tissue-resident memory T cell marker transcripts ITGAE (CD103) and CXCR6 and the CD69 protein epitope (CITE-seq data) ( 23 ), which we termed Trm1, Trm2, and Trm3, contained both CD4 + and CD8A + cells

summary:
In Homo sapiens skin, tissue-resident memory T cells express the marker transcripts CD3D, ITGAE, and CXCR6.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:a0f107929353e1b2ffb9
claim_id: claim:a0f107929353e1b2ffb9
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Three other CD4 + populations were identified as regulatory T cells based on the expression of FOXP3 , TIGIT , CTLA4 , IL2RA (CD25) , and IKZF2 (Helios)

summary:
In Homo sapiens skin, regulatory T cells are identified by expression of FOXP3, TIGIT, CTLA4, IL2RA, and IKZF2.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:f3ccc3257463d2165345
claim_id: claim:f3ccc3257463d2165345
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two of these regulatory T cell populations displayed effector markers ( TNFRSF18, PRDM1 ) ( 26 ) and were termed eTreg1 and eTreg2, while a third CD45RO + class harboring SELL and CCR7 transcript was classified as central memory Tregs (cmTreg, Fig. 1C , 1D )

summary:
In Homo sapiens skin, effector regulatory T cells (eTreg1 and eTreg2) are marked by TNFRSF18 and PRDM1, while central memory regulatory T cells express SELL and CCR7.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:714ccc0f0850fad0e2fe
claim_id: claim:714ccc0f0850fad0e2fe
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
A small CD3D + T cell cluster bearing elevated levels of numerous epigenetic regulators, transcription factors, and lncRNAs such as BATF , SNHG12 , and ZFAS1 , was named Tet.

summary:
In Homo sapiens skin, the Tet T cell cluster is marked by elevated expression of CD3D, BATF, SNHG12, and ZFAS1.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:8749848ca77b569877d1
claim_id: claim:8749848ca77b569877d1
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two CD8A + CD8B + clusters were defined as cytotoxic T cells based on expression of GZMB , NKG7 and CCL5 , including an activated cluster (CTLac) expressing TNFRSF4, TNFRSF18 , and CD96 ( 28 , 29 ) , and a closely related class enriched in canonical exhaustion markers such as PDCD1 and LAG3 (CTLex)

summary:
In Homo sapiens skin, cytotoxic T cells are defined by expression of CD8A, CD8B, GZMB, NKG7, and CCL5; the activated cytotoxic T cell cluster (CTLac) expresses TNFRSF4, TNFRSF18, and CD96; and the exhausted cytotoxic T cell cluster (CTLex) is enriched for PDCD1 and LAG3.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:6129c5ded3303bd48bc1
claim_id: claim:6129c5ded3303bd48bc1
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two CD8A + CD8B + clusters were defined as cytotoxic T cells based on expression of GZMB , NKG7 and CCL5 , including an activated cluster (CTLac) expressing TNFRSF4, TNFRSF18 , and CD96 ( 28 , 29 ) , and a closely related class enriched in canonical exhaustion markers such as PDCD1 and LAG3 (CTLex)

summary:
In Homo sapiens skin, the activated cytotoxic T cell cluster (CTLac) is marked by expression of TNFRSF4, TNFRSF18, and CD96.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:248b50accb84e9555ca8
claim_id: claim:248b50accb84e9555ca8
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two CD8A + CD8B + clusters were defined as cytotoxic T cells based on expression of GZMB , NKG7 and CCL5 , including an activated cluster (CTLac) expressing TNFRSF4, TNFRSF18 , and CD96 ( 28 , 29 ) , and a closely related class enriched in canonical exhaustion markers such as PDCD1 and LAG3 (CTLex)

summary:
In Homo sapiens skin, the exhausted cytotoxic T cell cluster (CTLex) is enriched for the exhaustion markers PDCD1 and LAG3.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:59dc238f098748fff724
claim_id: claim:59dc238f098748fff724
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
We also defined 3 innate lymphoid/natural killer cell populations as KLRB1 ( CD161) + with absent or relatively low CD3D , CD19/MS4A1 , CD14, HLA-DRA expression

summary:
In Homo sapiens skin, innate lymphoid/natural killer cell populations are marked by positive expression of KLRB1 and relatively low expression of CD3D, CD19, MS4A1, CD14, and HLA-DRA.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:2e4166c93b2a6512fabe
claim_id: claim:2e4166c93b2a6512fabe
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Of these, one small cluster expressed the type 2 transcriptional factors GATA3 and PTGDR2 , and was identified as an innate lymphoid cell population (ILC2)

summary:
In Homo sapiens skin, type 2 innate lymphoid cells (ILC2) are identified by expression of GATA3 and PTGDR2.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:0068c117bc169fd04878
claim_id: claim:0068c117bc169fd04878
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two populations of KLRD1 + , GNLY + , PRF1 + , GZMB + cells were assigned as either NK or ILC/NK cells, with the former expressing high levels of the CD56 epitope by CITE-seq

summary:
In Homo sapiens skin, natural killer cells and innate lymphoid cell/natural killer cells are marked by expression of KLRD1, GNLY, PRF1, and GZMB.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:e930cae0fe72ee835157
claim_id: claim:e930cae0fe72ee835157
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two were distinguished by complement transcripts C1QB and C1QC as well as the scavenger receptor CD163 (Mac1 and Mac3), another by alternative activation and suppression markers NR4A1, NR4A2, KLF4 (Mac2) ( 12 ), and the fourth by monocyte markers CD14 and S100A9 (Mac4).

summary:
In Homo sapiens skin, macrophage populations Mac1 and Mac3 are distinguished by C1QB, C1QC, and CD163; Mac2 is distinguished by NR4A1, NR4A2, and KLF4; and Mac4 is distinguished by CD14 and S100A9.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:9b4a95fadcf5eb1c6a5d
claim_id: claim:9b4a95fadcf5eb1c6a5d
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two were distinguished by complement transcripts C1QB and C1QC as well as the scavenger receptor CD163 (Mac1 and Mac3), another by alternative activation and suppression markers NR4A1, NR4A2, KLF4 (Mac2) ( 12 ), and the fourth by monocyte markers CD14 and S100A9 (Mac4).

summary:
In Homo sapiens skin, macrophage population Mac2 is distinguished by alternative activation and suppression markers NR4A1, NR4A2, and KLF4.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:2468c33ba170b3dc5686
claim_id: claim:2468c33ba170b3dc5686
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Two were distinguished by complement transcripts C1QB and C1QC as well as the scavenger receptor CD163 (Mac1 and Mac3), another by alternative activation and suppression markers NR4A1, NR4A2, KLF4 (Mac2) ( 12 ), and the fourth by monocyte markers CD14 and S100A9 (Mac4).

summary:
In Homo sapiens skin, macrophage population Mac4 is distinguished by monocyte markers CD14 and S100A9.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:e87e79570282fe26ab68
claim_id: claim:e87e79570282fe26ab68
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Three Langerhans cells populations were identified based on CD207 transcript and protein and CD1c and EPCAM expression (LC1, LC2, and LC3).

summary:
In Homo sapiens skin, Langerhans cell populations (LC1, LC2, and LC3) are identified by expression of CD207, CD1c, and EPCAM.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:1d8eabc949522099d5f1
claim_id: claim:1d8eabc949522099d5f1
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
Five monocyte or monocyte-derived cell populations shared expression of monocyte-associated genes MS4A7, LYZ , and SERPINA1

summary:
In Homo sapiens skin, monocyte or monocyte-derived cell populations share expression of MS4A7, LYZ, and SERPINA1.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:9ca1b223453b998fef90
claim_id: claim:9ca1b223453b998fef90
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
summary: In Homo sapiens skin, classical monocytes express higher levels of CD14 and S100A9.
span_literal:
One cluster representing classical monocytes (Mono) expressed higher levels of CD14 transcript and protein and S100A9


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:851c0ad896f3de4862f5
claim_id: claim:851c0ad896f3de4862f5
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
summary: In Homo sapiens skin, inflammatory monocytes are enriched for IL1B, IL23A, and CXCL3.
span_literal:
while we designated another inflammatory monocytes (InfMono), as it was enriched for inflammatory genes such as IL1B , IL23A , and CXCL3


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:039670e16cc0f0880955
claim_id: claim:039670e16cc0f0880955
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
We identified four DC classes ( HLA-DRA + ), one enriched in CD1C and CLEC10A (DC1), with two others expressing CLEC9A, CLEC10A and XCR1 (DC2 and DC3)

summary:
In Homo sapiens skin, dendritic cell class DC1 is enriched in HLA-DRA, CD1C, and CLEC10A, while DC2 and DC3 express HLA-DRA, CLEC9A, CLEC10A, and XCR1.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:95062a4f1aebd6c773f3
claim_id: claim:95062a4f1aebd6c773f3
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
We identified four DC classes ( HLA-DRA + ), one enriched in CD1C and CLEC10A (DC1), with two others expressing CLEC9A, CLEC10A and XCR1 (DC2 and DC3)

summary:
In Homo sapiens skin, dendritic cell classes DC2 and DC3 express HLA-DRA, CLEC9A, CLEC10A, and XCR1.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:8be9897882ba35066e3b
claim_id: claim:8be9897882ba35066e3b
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
summary: In Homo sapiens skin, migratory dendritic cells express CD1C, FSCN1, LAMP3, and CCR7.
span_literal:
There was an additional migratory DC (migDC) population which expressed CD1C and migratory/mature markers, such as FSCN1, LAMP3 , and CCR7


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:1dca46939b5453cab304
claim_id: claim:1dca46939b5453cab304
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
summary: In Homo sapiens skin, B cell lineage populations are enriched in IGHG, IGHA, IGKC, and JCHAIN.
span_literal:
Two minor populations were enriched in immunoglobulin genes ( IGHG, IGHA, IGKC , and JCHAIN ), consistent with B cell lineage.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:1dd0472f047a3cf927c2
claim_id: claim:1dd0472f047a3cf927c2
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
One was identified as B cells ( CD19 + , MS4A2 + , Fig. 1C ), also enriched for CD19 and CD21 epitopes ( Fig. 1D ), and one as plasma cells ( CD19 − , MS4A2 − , IGHG1/IGHG4 + )

summary:
In Homo sapiens skin, B cells are marked by positive expression of CD19 and MS4A2, while plasma cells are marked by negative expression of CD19 and MS4A2 and positive expression of IGHG1 and IGHG4.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:6c715165f5b89a540e72
claim_id: claim:6c715165f5b89a540e72
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal:
One was identified as B cells ( CD19 + , MS4A2 + , Fig. 1C ), also enriched for CD19 and CD21 epitopes ( Fig. 1D ), and one as plasma cells ( CD19 − , MS4A2 − , IGHG1/IGHG4 + )

summary:
In Homo sapiens skin, plasma cells are marked by negative expression of CD19 and MS4A2 and positive expression of IGHG1 and IGHG4.


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:f69c772eaac10687798d
claim_id: claim:f69c772eaac10687798d
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
summary: In Homo sapiens skin, mast cells are distinguished by expression of TPSAB1 and TPSB2.
span_literal:
A large population of mast cells (Mast) was easily distinguished by expression of TPSAB1 (tryptase) and TPSB2


claim_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2:claim:26902e48b18eec092f64
claim_id: claim:26902e48b18eec092f64
paper_key: hca:0099_10.1126_sciimmunol.abl9165_5f9974d5f2
span_literal: Five clusters showed elevated cell division transcripts, such as MKI67 , TOP2A, CENPF , and UBE2C
summary:
In Homo sapiens skin, cycling cell clusters show elevated expression of cell division transcripts MKI67, TOP2A, CENPF, and UBE2C.


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:296548bdb59b412fb082
claim_id: claim:296548bdb59b412fb082
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
summary: In Homo sapiens, B cells are marked by CD79A, CD79B, and MS4A1.
span_literal:
The marker genes used were CD79A , CD79B , MS4A1 (B cells); CD8A , CD8B , CD7 , CD3E (CD8+ T cells); CD4 , IL7R , CD7 , CD3E (CD4+ T cells); NKG7 , GNLY (NK cells); MZB1 , SDC1 , IGHG1 (Plasma cells); FCGR3A (Macrophages); CD14 , LYZ (Monocytes); FCER1A , CLEC10A (Dendritic cells); and AHSP1 , HBA , HBB (Erythrocytes).


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:2c51e9ddc3db9512d49e
claim_id: claim:2c51e9ddc3db9512d49e
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
summary: In Homo sapiens, primitive B cells exhibit high expression of SOX4, VPREB3, and MME.
span_literal:
There are three small B cell clusters (Fig. 3a, b ), predominantly from healthy donors, that exhibit high expression of SOX4, VPREB3 , and MME , suggesting a primitive B cell state 34 , 35 .


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:5c7e947ea8013b662809
claim_id: claim:5c7e947ea8013b662809
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
span_literal:
We found substantial B cell signatures in the plasma cells—with high expression of typical plasma cell markers, such as SDC1 and TNFRSF17 —for Patients 56203 and 83942, and to a lesser degree for 77570, as illustrated by expression of B cell marker MS4A1 (Supplementary Fig. 4c ).

summary:
In Homo sapiens, plasma cells show high expression of typical plasma cell markers SDC1 and TNFRSF17, while MS4A1 is a B cell marker.


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:db50f67de7a5257392f8
claim_id: claim:db50f67de7a5257392f8
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
summary: In Homo sapiens, primitive B cells are marked by SOX4, DNTT, HMGB1, and HMGB2.
span_literal:
The Primitive B group included SOX4 and DNTT , along with several less-investigated genes in terms of lineage, such as HMGB1 and HMGB2 , both of which are involved in DNA double-strand breakage 36 , 37 and might be associated with VDJ recombination.


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:6f5f5a0f1354eb3bb60e
claim_id: claim:6f5f5a0f1354eb3bb60e
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
span_literal: The Mature B group was defined by CD20 ( MS4A1 ) and MHC-associated genes.
summary:
In Homo sapiens, mature B cells are defined by CD20 (MS4A1) and major histocompatibility complex-associated genes.


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:736630920b71a928b81b
claim_id: claim:736630920b71a928b81b
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
summary: In Homo sapiens, plasma cells overexpress the endoplasmic reticulum stress response gene XBP1.
span_literal:
As expected, ER stress response gene XBP1 was overexpressed since plasma cells produce high levels of secreted proteins 38 .


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:4a93a843ea475dc9459b
claim_id: claim:4a93a843ea475dc9459b
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
span_literal:
All three clusters expressed high levels of standard plasma cell markers, such as SDC1 , SLAMF7 (CS1) , and TNFRSF17 (BCMA) , while FGFR3 and WHSC1 were primarily expressed in the malignant (RL2.1) and the “transitional” malignant (RL2.3) populations.

summary:
In Homo sapiens, plasma cells express high levels of standard plasma cell markers SDC1, SLAMF7, and TNFRSF17.


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:5eb7b66e7a5e4f5938ef
claim_id: claim:5eb7b66e7a5e4f5938ef
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
summary: In Homo sapiens, normal plasma cells are associated with CD27 expression.
span_literal:
CD27 , a marker associated with normal plasma cells 44 , CD79A , a member of the B cell antigen receptor complex, and CD19 , a marker for B cell development were exclusively detected in RL2.2, supporting the normal “B cell-like” classification (Fig. 5d and Supplementary Fig. 7c ).


claim_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9:claim:537a3a6fbfad1ba1b9c3
claim_id: claim:537a3a6fbfad1ba1b9c3
paper_key: hca:0100_10.1038_s41467-021-22804-x_e7667133b9
span_literal:
We found high expression of MKI67 and TOP2A , two proliferative markers for R.3 (Supplementary Fig. 7d ).

summary:
In Homo sapiens, the proliferative plasma cell subpopulation R.3 shows high expression of the proliferative markers MKI67 and TOP2A.


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:0804326877c25bc2808c
claim_id: claim:0804326877c25bc2808c
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
summary: In Homo sapiens, alveolar fibroblasts are marked by expression of NPNT and CES1.
span_literal:
Cluster 1, which was enriched with cells from normal lungs, expressed alveolar fibroblast markers such as NPNT and CES1


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:d963e4af863503895d58
claim_id: claim:d963e4af863503895d58
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
summary: In Homo sapiens, peribronchial fibroblasts are marked by expression of FGF18 and WIF1.
span_literal:
Cluster 5 markers include FGF18 and WIF1 , which were also expressed in peribronchial fibroblasts in mice


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:f764dd146f3ff4503217
claim_id: claim:f764dd146f3ff4503217
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
summary: In Homo sapiens, pericytes are marked by expression of RGS5 and MCAM.
span_literal:
Cluster 0 expressed pericyte markers including RGS5 and MCAM , and clusters 2, 6 expressed the highest levels of smooth muscle markers including MYH11 and MYL9


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:cde6372e044f829ba531
claim_id: claim:cde6372e044f829ba531
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
span_literal:
As seen in mice, CTHRC1 expression correlated with COL1A1 expression and was largely restricted to cells from fibrotic lungs, and ACTA2 expression was poorly correlated with COL1A1

summary:
In Homo sapiens, CTHRC1-expressing pathologic fibroblasts are marked by expression of CTHRC1 and COL1A1 in fibrotic lungs.


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:8f7d8e083de515bd6e5f
claim_id: claim:8f7d8e083de515bd6e5f
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
span_literal: Clusters 1, 3, 4 expressed PDGFRA , and clusters 0, 2, 6 expressed PDGFRB
summary:
In Homo sapiens, alveolar fibroblasts, adventitial fibroblasts, and peribronchial fibroblasts express PDGFRA, while pericytes and smooth muscle cells express PDGFRB.


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:3dca6a2096535d28c10e
claim_id: claim:3dca6a2096535d28c10e
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
summary: In Homo sapiens, pericytes are marked by expression of RGS5 and CSPG4.
span_literal:
After focusing on COL1A1 + cells, we found similar heterogeneous populations including RGS5 + CSPG4 + pericytes, MYH11 + MYL9 + smooth muscle cells, NPNT + CES1 + alveolar fibroblasts, and PI16 + DCN + adventitial fibroblasts


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:e455fce68e9c40eade0d
claim_id: claim:e455fce68e9c40eade0d
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
span_literal:
IPF lungs, highly expressed CTHRC1 and other ECM-related genes such as COL1A1 , COL3A1 , TNC , and POSTN

summary:
In Homo sapiens, CTHRC1-positive pathologic fibroblasts from idiopathic pulmonary fibrosis lungs highly express CTHRC1, COL1A1, COL3A1, TNC, and POSTN.


claim_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6:claim:419b872c366da5f25470
claim_id: claim:419b872c366da5f25470
paper_key: hca:0101_10.1038_s41467-020-15647-5_d22ec8f4b6
span_literal: COL1A1 + cells expressed CTHRC1
summary:
In Homo sapiens, CTHRC1-positive pathologic fibroblasts express CTHRC1 but do not express the highest level of ACTA2.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:d2fa6c3c9d1ac29ec62b
claim_id: claim:d2fa6c3c9d1ac29ec62b
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
summary: In Homo sapiens, BEST4/OTOP2 cells express GUCA2B, encoding the satiety peptide uroguanylin.
span_literal:
The cells of this cluster also expressed the endogenous paracrine hormone and satiety peptide uroguanylin 13 (encoded by GUCA2B ; Fig. 2a, iv, v, vi ), which is required for activation of guanylate cyclase 2C(GC-C) and epithelial cyclic GMP activity.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:47817b9ef755337ff199
claim_id: claim:47817b9ef755337ff199
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
summary: In Homo sapiens, BEST4/OTOP2 cells express the transcription factors SPIB and HES4.
span_literal:
Trajectory analysis indicated that these cells originate from the absorptive lineage and express the transcription factors SPIB and HES4 (Extended Data Fig. 2c, iv, v ), with the latter normally confined to undifferentiated epithelial populations (Extended Data Fig. 2b ).


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:032bd23d3a6a1687bfd5
claim_id: claim:032bd23d3a6a1687bfd5
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
span_literal:
Inflamed crypt-top colonocytes differentially expressed the oxidative-stress-pathway genes NOS2 (Fig. 3d ) and DDAH2 (ref. 29 ), and showed increased expression of SMAD3 (Extended Data Fig. 5b ) and JAK2 , which are associated with both Crohn’s disease and ulcerative colitis 25 , 30 .

summary:
In Homo sapiens, inflamed crypt-top colonocytes express the oxidative-stress-pathway genes NOS2 and DDAH2, and show increased expression of SMAD3 and JAK2.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:4393b71564408ceb9163
claim_id: claim:4393b71564408ceb9163
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
span_literal:
IBD-associated ITLN1 (Fig. 3d ) and IL1R2 (ref. 30 ) were expressed by goblet cells, while undifferentiated epithelia expressed IBD-associated RNF186 , the chemokines CXCL1 , CXCL2 and CXCL3 (ref. 31 ), the integrin ITGB8 (ref. 25 ) and the heat-shock-protein HSPA6 (ref. 28 ) (Extended Data Fig. 5b ).

summary:
In Homo sapiens, goblet cells express ITLN1 and IL1R2, while undifferentiated epithelial cells express RNF186, CXCL1, CXCL2, CXCL3, ITGB8, and HSPA6.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:8dcb0a868c2faf94f6c1
claim_id: claim:8dcb0a868c2faf94f6c1
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
span_literal:
IBD-associated ITLN1 (Fig. 3d ) and IL1R2 (ref. 30 ) were expressed by goblet cells, while undifferentiated epithelia expressed IBD-associated RNF186 , the chemokines CXCL1 , CXCL2 and CXCL3 (ref. 31 ), the integrin ITGB8 (ref. 25 ) and the heat-shock-protein HSPA6 (ref. 28 ) (Extended Data Fig. 5b ).

summary:
In Homo sapiens, undifferentiated epithelial cells express RNF186, CXCL1, CXCL2, CXCL3, ITGB8, and HSPA6.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:56006c1d6babb306528b
claim_id: claim:56006c1d6babb306528b
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
summary: In Homo sapiens, goblet cells express BCAS1, CLCA1, REGIV, WFDC2, and MUC2 proteins.
span_literal:
Figure 4b shows expression of the BCAS1 (cluster 5), CLCA1 (cluster 1), REGIV (cluster 1) and WFDC2 (cluster 2) proteins together with mucin 2 (MUC2) within goblet cells.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:01f3780cf015c2ffe3f2
claim_id: claim:01f3780cf015c2ffe3f2
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
span_literal:
LYZ , a Paneth-cell gene, was upregulated by lower-crypt goblet cells in inflammation (Fig. 3b and Extended Data Fig. 4e ), and may mark the ‘deep crypt secretory cells’ of the colon 22 that are required to maintain the colonic stem cell niche and to protect stem cells from bacterial damage during colitis.

summary:
In Homo sapiens, LYZ is upregulated by lower-crypt goblet cells in inflammation and may mark deep crypt secretory cells of the colon.


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:33dfc611db3b14fe6ba0
claim_id: claim:33dfc611db3b14fe6ba0
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
summary: In Homo sapiens, intra-epithelial T cells show high and specific expression of IL7R and TNFRSF9.
span_literal:
This association was driven by high and specific expression of genes such as IL7R and TNFRSF9 (refs. 25 , 28 ; Extended Data Fig. 5b ).


claim_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9:claim:e3b674f592e4b5141c89
claim_id: claim:e3b674f592e4b5141c89
paper_key: hca:0102_10.1038_s41586-019-0992-y_40614812e9
span_literal:
These cells selectively express uroguanylin, the endogenous paracrine hormone required for GC-C activation.

summary:
In Homo sapiens, BEST4/OTOP2 cells selectively express uroguanylin (GUCA2B), the endogenous paracrine hormone required for guanylate cyclase 2C activation.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:df95a933e824adfa405a
claim_id: claim:df95a933e824adfa405a
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
showed the expected enrichment of β cell–specific genes (e.g., INS, IAPP, MAFA ) as well as α cell–specific genes ( GCG, TM4SF4, ARX )

summary:
In Homo sapiens, beta cells are marked by INS, IAPP, and MAFA, while alpha cells are marked by GCG, TM4SF4, and ARX.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:eeb26210c1b78261332a
claim_id: claim:eeb26210c1b78261332a
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
PAX6 , RFX6 , NEUROD1 , and NKX2-2 were detected in all endocrine cell types, whereas PDX1 , NKX6-1 , and MAFA were enriched in β cells; IRX2 was specifically detected in α cells; and ARX was detected in α, γ, and ε cells, consistent with previous single-cell studies

summary:
In Homo sapiens, PAX6, RFX6, NEUROD1, and NKX2-2 are detected in all endocrine cell types, while PDX1, NKX6-1, and MAFA are enriched in beta cells.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:3720a7fd0c5abe148db1
claim_id: claim:3720a7fd0c5abe148db1
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
PAX6 , NEUROD1 , and MAFB were among the most prevalent endocrine factors, detected in more than 75% of α and β cells

summary:
In Homo sapiens, PAX6, NEUROD1, and MAFB are among the most prevalent endocrine transcription factors, detected in more than 75% of alpha cells.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:265b8e3b799733eaa535
claim_id: claim:265b8e3b799733eaa535
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
PAX6 , NEUROD1 , and MAFB were among the most prevalent endocrine factors, detected in more than 75% of α and β cells

summary:
In Homo sapiens, PAX6, NEUROD1, and MAFB are among the most prevalent endocrine transcription factors, detected in more than 75% of beta cells.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:5a64870e5ad3c8d73821
claim_id: claim:5a64870e5ad3c8d73821
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
MAFB — known in humans to be expressed in both α and β cells — was also enriched in the immune cell population, which had been overlooked in previous studies because of low abundance of immune cells in isolated islets

summary:
In Homo sapiens, MAFB is expressed in both alpha and beta cells and is also enriched in the immune cell population of pancreatic islets.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:4af6369fb923b78e4896
claim_id: claim:4af6369fb923b78e4896
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal: In α cells, MAFB is known to directly bind to the GCG promoter to regulate glucagon expression
summary:
In Homo sapiens, MAFB is expressed in alpha cells where it directly binds to the GCG promoter to regulate glucagon expression.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:8e586cfc3b8b39043c9e
claim_id: claim:8e586cfc3b8b39043c9e
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
MAFA is a bona fide β cell factor exerting direct control over insulin expression as well as key components of glucose-stimulated insulin secretion, and it is expressed relatively late in β cell development, making it a commonly used marker of fully mature β cells

summary:
In Homo sapiens, MAFA is a marker of fully mature beta cells, exerting direct control over insulin expression and glucose-stimulated insulin secretion.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:a6d3f951336b7ec19d7b
claim_id: claim:a6d3f951336b7ec19d7b
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
In α cells, aristaless related homeobox (ARX) factor is essential for α cell differentiation and function, a finding that has been confirmed in human α cells

summary:
In Homo sapiens, aristaless related homeobox (ARX) is essential for alpha cell differentiation and function.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:ecd0988faf1567789140
claim_id: claim:ecd0988faf1567789140
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
Specifically, numerous genes related to cell identity ( PDX1 , PAX6 , NEUROD1 , ISL1 , PCSK1 , IAPP ), glucose metabolism ( ACLY , G6PC2 , GPX3 ), ion channels ( ABCC8 , KCNJ6 ), and exocytosis ( VAMP2 , SYT7 , PCLO , TSPAN7 , RGS9 , FAM159B , BMP5 ) were all increased in MAFA- and MAFB-coexpressing cells compared with other subgroups

summary:
In Homo sapiens, beta cells coexpressing MAFA and MAFB show increased expression of PDX1, PAX6, NEUROD1, ISL1, PCSK1, IAPP, ACLY, G6PC2, GPX3, ABCC8, KCNJ6, VAMP2, SYT7, PCLO, TSPAN7, RGS9, FAM159B, and BMP5 compared with other beta cell subgroups.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:27bf74904066a8cd6850
claim_id: claim:27bf74904066a8cd6850
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal: HSPA5 , HERPUD1 , DDIT3 , ATF4 ) were either significantly reduced in the coexpression group
summary:
In Homo sapiens, stress genes HSPA5, HERPUD1, DDIT3, and ATF4 are reduced in MAFA and MAFB coexpressing beta cells or elevated in beta cells expressing neither MAFA nor MAFB.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:67b668082351c610dc0f
claim_id: claim:67b668082351c610dc0f
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
we observed that numerous α cell–enriched TFs ( RFX6 , PAX6 , NEUROD1 , ISL1 , IRX2 ) and genes related to nutrient sensing or glucagon secretion ( ACLY , PKM , GSTA4 , GPX3 , G6PC2 , KCTD12 , KCNK16 , KCNJ6 , ABCC8 ) were elevated in α cells in which MAFB and ARX were codetected compared with the other populations

summary:
In Homo sapiens, alpha cells coexpressing ARX and MAFB show elevated expression of RFX6, PAX6, NEUROD1, ISL1, IRX2, ACLY, PKM, GSTA4, GPX3, G6PC2, KCTD12, KCNK16, KCNJ6, and ABCC8 compared with other alpha cell populations.


claim_key: hca:0103_10.1172_jci.insight.151621_2faf375c31:claim:0a68d537411db49a4a1e
claim_id: claim:0a68d537411db49a4a1e
paper_key: hca:0103_10.1172_jci.insight.151621_2faf375c31
span_literal:
whereas genes related to cell stress ( DDIT , ATF4 ) were highest in the “None” group, suggesting that the presence of both factors may support increased metabolic activity and glucagon secretory capacity

summary:
In Homo sapiens, alpha cells expressing neither ARX nor MAFB show the highest expression of stress genes DDIT and ATF4.


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:e39e0fa0e36517819d91
claim_id: claim:e39e0fa0e36517819d91
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
span_literal:
the Takasato protocol produced more tubular epithelial cells based on the expression of EPCAM, SLC3A1 and WFDC2

summary:
In Homo sapiens, tubular epithelial cells are marked by the expression of EPCAM, SLC3A1, and WFDC2 in kidney organoids.


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:498ee14787e8c9faf44b
claim_id: claim:498ee14787e8c9faf44b
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
span_literal:
Organoids generated using the Takasato protocol contained four neuronal clusters and one cluster that we could not annotate but that expressed some melanocyte markers such as MLANA and PMEL

summary:
In Homo sapiens kidney organoids, a melanocyte-like cluster expressed melanocyte markers MLANA and PMEL.


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:118c1b86cf50fdd1f151
claim_id: claim:118c1b86cf50fdd1f151
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
summary: In Homo sapiens kidney organoids, podocytes are marked by NPHS1 expression.
span_literal:
We confirmed differences in relative abundance of both renal and non-renal cell types by comparing marker gene expression for podocytes (NPHS1) and loop of henle (SLC12A1) as well as muscle (MYLPF, MYOG) and neuronal (CRABP1, MAP2) by qPCR


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:ee851f8643ad2e38281d
claim_id: claim:ee851f8643ad2e38281d
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
summary: In Homo sapiens, MAP2, a microtubule-associated protein, is expressed exclusively in neurons.
span_literal:
We could identify co-expression of MAP2, a microtubule-associated protein expressed exclusively in neurons


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:fa97c90fe30e16c008f7
claim_id: claim:fa97c90fe30e16c008f7
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
span_literal:
NTRK2, which encodes Neurotrophic Tyrosine Kinase Receptor, type 2, was expressed exclusively in neural clusters N1 and N3.

summary:
In Homo sapiens kidney organoids, NTRK2, which encodes neurotrophic tyrosine kinase receptor type 2, is expressed exclusively in neural cells.


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:66f1ab1832d2998ee70a
claim_id: claim:66f1ab1832d2998ee70a
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
summary: In Homo sapiens, metanephric mesenchyme is marked by the expression of SALL1, FGF18, and HOXB9.
span_literal:
Pluripotency gene expression (e.g., POU5F1/Oct4) was completely downregulated by day 7 with upregulation of metanephric mesenchyme markers (SALL1, FGF18 and HOXB9, Figure 6B )


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:b5c62a365b7bc7abae9f
claim_id: claim:b5c62a365b7bc7abae9f
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
summary: In Homo sapiens, the pretubular aggregate is marked by enrichment of JAG1 and LHX1.
span_literal:
The day 12 cluster most closely resembled the pretubular aggregate, with genes such as JAG1 and LHX1 strongly enriched at this timepoint.


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:32f9c2f99717c4dc82b3
claim_id: claim:32f9c2f99717c4dc82b3
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
span_literal:
Both the Morizane M1 cluster and the Takasato Lp cluster expressed high levels of the cell cycle gene MKI67, but showed divergent expression of COL3A1 (M1) and POU3F3 (Lp)

summary:
In Homo sapiens kidney organoids, the mesenchymal M1 cluster expressed COL3A1, while the Lp cluster expressed POU3F3, and both expressed MKI67.


claim_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9:claim:d8baefa4744e7be9b0da
claim_id: claim:d8baefa4744e7be9b0da
paper_key: hca:0104_10.1016_j.stem.2018.10.010_b71866c4b9
span_literal:
Expression of S1 marker SLC5A12 and loop of henle marker UMOD is strong in adult kidney and undetectable in organoids.

summary:
In Homo sapiens adult kidney, SLC5A12 is a marker of S1 proximal tubule and UMOD is a marker of loop of Henle.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:bd2c89e6d3c83f49dae0
claim_id: claim:bd2c89e6d3c83f49dae0
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Immunofluorescence was used to establish the presence of classically patterned nephrons revealing the presence of podocytes (NEPHRIN), proximal tubules (LTL, CUBN), distal tubules/loop of Henle thick ascending limb (TAL; ECAD, SLC12A1) and connecting segments/ureteric epithelium (GATA3, ECAD)

summary:
In Homo sapiens kidney organoids, podocytes are marked by NPHS1 (NEPHRIN), proximal tubule cells by LTL and CUBN, distal tubule/loop of Henle thick ascending limb cells by CDH1 (ECAD) and SLC12A1, and connecting segment/ureteric epithelium cells by GATA3 and CDH1 (ECAD).


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:96cff1ac8c17091a1e20
claim_id: claim:96cff1ac8c17091a1e20
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Immunofluorescence was used to establish the presence of classically patterned nephrons revealing the presence of podocytes (NEPHRIN), proximal tubules (LTL, CUBN), distal tubules/loop of Henle thick ascending limb (TAL; ECAD, SLC12A1) and connecting segments/ureteric epithelium (GATA3, ECAD)

summary:
In Homo sapiens kidney organoids, distal tubule/loop of Henle thick ascending limb cells are marked by CDH1 (ECAD) and SLC12A1.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:62ab979532d228f7580a
claim_id: claim:62ab979532d228f7580a
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
summary:
In Homo sapiens kidney organoids, connecting segment/ureteric epithelium cells are marked by GATA3 and CDH1 (ECAD).


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:5bc750d62c79e45972ef
claim_id: claim:5bc750d62c79e45972ef
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
summary: In Homo sapiens kidney organoids, endothelial cells are marked by CD31 (PECAM1).
span_literal:
The presence of additional cellular components, including endothelial cells (CD31) and renal stroma (MEIS1/2) was also evident


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:b4f2ce6c764ffb99e218
claim_id: claim:b4f2ce6c764ffb99e218
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Doxorubicin also downregulated key podocyte markers NPHS1 and PODXL at 2μM, while the proximal tubule gene CUBN was only downregulated in response to 10μM Doxorubicin

summary:
In Homo sapiens kidney organoids, NPHS1 and PODXL are key markers of podocytes, while CUBN is a marker of proximal tubule cells.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:c18ac0cf0a57e5925bd7
claim_id: claim:c18ac0cf0a57e5925bd7
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Genes related to epithelial formation ( CDH1, EPCAM ) and tubule patterning and function ( HNF4A, CUBN, LRP2, SLC12A1 ) were upregulated at ratio 40 (R40), while genes related to vascular ( FLT1, SOX17, PECAM ) and stromal / fibroblast ( THY1, DCN ) development were upregulated at ratio 0 (R0)

summary:
In Homo sapiens kidney organoids, vascular cells express FLT1, SOX17, and PECAM1, while stromal/fibroblast cells express THY1 and DCN.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:38408a1a038e3a747e4f
claim_id: claim:38408a1a038e3a747e4f
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
with clear expression of MAFB in podocytes, HNF4A in proximal tubule and GATA3 in distal tubule clusters

summary:
In Homo sapiens kidney organoids, MAFB is expressed in podocytes, HNF4A in proximal tubule cells, and GATA3 in distal tubule cells.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:fb7d3f3c243272ae0ad4
claim_id: claim:fb7d3f3c243272ae0ad4
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Genes previously associated with mature tubule function and metabolism, including key solute channels ( SLC30A1, SLC51B and SULT1E1 ) and fatty acid metabolismrelated gene FABP3 24 – 27 were significantly increased in R40 versus manual organoid proximal tubule cells

summary:
In Homo sapiens kidney organoids, SLC30A1, SLC51B, SULT1E1, and FABP3 are markers of mature proximal tubule cells.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:c41f985632d5c9761913
claim_id: claim:c41f985632d5c9761913
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Clusters 2 and 3, with identify most similar to early kidney forming mesenchyme, showed a significant upregulation of kidney development genes in bioprinted R40 lines, including HOXA11 , FOXC2, EYA1 and SIX1 as well as developmental signalling genes WNT5A and RSPO3

summary:
In Homo sapiens kidney organoids, early kidney forming mesenchyme cells express HOXA11, FOXC2, EYA1, SIX1, WNT5A, and RSPO3.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:7dfcc2700de92f7f3d7e
claim_id: claim:7dfcc2700de92f7f3d7e
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal: Marker genes of main cells type, WT1 and PAX2 (nephron), PDGFRA (stroma) and SOX17 (endothelial).
summary:
In Homo sapiens kidney organoids, WT1 and PAX2 are marker genes of nephron cells, PDGFRA is a marker of stromal cells, and SOX17 is a marker of endothelial cells.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:872eab62ceafaded46a0
claim_id: claim:872eab62ceafaded46a0
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Marker genes identifying each cluster: GATA3 (distal), HNF1B (pre-tubule), CUBN (proximal), HNF4A (proximal), FOXC2 (pre-podocyte), MAFB (pre-podocyte / podocyte), PODXL (podocyte), SIX2 (progenitor), EYA1 (progenitor).

summary:
In Homo sapiens kidney organoids, GATA3 marks distal nephron cells, HNF1B marks pre-tubule cells, CUBN and HNF4A mark proximal tubule cells, FOXC2 marks pre-podocyte cells, MAFB marks pre-podocyte/podocyte cells, PODXL marks podocyte cells, and SIX2 and EYA1 mark progenitor cells.


claim_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313:claim:c7bf054eb38e4b2100d8
claim_id: claim:c7bf054eb38e4b2100d8
paper_key: hca:0105_10.1038_s41563-020-00853-9_ec3e5ef313
span_literal:
Markers of specific stromal clusters; SIX2 , LYPD1 , FOXC2 , HOXA11 (Cluster 3, nephron progenitor-like), WNT5A , LHX9 (Cluster 7) and ZIC1 and ZIC4 (Cluster 10).

summary:
In Homo sapiens kidney organoids, stromal cluster 3 (nephron progenitor-like) is marked by SIX2, LYPD1, FOXC2, and HOXA11; stromal cluster 7 is marked by WNT5A and LHX9; and stromal cluster 10 is marked by ZIC1 and ZIC4.


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:1496cdac427538274e34
claim_id: claim:1496cdac427538274e34
paper_key: hca:0106_10.1101_585901_f6794b9c1b
summary: In Homo sapiens, induced pluripotent stem cells express the characteristic marker DPPA4.
span_literal:
The cluster formed by cells from early time-points day 0 and day 1 contained pluripotent stem cells (Fig. 3A,B , ‘iPSC’, orange cluster), in agreement with the expression of characteristic markers such as DPPA4.


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:6d4ce7ea1f73a234c93f
claim_id: claim:6d4ce7ea1f73a234c93f
paper_key: hca:0106_10.1101_585901_f6794b9c1b
summary: In Homo sapiens, cardiac progenitors express EOMES, a mesendoderm progenitor marker gene.
span_literal:
Cells harvested on day 3 mostly formed a separate cluster (‘Cardiac progenitors’, green cluster) composed of cells expressing markers concordant with cardiac progenitors (e.g. expression of EOMES (logFC = 1.08), a mesendoderm progenitor marker gene).


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:e1739d1372dce723b106
claim_id: claim:e1739d1372dce723b106
paper_key: hca:0106_10.1101_585901_f6794b9c1b
summary: In Homo sapiens, cardiomyocyte 2 cells express markers MYH6, TNNT2, MYL, and MYBPC3.
span_literal:
MYH6 , TNNT2 , MYL , and MYBPC3 (Fig. 3A , cyan cluster, ‘Cardiomyocyte 1’ and blue cluster, ‘Cardiomyocyte 2


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:7312ac2aa10cd6be9bf6
claim_id: claim:7312ac2aa10cd6be9bf6
paper_key: hca:0106_10.1101_585901_f6794b9c1b
span_literal:
A cluster was identified as CMs (Fig. 4A , pink cluster) based on marker genes TNNT2 (logFC = 0.71), MYH6 (logFC = 0.87), and MYBPC3 (logFC = 1.38).

summary:
In Homo sapiens, cardiomyocytes in heart tissue are identified by marker genes TNNT2, MYH6, and MYBPC3.


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:e0ccb9f5cdbf5b31e713
claim_id: claim:e0ccb9f5cdbf5b31e713
paper_key: hca:0106_10.1101_585901_f6794b9c1b
span_literal:
A second cluster was identified as likely myofibroblasts (Fig. 4A , dark-green cluster) expressing the collagen genes COL5A2 (logFC = 1.95) and COL6A3 (logFC = 1.92) and periostin (POSTN).

summary:
In Homo sapiens, myofibroblasts in heart tissue express the collagen genes COL5A2 and COL6A3 and periostin (POSTN).


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:374ab524a8f312d7861e
claim_id: claim:374ab524a8f312d7861e
paper_key: hca:0106_10.1101_585901_f6794b9c1b
span_literal:
Finally, a third cluster was identified as endothelial cells (Fig. 4A , grey cluster) based on vascular endothelial growth factor receptor FLT1 (logFC = 2.4) and blood clotting protein VWF (logFC = 1.77).

summary:
In Homo sapiens, endothelial cells in heart tissue are identified by vascular endothelial growth factor receptor FLT1 and von Willebrand factor VWF.


claim_key: hca:0106_10.1101_585901_f6794b9c1b:claim:d7af9afe4570fb79d94a
claim_id: claim:d7af9afe4570fb79d94a
paper_key: hca:0106_10.1101_585901_f6794b9c1b
summary: In Homo sapiens, a second cluster of myofibroblasts in heart tissue expresses CPE and ENPEP.
span_literal:
A fourth cluster expressing CPE (logFC = 2.4) and ENPEP (logFC = 2.5) was identified likely representing myofibroblasts (Fig. 4A , black cluster).


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:81cdcc73888d5d275f25
claim_id: claim:81cdcc73888d5d275f25
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
radial glia (defined by expression of HES1), neuroblasts (NHLH1), neuronal intermediate progenitor cells (IPCs; defined as neuroblasts and immature neurons expressing cell cycle genes), and immature neurons (expressing the neurofilament gene INA)

summary:
In Homo sapiens developing brain, radial glia are defined by expression of HES1, neuroblasts by NHLH1, and immature neurons by the neurofilament gene INA.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:a562ce803d4116b8e2f5
claim_id: claim:a562ce803d4116b8e2f5
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
radial glia (defined by expression of HES1), neuroblasts (NHLH1), neuronal intermediate progenitor cells (IPCs; defined as neuroblasts and immature neurons expressing cell cycle genes), and immature neurons (expressing the neurofilament gene INA)

summary:
In Homo sapiens developing brain, immature neurons are defined by expression of the neurofilament gene INA.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:a70b3a5e64c97235b098
claim_id: claim:a70b3a5e64c97235b098
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
summary: In Homo sapiens developing brain, glioblasts are defined by expression of TNC and BCAN.
span_literal:
radial glia matured into putative glioblasts (defined here by expression of TNC and BCAN) and oligodendrocyte precursor cells (OPCs; expressing PDGFRA and OLIG1)


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:640a03efc299e60a5a2c
claim_id: claim:640a03efc299e60a5a2c
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
radial glia matured into putative glioblasts (defined here by expression of TNC and BCAN) and oligodendrocyte precursor cells (OPCs; expressing PDGFRA and OLIG1)

summary:
In Homo sapiens developing brain, oligodendrocyte precursor cells are defined by expression of PDGFRA and OLIG1.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:dc3a5627a69b8a372b2e
claim_id: claim:dc3a5627a69b8a372b2e
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal: SOX2, radial glia
summary:
In Homo sapiens developing brain, SOX2 is a maturation marker of radial glia, NHLH1 marks early neuroblasts, NRXN3 marks late GABAergic neuroblasts, and STMN2 marks neurons.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:79d2b3919efe51f2d6ce
claim_id: claim:79d2b3919efe51f2d6ce
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
we computationally isolated those cortical clusters expressing EMX1, a transcription factor that marks the cortical excitatory lineage

summary:
In Homo sapiens developing brain, EMX1 is a transcription factor that marks the cortical excitatory lineage.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:9aa6919ab2b4dcfbc2d4
claim_id: claim:9aa6919ab2b4dcfbc2d4
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal: choroid plexus (FOLR1, TTR
summary:
In Homo sapiens developing brain, choroid plexus cells are identified by expression of FOLR1 and TTR, and ependymal cells are identified by expression of PIFO and CCNO.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:636c7a13298a6b89b30e
claim_id: claim:636c7a13298a6b89b30e
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
About half of all glioblasts additionally expressed the astrocyte-specific water channel AQP4 and tight-junction Connexin-43 (encoded by GJA1), and we designated those as pre-astrocytes

summary:
In Homo sapiens developing brain, pre-astrocytes are designated by expression of the astrocyte-specific water channel AQP4 and tight-junction Connexin-43 encoded by GJA1.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:6108b803af103ca26580
claim_id: claim:6108b803af103ca26580
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
One cluster (#510, [fig. S9A](513487v1_figS9.tif)) was identified as pre-OPCs based on expression of EGFR and DLL3 (51), and comprised cells from all major brain regions.

summary:
In Homo sapiens developing brain, pre-oligodendrocyte precursor cells are identified based on expression of EGFR and DLL3.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:e13b2d1fbd5985ec5c53
claim_id: claim:e13b2d1fbd5985ec5c53
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
we found that cells expressing both BCAN (51) and TNC identified putative glioblasts in all brain regions

summary:
In Homo sapiens developing brain, cells expressing both BCAN and TNC are identified as putative glioblasts.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:c6a80e0202ce787c1975
claim_id: claim:c6a80e0202ce787c1975
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal: PDGFRA (OPCs
summary:
In Homo sapiens developing brain, PDGFRA is a prototypical marker gene of oligodendrocyte precursor cells, while ENPP6 and MAG are markers of committed oligodendrocyte precursor cells.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:927ea0c11b8264d26565
claim_id: claim:927ea0c11b8264d26565
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal: ENPP6 and MAG (COPs
summary:
In Homo sapiens developing brain, ENPP6 and MAG are prototypical marker genes of committed oligodendrocyte precursor cells.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:495e3c35bb5fcd37375a
claim_id: claim:495e3c35bb5fcd37375a
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
For example, RIT2 (OPCs) and BMP-binding endothelial regulator (BMPER; COPs) clearly distinguished the two populations in human

summary:
In Homo sapiens developing brain, RIT2 is a marker of oligodendrocyte precursor cells and BMP-binding endothelial regulator (BMPER) is a marker of committed oligodendrocyte precursor cells, distinguishing the two populations.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:5bf397346dcad2842f60
claim_id: claim:5bf397346dcad2842f60
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
For example, RIT2 (OPCs) and BMP-binding endothelial regulator (BMPER; COPs) clearly distinguished the two populations in human

summary:
In Homo sapiens developing brain, BMP-binding endothelial regulator (BMPER) is a marker of committed oligodendrocyte precursor cells, distinguishing them from oligodendrocyte precursor cells.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:38be824e6f922014b51c
claim_id: claim:38be824e6f922014b51c
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
PRRX1, a transcription factor typically expressed in mesoderm-associated tissues and that is involved in craniofacial and limb development, was specific to the forebrain-derived OPCs

summary:
In Homo sapiens developing brain, PRRX1 is a transcription factor specific to forebrain-derived oligodendrocyte precursor cells.


claim_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68:claim:c8f127934f86bbe4096a
claim_id: claim:c8f127934f86bbe4096a
paper_key: hca:0107_10.1101_2022.10.24.513487_4d505f4f68
span_literal:
This resulted in a list of differentially expressed genes (see table S8) per region, some of them being developmental regional patterning genes such as FOXG1 (forebrain), EN1 (midbrain-hindbrain boundary) and HOXD3 (hindbrain)

summary:
In Homo sapiens developing brain, FOXG1 is a forebrain patterning gene in oligodendrocyte precursor cells, EN1 marks the midbrain-hindbrain boundary, and HOXD3 marks the hindbrain.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:7a9f4a47a3c2e3c380cf
claim_id: claim:7a9f4a47a3c2e3c380cf
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
The cell populations inferred from this analysis were readily matched to the tumor cells and infiltrating lymphocytes, including macrophages and T cell classes, based on the specific expression of known markers such as CD3D and CD68

summary:
In Homo sapiens endometrioid adenocarcinoma tissue, T cells were identified by expression of CD3D and macrophages were identified by expression of CD68.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:d24bd152784b20ed8dfc
claim_id: claim:d24bd152784b20ed8dfc
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
The cell populations inferred from this analysis were readily matched to the tumor cells and infiltrating lymphocytes, including macrophages and T cell classes, based on the specific expression of known markers such as CD3D and CD68

summary:
In Homo sapiens endometrioid adenocarcinoma tissue, macrophages were identified by expression of CD68.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:d15481e7ba5b41a7fb62
claim_id: claim:d15481e7ba5b41a7fb62
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
We screened for cancer cells expressing at least one EMT marker, such as ACTA2 , EPCAM , CD44 , THY1 , VIM , FN1 , ZEB1 or CDH1

summary:
In Homo sapiens endometrioid adenocarcinoma, epithelial-to-mesenchymal transition cancer cells were screened using markers ACTA2, EPCAM, CD44, THY1, VIM, FN1, ZEB1, and CDH1.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:191451ba2ee63380814a
claim_id: claim:191451ba2ee63380814a
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
Genes that highly expressed in EA EMT compared with EA type cells were TCEAL4 , BAG1 , VAT1 , and GPI which are known to be gynecological tumor markers

summary:
In Homo sapiens endometrioid adenocarcinoma, TCEAL4, BAG1, VAT1, and GPI are highly expressed in endometrioid adenocarcinoma epithelial-to-mesenchymal transition cells compared with endometrioid adenocarcinoma cells.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:3c8de6db7119763fad50
claim_id: claim:3c8de6db7119763fad50
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
Sph cells, the gene expressed in the largest proportion of cells was FADS2 , followed by CTSV , S100B , and SCG2

summary:
In Homo sapiens endometrioid adenocarcinoma, spheroid cells highly express FADS2, CTSV, S100B, and SCG2.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:d40166f8d7c1b0cdf76d
claim_id: claim:d40166f8d7c1b0cdf76d
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
Moreover, EMT ( VIM , ZEB1 and ACTA2 ) and stem cell markers ( SOX2 , POU5F1 , NANOG , BMI1 , THY1 , CD24 , CD44 , PROM1 and REXO1 ) were also observed in Sph and Ser cells

summary:
In Homo sapiens endometrioid adenocarcinoma, stem cell markers SOX2, POU5F1, NANOG, BMI1, THY1, CD24, CD44, PROM1, and REXO1 were observed in spheroid cells.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:ae45a71f970522146a91
claim_id: claim:ae45a71f970522146a91
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
SOX2 , THY1 , CD24 and ZEB1 genes were expressed at a higher level in Sph cells compared with Ser cells

summary:
In Homo sapiens endometrioid adenocarcinoma, SOX2, THY1, CD24, and ZEB1 are expressed at higher levels in spheroid cells compared with serum-cultured cells.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:11e181e8b5412bf28707
claim_id: claim:11e181e8b5412bf28707
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal:
Single cell gene analysis showed that some SCCs positive for KRT14 expressed the adenocarcinoma marker KRT8 as well as the EMT markers VIM, and ZEB2

summary:
In Homo sapiens, squamous cell carcinoma cells positive for KRT14 expressed the adenocarcinoma marker KRT8 and the epithelial-to-mesenchymal transition markers VIM and ZEB2.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:b9d6ecf19da305b6c5ff
claim_id: claim:b9d6ecf19da305b6c5ff
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
span_literal: Loss of ER and PR is linked to aggressive tumors, specifically to the endometrioid subtype.
summary:
In Homo sapiens, loss of estrogen receptor and progesterone receptor is linked to aggressive endometrioid adenocarcinoma cells.


claim_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700:claim:8a6a42b155bc4d163ae1
claim_id: claim:8a6a42b155bc4d163ae1
paper_key: hca:0108_10.1038_s41598-017-14676-3_ca30704700
summary: In Homo sapiens, STMN1 and HER2 overexpression identifies high-risk endometrial cancer cells.
span_literal:
In addition, STMN1 and HER2 overexpression identifies high-risk patients and lymph node metastasis in endometrial cancer


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:db82ded05ac99c8d0e6d
claim_id: claim:db82ded05ac99c8d0e6d
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
Within myeloid cells we identified some of the most significantly upregulated genes in pediCD versus FGID to be CXCL9 and CXCL10 , canonical IFNγ-stimulated genes, and S100A8 and S100A9 which form the biomarker fecal calprotectin

summary:
In Homo sapiens, myeloid cells in pediatric Crohn's disease show upregulation of CXCL9, CXCL10, S100A8, and S100A9 compared to functional gastrointestinal disorder.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:cca0c84c0f3e3b70f420
claim_id: claim:cca0c84c0f3e3b70f420
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
In T cells, we noted that the cytotoxic genes GNLY and GZMA were amongst the most significantly upregulated in pediCD, with almost no genes downregulated

summary:
In Homo sapiens, T cells in pediatric Crohn's disease show upregulation of the cytotoxic genes GNLY and GZMA.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:cefe4a8f56e93b5017fd
claim_id: claim:cefe4a8f56e93b5017fd
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
summary: In Homo sapiens, a natural killer cell cluster is marked by enrichment of CCL3 and CD160.
span_literal:
using this ranking system, we identified CCL3 and CD160 as two genes significantly enriched in one NK cluster


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:576a9f5b0d4906ae27db
claim_id: claim:576a9f5b0d4906ae27db
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
Within B cells, we identified a strong division between non-cycling and cycling B cells, with those found in the cycling compartment readily identifiable by germinal center markers and further dark zone ( AICDA ) and light zone ( CD83 ) genes resulting in FG.B/DZ.AICDA.IGKC and FG.B/LZ.CD74.CD83 clusters

summary:
In Homo sapiens, germinal center dark zone B cells are marked by AICDA expression, while germinal center light zone B cells are marked by CD83 expression.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:40ff587d9ba75888f485
claim_id: claim:40ff587d9ba75888f485
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
cell subsets corresponding to monocytes ( CD14, FCGR3A, FCN1, S100A8, S100A9 , etc.), macrophages ( CSF1R, MERTK, MAF, C1QA , etc.), cDC1 ( CLEC9A, XCR1, BATF3 ), cDC2 ( FCER1A, CLEC10A, CD1C, IRF4 etc.), and pDCs ( IL3RA, LILRA4, IRF7 )

summary:
In Homo sapiens, monocytes are marked by CD14, FCGR3A, FCN1, S100A8, and S100A9; macrophages by CSF1R, MERTK, MAF, and C1QA; conventional dendritic cell type 1 by CLEC9A, XCR1, and BATF3; conventional dendritic cell type 2 by FCER1A, CLEC10A, CD1C, and IRF4; and plasmacytoid dendritic cells by IL3RA, LILRA4, and IRF7.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:b9a5736183722d17a70c
claim_id: claim:b9a5736183722d17a70c
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
T cells (joint expression of CD247, CD3D, CD3E, CD3G with TRAC, TRBC1, TRBC2 , or TRGC1, TRGC2 and TRDC ), and a combined cluster of cytotoxic cells (FG.T/NK/ILC.GNLY.TYROBP) likely including T cells, NK cells (lower expression of TCR-complex genes with NCAM1 , NCR1 and TYROBP ), and some ILCs ( KIT, NCR2, RORC and low expression of CD3-complex genes)

summary:
In Homo sapiens, T cells are identified by joint expression of CD247, CD3D, CD3E, CD3G with TRAC, TRBC1, and TRBC2; natural killer cells by NCAM1, NCR1, and TYROBP; and innate lymphoid cells by KIT, NCR2, and RORC.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:d9780401d40180c77f1a
claim_id: claim:d9780401d40180c77f1a
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
T cells (joint expression of CD247, CD3D, CD3E, CD3G with TRAC, TRBC1, TRBC2 , or TRGC1, TRGC2 and TRDC ), and a combined cluster of cytotoxic cells (FG.T/NK/ILC.GNLY.TYROBP) likely including T cells, NK cells (lower expression of TCR-complex genes with NCAM1 , NCR1 and TYROBP ), and some ILCs ( KIT, NCR2, RORC and low expression of CD3-complex genes)

summary:
In Homo sapiens, innate lymphoid cells are marked by KIT, NCR2, and RORC with low expression of CD3-complex genes.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:f49f4874b79bd73a946e
claim_id: claim:f49f4874b79bd73a946e
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
We note that the numerical majority of CD4 T cells (FG.T/NK/ILC.MAF.RPS26) and CD8 T cells (FG.T/NK/ILC.CCR7.SELL) expressed SELL and CCR7 thus identifying them as naïve T cells.

summary:
In Homo sapiens, the majority of CD4 and CD8 T cells in functional gastrointestinal disorder express SELL and CCR7, identifying them as naïve T cells.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:59af78c98d5538d0e2b2
claim_id: claim:59af78c98d5538d0e2b2
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
We readily identified subsets of stem cells ( LGR5 ), proliferating cells ( TOP2A ), goblet cells ( SPINK4 , ZG16 , various MUCs ), enteroendocrine cells ( SCG3, ISL1 ), Paneth cells ( ITLN2, PRSS2, LYZ ), tuft cells ( GNG13, SH2D6, TRPM5 ) and enterocytes ( APOC3, APOA1, FABP6, etc.)

summary:
In Homo sapiens, intestinal stem cells are marked by LGR5; goblet cells by SPINK4 and ZG16; enteroendocrine cells by SCG3 and ISL1; Paneth cells by ITLN2, PRSS2, and LYZ; tuft cells by GNG13, SH2D6, and TRPM5; and enterocytes by APOC3, APOA1, and FABP6.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:a8dbccf75da60896609a
claim_id: claim:a8dbccf75da60896609a
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
we readily identified vascular and lymphatic endothelial cells ( LYVE1, PROX1 ), with the vascular cells able to be further identified as capillaries ( CA4 ) or venular endothelial cells ( ACKR1, MADCAM1 )

summary:
In Homo sapiens, lymphatic endothelial cells are marked by LYVE1 and PROX1; capillary endothelial cells by CA4; and venular endothelial cells by ACKR1 and MADCAM1.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:b9a064b4b15f78a98ecf
claim_id: claim:b9a064b4b15f78a98ecf
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
We also identified a subset of cells (FG.Endth/Peri.FRZB.NOTCH3) expressing high levels of FRZB and NOTCH3 , which, rather than being arterioles, likely represent arteriole-associated pericytes or smooth muscle cells given the absence of EFNB2, SOX17, BMX, and HEY1, and the presence of ACTA2 and MYL9 , as cluster-defining genes

summary:
In Homo sapiens, arteriole-associated pericytes are marked by FRZB, NOTCH3, ACTA2, and MYL9, and lack EFNB2, SOX17, BMX, and HEY1.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:6cb7fa9f81ab97991879
claim_id: claim:6cb7fa9f81ab97991879
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
Within fibroblasts, we identified principal subsets characterized by their structural roles ( COL3A1, ADAMDEC1, FBLN1, LUM, etc.), myofibroblasts ( MYH11, ACTA2, ACTG2, etc.), and organization of lymphoid cells ( CCL19, CCL21 etc.)

summary:
In Homo sapiens, fibroblasts are characterized by COL3A1, ADAMDEC1, FBLN1, and LUM; myofibroblasts by MYH11, ACTA2, and ACTG2.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:af153e2218673c811d9a
claim_id: claim:af153e2218673c811d9a
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
summary: In Homo sapiens, follicular dendritic cells express FDCSP, CXCL13, and CR2.
span_literal:
FDCSP, CXCL13, and CR2, a key complement receptor which allows for complement-bound antigens to be recycled and presented by follicular dendritic cells


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:563a50004feaa5767b09
claim_id: claim:563a50004feaa5767b09
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
The mast cells recovered did not further sub-cluster in an automated fashion, and were largely marked by TPSB2 and TPSAB1 (>97%), with minimal CMA1 (<20%) expressing cells, suggesting they are largely classical MC-T cells in FGID intestine

summary:
In Homo sapiens, mast cells in functional gastrointestinal disorder intestine are largely marked by TPSB2 and TPSAB1, with minimal CMA1 expression, suggesting they are classical MC-T cells.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:dd8ff26a88b12b4a290d
claim_id: claim:dd8ff26a88b12b4a290d
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
The CD.B/LZ.CCL22.NPW was characterized by high levels of MYC , which has been shown to allow for further rounds of germinal center affinity maturation

summary:
In Homo sapiens, a germinal center light zone B cell cluster (CD.B/LZ.CCL22.NPW) is characterized by high levels of MYC.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:07d57e76d227fe7f6f40
claim_id: claim:07d57e76d227fe7f6f40
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
summary: In Homo sapiens, B cell clusters are characterized by expression of GPR183.
span_literal:
More numerous B cell clusters included ones characterized by expression of GPR183 , such as CD.B.CD69.GPR183 (also expressing IGHG1 ) and CD.B.RPS29.RPS21.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:c8853c61adb88fc49296
claim_id: claim:c8853c61adb88fc49296
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
We also noted a substantial expansion of clusters characterized by expression of CXCL9, CXCL10, and STAT1, canonical interferon-stimulated genes, observed in clusters such as CD.Mono/Mac.CXCL10.FCN1

summary:
In Homo sapiens, a monocyte/macrophage cluster (CD.Mono/Mac.CXCL10.FCN1) is characterized by expression of CXCL9, CXCL10, and STAT1.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:095c44fa8a82b0a7f8ab
claim_id: claim:095c44fa8a82b0a7f8ab
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
Moreover, we identified a cluster of inflammatory monocytes, CD.Mono.S100A8.S100A9, characterized by both CD14 and FCGR3A expression.

summary:
In Homo sapiens, inflammatory monocytes (CD.Mono.S100A8.S100A9) are characterized by CD14 and FCGR3A expression.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:900a44e23e9d96c9e96d
claim_id: claim:900a44e23e9d96c9e96d
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
NK cell clusters also expressed the highest levels of TYROBP , which encodes DAP12 and mediates signaling downstream from many NK receptors

summary:
In Homo sapiens, natural killer cell clusters express the highest levels of TYROBP, which encodes DAP12.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:9e703e59572034ed4045
claim_id: claim:9e703e59572034ed4045
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
ILC clusters such as CD.ILC.LST1.AREG or CD.ILC.IL22.KIT were characterized by an apparent ILC3 phenotype, with expression of KIT , RORC and IL22 , though they also expressed detectable transcripts of GATA3 in the same clusters

summary:
In Homo sapiens, innate lymphoid cell type 3 clusters are characterized by expression of KIT, RORC, IL22, and detectable GATA3.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:29d979e1f3be2b49a449
claim_id: claim:29d979e1f3be2b49a449
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
We detected several clusters expressing CD4 and lacking CD8A/CD8B , including regulatory T cells (CD.T.TNFRSF18.FOXP3), and MAF - and CCR6 -expressing helper T cells (CD.T.MAF.CTLA4).

summary:
In Homo sapiens, regulatory T cells (CD.T.TNFRSF18.FOXP3) express FOXP3 and TNFRSF18, while helper T cells (CD.T.MAF.CTLA4) express MAF and CCR6.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:1a76eb94adfbfbdc732e
claim_id: claim:1a76eb94adfbfbdc732e
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
summary: In Homo sapiens, intestinal stem cells are marked by LGR5, CCL25, and OLFM4 expression.
span_literal:
Amongst several clusters characterized by CCL25 and OLFM4 expression, we identified a subset marked by LGR5 expression, characteristic of intestinal stem cells (CD.EpithStem.LINC00176.RPS4YA1)


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:0418918b664c3765cbd2
claim_id: claim:0418918b664c3765cbd2
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
summary: In Homo sapiens, M cells are identified based on expression of SPIB.
span_literal:
We also found two clusters we labeled as M cells based on expression of SPIB (CD.Mcell.CCL23.SPIB; CD.MCell.CSRP2.SPIB)


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:e6f99b8c13eb780a7de4
claim_id: claim:e6f99b8c13eb780a7de4
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
we also identified a cluster of arteriolar endothelial cells, CD.Endth/Art.SEMA3G.SSUH2, identified by expression of HEY1, EFNB2, and SOX17

summary:
In Homo sapiens, arteriolar endothelial cells are identified by expression of HEY1, EFNB2, and SOX17.


claim_key: hca:0109_10.7554_elife.91792.1_056dda27be:claim:44891da6f2f78203924e
claim_id: claim:44891da6f2f78203924e
paper_key: hca:0109_10.7554_elife.91792.1_056dda27be
span_literal:
T.KLF2.FAM65B.CCR7.SELL (expressing markers of naïve T cells), T.GZMK.CCL5.HLA-B.TRAC (expressing markers of CD8 cytotoxic T cells) and T.S100A4.CCR6.TMSB4X.PFN1 (expressing markers of Th17 cells) were significantly decreased with anti-TNF treatment in pediatric and adult patients.

summary:
In Homo sapiens, naïve T cells express KLF2, CCR7, and SELL; CD8 cytotoxic T cells express GZMK and CCL5; and Th17 cells express S100A4 and CCR6.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:46ba7c2255564009df93
claim_id: claim:46ba7c2255564009df93
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
We defined 75 transcriptomically distinct cell types, including 45 inhibitory neuron types that express the GABAergic interneuron marker GAD1 , 24 excitatory neuron types that express the vesicular glutamate transporter SLC17A7 , and 6 non-neuronal types that express the glutamate transporter SLC1A3 .

summary:
In Homo sapiens middle temporal gyrus, inhibitory neuron types express the GABAergic interneuron marker GAD1.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:cce135de68c9bfa6ee1f
claim_id: claim:cce135de68c9bfa6ee1f
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
We defined 75 transcriptomically distinct cell types, including 45 inhibitory neuron types that express the GABAergic interneuron marker GAD1 , 24 excitatory neuron types that express the vesicular glutamate transporter SLC17A7 , and 6 non-neuronal types that express the glutamate transporter SLC1A3 .

summary:
In Homo sapiens middle temporal gyrus, excitatory neuron types express the vesicular glutamate transporter SLC17A7.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:ec23c833e58e81ac9791
claim_id: claim:ec23c833e58e81ac9791
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
We defined 75 transcriptomically distinct cell types, including 45 inhibitory neuron types that express the GABAergic interneuron marker GAD1 , 24 excitatory neuron types that express the vesicular glutamate transporter SLC17A7 , and 6 non-neuronal types that express the glutamate transporter SLC1A3 .

summary:
In Homo sapiens middle temporal gyrus, non-neuronal cell types express the glutamate transporter SLC1A3.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:16a6d6b98b4f4a8b7350
claim_id: claim:16a6d6b98b4f4a8b7350
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
Inhibitory neurons formed two major branches, distinguished by expression of ADARB2 and LHX6 , like mouse cortex where these branches correlate with developmental origins in CGE and medial ganglionic eminence (MGE), respectively 22 .

summary:
In Homo sapiens cortex, inhibitory neurons from the caudal ganglionic eminence branch are distinguished by expression of ADARB2, while the medial ganglionic eminence branch is distinguished by expression of LHX6.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:162f1cd5030382272de6
claim_id: claim:162f1cd5030382272de6
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
The LHX6 branch 36 , 37 included PVALB and SST subclasses and the ADARB2 branch had LAMP5/PAX6 and VIP subclasses.

summary:
In Homo sapiens cortex, the LHX6 branch of inhibitory neurons includes PVALB and SST subclasses, while the ADARB2 branch includes LAMP5/PAX6 and VIP subclasses.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:c3766e43c71f0c074f36
claim_id: claim:c3766e43c71f0c074f36
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
The LHX6 branch 36 , 37 included PVALB and SST subclasses and the ADARB2 branch had LAMP5/PAX6 and VIP subclasses.

summary:
In Homo sapiens cortex, the ADARB2 branch of inhibitory neurons includes LAMP5, PAX6, and VIP subclasses.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:87fd08c426de8ddf2f0c
claim_id: claim:87fd08c426de8ddf2f0c
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
summary: In Homo sapiens, caudal ganglionic eminence interneuron types do not express HTR3A.
span_literal:
Surprisingly, the mouse CGE interneuron marker HTR3A 38 was not expressed in human CGE types ( Fig. 3c ).


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:a320f69fc566e5c811d0
claim_id: claim:a320f69fc566e5c811d0
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
Among LAMP5/PAX6 types, only Inh L2-6 LAMP5 CA1 expressed LHX6 , suggesting possible origins in MGE like Lamp5 Lhx6 cells described in mouse 22 .

summary:
In Homo sapiens middle temporal gyrus, among LAMP5/PAX6 inhibitory neuron types, only Inh L2-6 LAMP5 CA1 expresses LHX6.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:103871e866e7a2d3e80c
claim_id: claim:103871e866e7a2d3e80c
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
Inh L2-5 PVALB SCUBE3 is a distinctive type that expresses chandelier cell marker UNC5B 41 and likely corresponds to these specialized cells.

summary:
In Homo sapiens middle temporal gyrus, Inh L2-5 PVALB SCUBE3 expresses the chandelier cell marker UNC5B.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:06d9876ace69442cc02c
claim_id: claim:06d9876ace69442cc02c
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
SnRNA-seq showed that Astro L1-2 FGFR3 GFAP expressed ID3 and had higher GFAP and AQP4 expression than Astro L1-6 FGFR3 SLC14A1 ( Fig. 4b , d ).

summary:
In Homo sapiens middle temporal gyrus, Astro L1-2 FGFR3 GFAP expresses ID3 and has higher GFAP and AQP4 expression than Astro L1-6 FGFR3 SLC14A1.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:00d53fffe5df8355d4ee
claim_id: claim:00d53fffe5df8355d4ee
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
summary: In Homo sapiens, chandelier cells express COL15A1 and NOG.
span_literal:
For example, chandelier cells express Vipr2 in mouse but COL15A1 and NOG in human ( Extended Data Fig. 10d .).


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:aeb5b03020b47cc01772
claim_id: claim:aeb5b03020b47cc01772
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
Clusters were assigned a broad class of interneuron, excitatory neuron, microglia, astrocyte, oligodendrocyte precursor, oligodendrocyte, or endothelial cell based on maximal median cluster CPM of GAD1, SLC17A7, TYROBP, AQP4, PDGFRA, OPALIN , or NOSTRIN, respectively.

summary:
In Homo sapiens middle temporal gyrus, interneurons are marked by GAD1, excitatory neurons by SLC17A7, microglia by TYROBP, astrocytes by AQP4, oligodendrocyte precursor cells by PDGFRA, oligodendrocytes by OPALIN, and endothelial cells by NOSTRIN.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:db0e2156d44dffe53063
claim_id: claim:db0e2156d44dffe53063
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
span_literal:
Three types were enriched in L2-L3, 10 RORB -expressing types were enriched in L3-6, and 4 THEMIS -expressing and 7 FEZF2− expressing types in L5-L6 ( Fig. 2a , Extended Data Fig. 6a ).

summary:
In Homo sapiens middle temporal gyrus, 10 excitatory neuron types enriched in layers 3-6 express RORB, 4 types in layers 5-6 express THEMIS, and 7 types in layers 5-6 express FEZF2.


claim_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941:claim:48bde882c48174e7cf8f
claim_id: claim:48bde882c48174e7cf8f
paper_key: hca:0110_10.1038_s41586-019-1506-7_3d44de0941
summary: In Homo sapiens cortex, some caudal ganglionic eminence-derived cell types in layer 1 express SST.
span_literal:
Some CGE-derived cell types in L1 expressed SST ( Fig. 3a , c ), as described in human 14 but not in mouse L1 interneurons 22 .


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:2da8405a119a6186df97
claim_id: claim:2da8405a119a6186df97
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
The alveolar bipotent/intermediate cells (AC14) express KRT8 , cell cyclin genes, and lineage markers from both AT1 and AT2.

summary:
In Homo sapiens, alveolar bipotent/intermediate cells express KRT8, cell cyclin genes, and lineage markers from both alveolar type 1 and alveolar type 2 cells.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:b8fd4dc5b73c1f0c5950
claim_id: claim:b8fd4dc5b73c1f0c5950
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
Notably, we identified endothelial cell populations that expressed major histocompatibility complex (MHC) class II genes such as HLA-DPA1 and HLA-DRA in a variety of adult tissues, including bladder (Fig. 2a ) and kidney.

summary:
In Homo sapiens, endothelial cell populations express major histocompatibility complex class II genes such as HLA-DPA1 and HLA-DRA in a variety of adult tissues including bladder and kidney.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:5d207f92b142adfe2821
claim_id: claim:5d207f92b142adfe2821
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
PECAM1 (also known as CD31 ) and the MHC class II marker HLA-DR further confirmed the existence of antigen-presenting endothelial cells in the adult human bladder

summary:
In Homo sapiens adult bladder, antigen-presenting endothelial cells are marked by PECAM1 (also known as CD31) and HLA-DR.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:4cf9fd7d418904c2445d
claim_id: claim:4cf9fd7d418904c2445d
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
C1 endothelial cells can be found in a wide range of adult organs such as bladder, kidney, artery, thyroid and omentum; they express HLA-DRA , CD74 and HLA-DRB1

summary:
In Homo sapiens, C1 endothelial cells express HLA-DRA, CD74, and HLA-DRB1 across a wide range of adult organs.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:a6d0bd838d79ff548989
claim_id: claim:a6d0bd838d79ff548989
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal: C7 endothelial cells come from adult kidney and express high levels of HLA-DQA1 , HLA-DPA1 and EMCN
summary:
In Homo sapiens adult kidney, C7 endothelial cells express high levels of HLA-DQA1, HLA-DPA1, and EMCN.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:958706329f425db9d8fc
claim_id: claim:958706329f425db9d8fc
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
Cells of C3, C5 and C8 highly expressed GCG , INS and SST , respectively, representing a tendency towards differentiation into alpha, beta and delta cells.

summary:
In Homo sapiens, pancreatic alpha cells highly express GCG, pancreatic beta cells highly express INS, and pancreatic delta cells highly express SST.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:5ea03165c3bab59cc8b6
claim_id: claim:5ea03165c3bab59cc8b6
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
Cells of C3, C5 and C8 highly expressed GCG , INS and SST , respectively, representing a tendency towards differentiation into alpha, beta and delta cells.

summary:
In Homo sapiens, pancreatic beta cells highly express INS, representing a tendency towards differentiation into beta cells.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:e4b8b7f7c3d2ed934cc9
claim_id: claim:e4b8b7f7c3d2ed934cc9
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal:
Cells of C3, C5 and C8 highly expressed GCG , INS and SST , respectively, representing a tendency towards differentiation into alpha, beta and delta cells.

summary:
In Homo sapiens, pancreatic delta cells highly express SST, representing a tendency towards differentiation into delta cells.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:d18ff2355d5474927c08
claim_id: claim:d18ff2355d5474927c08
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal: endothelial cell-related gene EDNRB
summary:
In Homo sapiens, endothelial cells are associated with expression of EDNRB, and neurons are associated with expression of MPZ.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:096007ee6c0579107dee
claim_id: claim:096007ee6c0579107dee
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal: SOX10 regulon for oligodendrocytes and SOX11 regulon for neurons are shared between human
summary:
In Homo sapiens, the SOX10 regulon is specific to oligodendrocytes and the SOX11 regulon is specific to neurons, and both are conserved between human and mouse.


claim_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09:claim:77f7cbbe794aa3b032dc
claim_id: claim:77f7cbbe794aa3b032dc
paper_key: hca:0111_10.1038_s41586-020-2157-4_a7b8710c09
span_literal: SOX11 regulon for neurons are shared between human
summary:
In Homo sapiens, the SOX11 regulon is specific to neurons, and is conserved between human and mouse.


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:0708d21861a1a6745a2e
claim_id: claim:0708d21861a1a6745a2e
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
summary: In Homo sapiens transplanted livers, B cells are marked by MS4A1 and BANK1.
span_literal:
B cells (MS4A1, BANK1), cholangiocyte (KRT7, KRT19), endothelial cells (FCN3, TSPAN7), erythroid cells (HBB, HBA1), hepatocytes (AHSG, APOC3), hepatic stellate cells (ACTA2), macrophages (CD68, MS4A7, MAFB), mast cells (TSPAB1, CPA3), monocytes (FCGR3B, CXCL8), neutrophils (RETN, CEACAM8), dendritic cells (PLD4, LILRA4), plasma cells (IGHG1, IGHA1), progenitor cells (TOP2A, ASPM), and T/ natural killer (NK) cells (CD3D, CD3E, KLRC1, GZMB, NCAM1)


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:240ab66718929b5b9e9c
claim_id: claim:240ab66718929b5b9e9c
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
summary:
In Homo sapiens transplanted livers, T/natural killer cells are marked by CD3D, CD3E, KLRC1, GZMB, and NCAM1.


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:9ec1c01e0ed663838622
claim_id: claim:9ec1c01e0ed663838622
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
summary: In Homo sapiens transplanted livers, S100A12+ neutrophils are marked by S100A12 and LTF.
span_literal:
wherein S100A12 and LTF are markers of S100A12+ neutrophils and PRTN3 is a marker of S100A12- neutrophils


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:0aca8a3058409db8b172
claim_id: claim:0aca8a3058409db8b172
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
span_literal:
MAIT cells in transplanted livers were associated with immune regulation effects according to the high expression levels of associated genes such as LTB, CCR6, IL4I1, and CCL20, along with significant enrichment of lymphocyte activation, leukocyte proliferation, and cytokine production and signaling.

summary:
In Homo sapiens transplanted livers, mucosal-associated invariant T cells show high expression of LTB, CCR6, IL4I1, and CCL20.


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:39b0da7badc7eebc5d88
claim_id: claim:39b0da7badc7eebc5d88
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
summary: In Homo sapiens, S100A12 is almost exclusively expressed by neutrophils.
span_literal:
Human S100A12 is almost exclusively expressed and secreted by neutrophils and is dramatically overexpressed at inflammation sites.


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:49ca96ce70c8ed1a611c
claim_id: claim:49ca96ce70c8ed1a611c
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
span_literal:
MAIT cells and GZMB+GZMK+ NK cells showed high expression of genes related to the IL18 signaling pathway and lymphocyte activation (IRF1, IL18, RAP, and TNFAIP3), whereas S100A12+ neutrophils showed high expression of S100A8 and S100A9 in our single-cell data

summary:
In Homo sapiens transplanted livers, mucosal-associated invariant T cells show high expression of IRF1, IL18, RAP, and TNFAIP3.


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:14f2f4dbdfcd035e96c4
claim_id: claim:14f2f4dbdfcd035e96c4
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
span_literal:
MAIT cells and GZMB+GZMK+ NK cells showed high expression of genes related to the IL18 signaling pathway and lymphocyte activation (IRF1, IL18, RAP, and TNFAIP3), whereas S100A12+ neutrophils showed high expression of S100A8 and S100A9 in our single-cell data

summary:
In Homo sapiens transplanted livers, granzyme B+ granzyme K+ natural killer cells show high expression of IRF1, IL18, RAP, and TNFAIP3.


claim_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08:claim:c14fe7195f598c0f10f9
claim_id: claim:c14fe7195f598c0f10f9
paper_key: hca:0112_10.1101_2022.02.09.479667_caaafb2f08
span_literal:
MAIT cells and GZMB+GZMK+ NK cells showed high expression of genes related to the IL18 signaling pathway and lymphocyte activation (IRF1, IL18, RAP, and TNFAIP3), whereas S100A12+ neutrophils showed high expression of S100A8 and S100A9 in our single-cell data

summary:
In Homo sapiens transplanted livers, S100A12+ neutrophils show high expression of S100A8 and S100A9.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:5ae30d0fb9319cd266a9
claim_id: claim:5ae30d0fb9319cd266a9
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
MAC-I and MAC-II expressing GPNMB and TREM2, which have been related to alveolar macrophages(23) and disease-associated macrophages (24), respectively.

summary:
In Homo sapiens, MAC-I lung-resident macrophages express GPNMB and MAC-II lung-resident macrophages express TREM2.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:708f1fed4069bbd423cf
claim_id: claim:708f1fed4069bbd423cf
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
summary: In Homo sapiens, MAC-IV macrophages in the lung express the highest levels of S100A8 and S100A9.
span_literal:
among lung macrophages, MAC-IV also expressed the highest levels of S100A8/9, which together form calprotectin, an antimicrobial peptide due to its ability to sequester iron and zinc.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:27658f5491c2f7276cf5
claim_id: claim:27658f5491c2f7276cf5
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Red pulp macrophages and Kupffer cells mainly populated the spleen and liver, as expected, and shared high expression of CD5L, SCL40A1 and the transcription factor SPIC(26), with higher expression of LYVE1 and ITGA9 distinguishing the Kupffer cells.

summary:
In Homo sapiens, red pulp macrophages and Kupffer cells share high expression of CD5L, SLC40A1, and SPIC, with higher expression of LYVE1 and ITGA9 distinguishing Kupffer cells from red pulp macrophages.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:9ab04b40bfaa7c0b4b34
claim_id: claim:9ab04b40bfaa7c0b4b34
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Red pulp macrophages and Kupffer cells mainly populated the spleen and liver, as expected, and shared high expression of CD5L, SCL40A1 and the transcription factor SPIC(26), with higher expression of LYVE1 and ITGA9 distinguishing the Kupffer cells.

summary:
In Homo sapiens, Kupffer cells are distinguished from red pulp macrophages by higher expression of LYVE1 and ITGA9, and share expression of CD5L, SLC40A1, and SPIC.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:21e76fe68dffc82194cf
claim_id: claim:21e76fe68dffc82194cf
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
summary: In Homo sapiens, a macrophage subtype in the thoracic lymph node expresses CHIT1 and CTSK.
span_literal:
We also found a macrophage subtype in the thoracic lymph node which expressed the chitin- and kinin-degrading enzymes CHIT1 and CTSK, respectively


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:e1d3fd983023162c301c
claim_id: claim:e1d3fd983023162c301c
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
In addition to three subsets of classical S100A8/9/12+ monocytes, we identified one non-classical monocyte subtype expressing FCGR3A and CX3CR1, and an intermediate monocyte subtype mainly restricted to the bone marrow with modest CD14 expression

summary:
In Homo sapiens, classical monocytes express S100A8, S100A9, and S100A12, non-classical monocytes express FCGR3A and CX3CR1, and intermediate monocytes express modest CD14.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:b2dbe7e00434abda0c43
claim_id: claim:b2dbe7e00434abda0c43
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
summary: In Homo sapiens, conventional dendritic cell type 1 expresses XCR1 and CLEC9A.
span_literal:
Among dendritic cells, DC1 expressed XCR1 and CLEC9A, consistent with their identity as conventional/classical DCs (cDC1), specialised for cross-presentation of antigen


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:e13e048411cfc2a92593
claim_id: claim:e13e048411cfc2a92593
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal: Two CD1C/IRF4+ subsets were evident, DC2 and a CCR7+ subset.
summary:
In Homo sapiens, DC2 and migratory dendritic cells express CD1C and IRF4, with the migratory subset also expressing CCR7.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:4cfa0978355ef971a85c
claim_id: claim:4cfa0978355ef971a85c
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
migDCs showed upregulation of AIRE, PDLIM4 and EBI3 in the TLN, and to a lesser extent in the MLN, while in the lung they upregulate CRLF2 (encoding TLSPR), chemokines (CCL22, CCL17), CSF2RA and GPR157

summary:
In Homo sapiens, migratory dendritic cells upregulate AIRE, PDLIM4, and EBI3 in the thoracic lymph node, and upregulate CRLF2, CCL22, CCL17, CSF2RA, and GPR157 in the lung.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:011b7ca0a0446ab9f1d3
claim_id: claim:011b7ca0a0446ab9f1d3
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Within the memory B cells, which were characterized by expression of B-cell lineage markers (MS4A1, CD19) and TNFRSF13B, we found a transcriptomically distinct cluster (MemB_ITGAX) positive for ITGAX, TBX21 and FCRL2, encoding CD11c, T-bet and the Fc receptor-like protein 2, respectively

summary:
In Homo sapiens, memory B cells express MS4A1, CD19, and TNFRSF13B, and the MemB_ITGAX subset is positive for ITGAX, TBX21, and FCRL2.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:a4307996c56719aef3cd
claim_id: claim:a4307996c56719aef3cd
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal: unlike conventional memory B cells, they showed low expression of CR2 (encoding CD21) and CD27
summary:
In Homo sapiens, MemB_ITGAX memory B cells show low expression of CR2 and CD27 unlike conventional memory B cells.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:9ec29099f19535668bc9
claim_id: claim:9ec29099f19535668bc9
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
we observed a small population that was distinct from the bulk of naive B cells, with unique expression of ITGA2B and SPARC (encoding the matricellular protein - secreted protein acidic rich in cysteine - that plays a key role in tissue stroma remodeling)

summary:
In Homo sapiens, a distinct naive B cell population uniquely expresses ITGA2B and SPARC (secreted protein acidic and rich in cysteine).


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:d4c5e824a045ba884323
claim_id: claim:d4c5e824a045ba884323
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
we identified two small populations of germinal center B cells expressing AICDA and BCL6 differing in their proliferative states (marked by MKI67).

summary:
In Homo sapiens, germinal center B cells express AICDA and BCL6, with proliferative states marked by MKI67.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:3cb82b4acf7299f5b460
claim_id: claim:3cb82b4acf7299f5b460
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
summary: In Homo sapiens, plasmablasts and plasma cells are marked by expression of CD38, XBP1, and SDC1.
span_literal:
We also uncovered two populations of plasmablasts (Plasma_prolif) and plasma cells (Plasma_ITGA8) marked by expression of CD38, XBP1 and SDC1.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:4eadc5d2d509f6b21340
claim_id: claim:4eadc5d2d509f6b21340
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Whereas the former expressed MKI67 and were found in the spleen, liver, bone marrow and blood, the latter expressed the integrin alpha-8-encoding gene ITGA8, the adhesion molecule CERCAM and was detected in the large intestine (CAE and TCL) in addition to the tissues of the Plasma_prolif population

summary:
In Homo sapiens, plasmablasts express MKI67, while Plasma_ITGA8 plasma cells express ITGA8 and CERCAM.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:467956e0b15ae48aea66
claim_id: claim:467956e0b15ae48aea66
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Naive/central memory CD4+ T cells were transcriptionally close to naive CD8+ T cells as defined by high expression of CCR7 and SELL

summary:
In Homo sapiens, naive/central memory CD4+ T cells and naive CD8+ T cells are defined by high expression of CCR7 and SELL.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:30933ec0461c6667c818
claim_id: claim:30933ec0461c6667c818
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
follicular helper T cells (Tfh) expressing CXCR5, regulatory T cells (Tregs) expressing FOXP3 and CTLA4, and effector memory CD4+ T cells.

summary:
In Homo sapiens, follicular helper T cells express CXCR5, and regulatory T cells express FOXP3 and CTLA4.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:ca24b39cc4c81ca88e7f
claim_id: claim:ca24b39cc4c81ca88e7f
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Within the effector memory CD8+ T compartment, we found three major subsets characterized by expression of the activation molecule CRTAM and the chemokine receptors CCR9 and CX3CR1, respectively.

summary:
In Homo sapiens, three effector memory CD8+ T cell subsets are characterized by expression of CRTAM, CCR9, and CX3CR1, respectively.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:e4d5b6476b6bdd887d29
claim_id: claim:e4d5b6476b6bdd887d29
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal: The CCR9+ population, which also expressed tissue-resident markers ITGAE and ITGA1
summary:
In Homo sapiens, the CCR9+ effector memory CD8+ T cell population expresses tissue-resident markers ITGAE and ITGA1.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:48c2fd5dd2a788ac9609
claim_id: claim:48c2fd5dd2a788ac9609
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
We also detected unconventional T cell subsets such as MAIT cells, characterised by expression of TRAV1-2 and SLC4A10, and a γδ T cell population overexpressed the integrin molecule ITGAD (CD11d)

summary:
In Homo sapiens, mucosal-associated invariant T cells are characterized by expression of TRAV1-2 and SLC4A10, and a gamma delta T cell population overexpresses ITGAD.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:6fd9296310f5f05ef1cd
claim_id: claim:6fd9296310f5f05ef1cd
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
NK cells in our data were represented by two clusters with high expression of either FCGR3A (encoding CD16) or NCAM1 (encoding CD56).

summary:
In Homo sapiens, natural killer cells are represented by two clusters with high expression of either FCGR3A or NCAM1.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:026595a4d40945ba6921
claim_id: claim:026595a4d40945ba6921
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
summary: In Homo sapiens, innate lymphoid cell type 3 is defined based on markers including PCDH9.
span_literal:
We defined the ILC3 population, within a small cluster mixed with NK cells, based on markers including PCDH9


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:1ced9c887983ef6a6bba
claim_id: claim:1ced9c887983ef6a6bba
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
summary: In Homo sapiens, a gamma delta T cell cluster expresses ITGAD, which encodes CD11d.
span_literal:
Here we manually annotated a γδ T cell cluster expressing ITGAD which encodes CD11d, part of a CD11d/CD18 heterodimer with the potential to interact with the cell adhesion molecule VCAM1 (48).


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:0e7768ce3308ba49cccf
claim_id: claim:0e7768ce3308ba49cccf
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
In the locations where γδ T cells were identified (liver, spleen and bone marrow), resident macrophages, such as red pulp macrophages, expressed high levels of VCAM1

summary:
In Homo sapiens, red pulp macrophages in the liver, spleen, and bone marrow express high levels of VCAM1.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:be615a0083e681f3f7e4
claim_id: claim:be615a0083e681f3f7e4
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
Comparisons of the two subpopulations with the blood TCRVδ1 and TCRVδ2 showed that they shared common markers for TCRVδ1 (CCL3, FCGR3A, CMC1, CD63) and TCRVδ2 (IL7R, LTB, SPOCK2, NFKBIA).

summary:
In Homo sapiens, TRDV1 gamma delta T cells share markers CCL3, FCGR3A, CMC1, and CD63, while TRDV2 gamma delta T cells share markers IL7R, LTB, SPOCK2, and NFKBIA.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:22a0e2226402427809af
claim_id: claim:22a0e2226402427809af
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
γδ T cells derived from the spleen, liver and bone marrow were uniquely overrepresented by specific markers, such as expression of TOX and TRGV4 in the TRDV1 subcluster, as well as CD55 and TRGV9 in the TRDV2 subcluster

summary:
In Homo sapiens, tissue-derived TRDV1 gamma delta T cells uniquely express TOX and TRGV4, while TRDV2 gamma delta T cells uniquely express CD55 and TRGV9.


claim_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4:claim:b1e9c58d439d01516506
claim_id: claim:b1e9c58d439d01516506
paper_key: hca:0113_10.1101_2021.04.28.441762_c83625bbe4
span_literal:
This CellTypist-annotated γδ T cell population was primarily derived from the gut and had high expression of the gut homing receptor CCR9, as well as several integrin-related genes including ITGAE and ITGA1

summary:
In Homo sapiens, a gut-derived gamma delta T cell population has high expression of CCR9, ITGAE, and ITGA1.


claim_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b:claim:00153bb84e4db26c343b
claim_id: claim:00153bb84e4db26c343b
paper_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b
span_literal:
Epithelial cell adhesion molecule (EpCAM), a surface marker of epithelial cells including acinar, ductal, and islet cells, is detected in the majority of fresh cells (>80%).

summary:
In Homo sapiens, epithelial cell adhesion molecule (EpCAM) is a positive surface marker of epithelial cells, including acinar, ductal, and islet cells in the pancreas.


claim_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b:claim:cf2369a6ee6db35cf621
claim_id: claim:cf2369a6ee6db35cf621
paper_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b
span_literal:
Among EpCAM + epithelial cells, HPx1, an exocrine cell marker (of acinar cells) was at very low abundance in fresh and cryopreserved cells, whereas HPi2, an endocrine pan-islet cell marker, was highly expressed in both fresh and cryopreserved epithelial cells, indicating the purity of the islet preparations used and the retention of characteristic surface markers after freeze-thaw.

summary:
In Homo sapiens, HPx1 is a marker of exocrine acinar cells, while HPi2 is an endocrine pan-islet cell marker highly expressed in islet cells.


claim_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b:claim:f49e97b2921b261f15a1
claim_id: claim:f49e97b2921b261f15a1
paper_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b
span_literal:
Among EpCAM + epithelial cells, HPx1, an exocrine cell marker (of acinar cells) was at very low abundance in fresh and cryopreserved cells, whereas HPi2, an endocrine pan-islet cell marker, was highly expressed in both fresh and cryopreserved epithelial cells, indicating the purity of the islet preparations used and the retention of characteristic surface markers after freeze-thaw.

summary:
In Homo sapiens, HPi2 is an endocrine pan-islet cell marker that is highly expressed in islet cells.


claim_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b:claim:a2400666f311f90eeb55
claim_id: claim:a2400666f311f90eeb55
paper_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b
summary: In Homo sapiens, CD31 is a surface marker for endothelial cells in the pancreas.
span_literal:
The cells were first stained with LIVE/DEAD Fixable near-IR dead cell dye to assess cell viability and analyzed using specific cell surface markers to stain distinct cell populations: CD31 for endothelial cells; CD45 for leukocytes; CD90 for mesenchymal cells; EpCAM for epithelial cells including acinar, ductal and islet cells; HPx1 for acinar cells and HPi2 for islet cells.


claim_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b:claim:c77b8c98ad9f64914b07
claim_id: claim:c77b8c98ad9f64914b07
paper_key: hca:0114_10.1371_journal.pone.0263005_b233a49b2b
summary:
In Homo sapiens, EpCAM is a surface marker for epithelial cells including acinar, ductal, and islet cells in the pancreas.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:b0d79cb855fa75d4b73d
claim_id: claim:b0d79cb855fa75d4b73d
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
summary: In Homo sapiens fetal liver, natural killer cells express NCAM1, CD7, IL2RB, and CD3E.
span_literal:
NK cells (expressing NCAM1 , CD7 , IL2RB and CD3E ) and ILC precursors (expressing KIT , KLRB1 , IL7R , RORC ) share a common origin in the lymphoid branch by PAGA and diffusion map analyses


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:134d1f66051d2e359461
claim_id: claim:134d1f66051d2e359461
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
summary: In Homo sapiens fetal liver, pre pro-B cells express CD34, SPINK2, and IGLL1.
span_literal:
The B-lineage cells are a continuum of differentiation states, from primitive ‘pre pro-B’ clusters expressing CD34 , SPINK2, and IGLL1 to ‘ pro-B’ and ‘pre-B’ clusters with increasing expression of B cell transcripts MS4A1 , CD79B, DNTT and HLA-DRA and reducing expression of JCHAIN and LTB


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:c1f3bd786ce2ea01e472
claim_id: claim:c1f3bd786ce2ea01e472
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
The B-lineage cells are a continuum of differentiation states, from primitive ‘pre pro-B’ clusters expressing CD34 , SPINK2, and IGLL1 to ‘ pro-B’ and ‘pre-B’ clusters with increasing expression of B cell transcripts MS4A1 , CD79B, DNTT and HLA-DRA and reducing expression of JCHAIN and LTB

summary:
In Homo sapiens fetal liver, pro-B and pre-B cells show increasing expression of MS4A1, CD79B, DNTT, and HLA-DRA and reducing expression of JCHAIN and LTB.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:267e10fb6ca8a6f49f4d
claim_id: claim:267e10fb6ca8a6f49f4d
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
Myeloid lineages stem from HSC/MPP via three intermediates: a neutrophil-myeloid progenitor expressing CD34 , SPINK2 , AZU1, PRTN3, ELANE , MPO and LYZ, monocyte- and DC-precursors

summary:
In Homo sapiens fetal liver, neutrophil-myeloid progenitors express CD34, SPINK2, AZU1, PRTN3, ELANE, MPO, and LYZ.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:ab73ed331f7eeb1d8069
claim_id: claim:ab73ed331f7eeb1d8069
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
DC and monocyte differentiation involve dynamic regulation of CLEC11A , BATF3 and ID2 while monocyte differentiation involves S100A8/A9, FCGR1A/2A and S100A12

summary:
In Homo sapiens fetal liver, monocyte differentiation involves dynamic regulation of S100A8, S100A9, FCGR1A, FCGR2A, and S100A12.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:afeb8b14f4b13bfc6458
claim_id: claim:afeb8b14f4b13bfc6458
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
NLT monocytes and DCs correlate strongly to fetal liver counterparts but macrophages are more tissue-specific, with VCAM1 expression in liver and F13A1 in skin, as is observed in adult tissue macrophages

summary:
In Homo sapiens, liver macrophages express VCAM1 while skin macrophages express F13A1. In Homo sapiens, skin macrophages express F13A1.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:d31d2b3fec90dc496597
claim_id: claim:d31d2b3fec90dc496597
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
Tissue specific gene expression patterns conferring functional specialization are discernible for DCs, for example S100A4 in skin DC1 (a molecule involved in T cell activation)

summary:
In Homo sapiens, skin dendritic cell type 1 expresses S100A4, a molecule involved in T cell activation.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:df231bed3535a761a9d1
claim_id: claim:df231bed3535a761a9d1
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
Tissue specific gene expression patterns conferring functional specialization are discernible for DCs, for example S100A4 in skin DC1 (a molecule involved in T cell activation) 39 and AOAH in liver DC2 (an enzyme involved in lipopolysaccharide response modulation)

summary:
In Homo sapiens, liver dendritic cell type 2 expresses AOAH, an enzyme involved in lipopolysaccharide response modulation.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:d168b92189a907058b74
claim_id: claim:d168b92189a907058b74
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
At the base of this cluster by FDG visualization is a population expressing CLEC9A, HLA-DRA and highest levels of primitive genes including MLLT3 consistent with a multipotent long-term repopulating (LT)-HSC

summary:
In Homo sapiens fetal liver, long-term repopulating haematopoietic stem cells express CLEC9A, HLA-DRA, and MLLT3.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:331736cb0365b5757636
claim_id: claim:331736cb0365b5757636
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
summary: In Homo sapiens fetal liver, erythroid cell specification involves TAL1 and KLF1.
span_literal:
Genes dynamically modulated in the specification of erythroid, megakaryocyte and mast cell lineages are distinct: TAL1 and KLF1 in erythroid; F11R , PBX1 and MEIS1 in megakaryocyte; and HES1 in mast cell differentiation


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:571d720c3bc932ef984f
claim_id: claim:571d720c3bc932ef984f
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal: Differentially regulated genes in the HSC/MPPs to B cell transition include SPIB , SP100 and CTSS
summary:
In Homo sapiens fetal liver, the haematopoietic stem cell/multipotent progenitor to B cell transition involves differentially regulated genes SPIB, SP100, and CTSS.


claim_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b:claim:2ffb2af4aaac554b6532
claim_id: claim:2ffb2af4aaac554b6532
paper_key: hca:0117_10.1038_s41586-019-1652-y_d63955188b
span_literal:
Fetal liver HSC/MPP have higher expression of genes encoding a heat shock protein ( HSPA1A ), potentially for maintenance of genome and proteome integrity, and lower levels of MHC-I ( HLA-B ) suggesting reduced antigen presenting potential compared to cord blood and adult BM HSC/MPPs

summary:
In Homo sapiens, fetal liver haematopoietic stem cells/multipotent progenitors have higher expression of HSPA1A and lower expression of HLA-B compared to cord blood and adult bone marrow haematopoietic stem cells/multipotent progenitors.


claim_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05:claim:76a28096d17dc4fce8bc
claim_id: claim:76a28096d17dc4fce8bc
paper_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05
span_literal:
Specifically, DAPL1 was predicted to be expressed in the cortex/medulla; DCD in sweat gland; DSC1 in IRS; DSG4 in cortex/medulla; CD74 in Langerhans cells; ELOVL5 in sebaceous glands; FABP9 in IRS; S100A3 in cuticle; and CD59 in melanocytes.

summary:
In Homo sapiens, DAPL1 was predicted to be expressed in the cortex/medulla of the hair follicle. In Homo sapiens, DSG4 was predicted to be expressed in cortex/medulla cells of the hair follicle.


claim_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05:claim:8f4617e8464b1eb9030f
claim_id: claim:8f4617e8464b1eb9030f
paper_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05
span_literal:
Specifically, DAPL1 was predicted to be expressed in the cortex/medulla; DCD in sweat gland; DSC1 in IRS; DSG4 in cortex/medulla; CD74 in Langerhans cells; ELOVL5 in sebaceous glands; FABP9 in IRS; S100A3 in cuticle; and CD59 in melanocytes.

summary:
In Homo sapiens, DSC1 was predicted to be expressed in inner root sheath cells. In Homo sapiens, FABP9 was predicted to be expressed in inner root sheath cells.


claim_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05:claim:735a49146f6f9145e911
claim_id: claim:735a49146f6f9145e911
paper_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05
span_literal:
To confirm the utility of scRNA-seq analysis in identifying previously undescribed subpopulation markers, we looked for enrichment of immunostaining with markers such as CXCL14 through immunostaining of hair follicle sections alongside known bulge marker, CD200, demonstrating co-localization

summary:
In Homo sapiens, CXCL14 and CD200 are markers of the hair follicle bulge cell population, with co-localization confirmed by immunostaining.


claim_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05:claim:9de890339d2a430b756d
claim_id: claim:9de890339d2a430b756d
paper_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05
span_literal:
Gene ontology analysis indicated enrichment of ECM protein synthesis associated with the bulge ( Figure S3 ), confirmed by co-localization of ECM markers TNC and EFEMP1

summary:
In Homo sapiens, TNC and EFEMP1 are extracellular matrix markers associated with the hair follicle bulge cell population.


claim_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05:claim:e21d210457d2bd643cb9
claim_id: claim:e21d210457d2bd643cb9
paper_key: hca:0118_10.1016_j.jid.2019.07.726_f70095db05
span_literal:
Also, as predicted, progressive loss of basal markers, KRT5, KRT14, and COL17A1 is observed coincident with a gain of spinous markers KRT10 and granular markers CALML5 expression as differentiation progresses

summary:
In Homo sapiens, KRT5, KRT14, and COL17A1 are positive markers of basal interfollicular epidermal cells, which are progressively lost during differentiation.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:bb7fb97eefd3a9a73b96
claim_id: claim:bb7fb97eefd3a9a73b96
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
We previously identified a role for cardiac resident macrophages in adaptive remodeling of the heart 25 – 27 . To assess whether cardiac resident macrophages are involved in cardiac recovery, we generated ridge plots and found that CD163 (specific marker of cardiac resident macrophages) expression was decreased pre-LVAD HF groups compared to donor controls.

summary:
In Homo sapiens, CD163 is a specific marker of cardiac resident macrophages, with expression decreased in heart failure groups compared to donor controls.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:1568b7207bb26aacb97a
claim_id: claim:1568b7207bb26aacb97a
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
Cell composition analysis showed expansion of Mac1 ( SPP1 and TPRG1 ) and Mac2 ( PLAUR and FOSB ) and reduction of Mac5 in the U-pre and U-post groups relative to donors and RR-pre and RR-post groups

summary:
In Homo sapiens, macrophage subtype 1 is marked by SPP1 and TPRG1, while macrophage subtype 2 is marked by PLAUR and FOSB.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:64633ac8bc55d717d34f
claim_id: claim:64633ac8bc55d717d34f
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
summary: In Homo sapiens, macrophage subtype 2 is an inflammatory population that expresses PLAUR.
span_literal:
Mac2 represented an inflammatory population that expressed PLAUR and several chemokines and cytokines


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:86d27d3f6395e2687328
claim_id: claim:86d27d3f6395e2687328
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
Notably, post-LVAD implantation RR-post converged toward a Mac5 phenotype, whereas U-post displayed a divergence toward Mac5 ( F13A1 and CD163 ), Mac2 ( PLAUR and FOSB ) and Mac4 ( IFI44L and MX2 )

summary:
In Homo sapiens, macrophage subtype 5 is marked by F13A1 and CD163, macrophage subtype 2 by PLAUR and FOSB, and macrophage subtype 4 by IFI44L and MX2.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:4fe78decf018cf52d291
claim_id: claim:4fe78decf018cf52d291
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
Cell composition and density analysis demonstrated that Fib1 ( SCN7A ) was enriched in donors, whereas Fib3 ( POSTN , THBS4 and MEOX1 ) and Fib7 were enriched in HF ( GPC6 )

summary:
In Homo sapiens, fibroblast subtype 1 is marked by SCN7A, fibroblast subtype 3 by POSTN, THBS4, and MEOX1, and fibroblast subtype 7 by GPC6.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:7a63f4e2eb99c1987f91
claim_id: claim:7a63f4e2eb99c1987f91
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
summary: In Homo sapiens, fibroblast subtype 3 expresses RUNX1, POSTN, FAP, and MEOX1.
span_literal:
Density plots revealed that RUNX1 was expressed in Fib3 along with genes known to contribute to myocardial fibrosis, including POSTN , FAP and MEOX1


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:f93cccd22873504f4afa
claim_id: claim:f93cccd22873504f4afa
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
Patients who did not recover displayed an enrichment in monocyte-derived macrophages expressing genes implicated in myocardial inflammation and HF ( PLAUR , IL1B , TNF and CCL4 )

summary:
In Homo sapiens, monocyte-derived macrophages express PLAUR, IL1B, TNF, and CCL4, genes implicated in myocardial inflammation and heart failure.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:cdbeab59df5a79686d97
claim_id: claim:cdbeab59df5a79686d97
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal: MYH6 and NPPA expression was enriched in CM0 and CM1, respectively
summary:
In Homo sapiens, MYH6 expression is enriched in cardiomyocyte subtype 0, and NPPA expression is enriched in cardiomyocyte subtype 1.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:e5c6bbb60f8f64a4012c
claim_id: claim:e5c6bbb60f8f64a4012c
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
The gene signature downregulated in recovery was most enriched in the CM2 subset, which expressed canonical HF genes, including ANKRD1 and NPPA

summary:
In Homo sapiens, cardiomyocyte subtype 2 expresses canonical heart failure genes including ANKRD1 and NPPA.


claim_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a:claim:3513a8b1d6f2623ba9ab
claim_id: claim:3513a8b1d6f2623ba9ab
paper_key: hca:0119_10.1038_s44161-023-00260-8_10d672103a
span_literal:
Within the recovered heart, cardiac fibroblasts retained signatures of fibroblast activation, including the expression of FAP , MEOX1 and POSTN

summary:
In Homo sapiens, cardiac fibroblasts express FAP, MEOX1, and POSTN as markers of fibroblast activation.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:962300a1a6ce1448c4cf
claim_id: claim:962300a1a6ce1448c4cf
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
The two smallest clusters expressed uroepithelial marker genes ( UPK3A , PSCA ), suggesting that they were probably uroepithelium (Fig. 1b ).

summary:
In Homo sapiens, uroepithelium is marked by expression of uroepithelial marker genes UPK3A and PSCA.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:a1c86557c2c7ebdf822d
claim_id: claim:a1c86557c2c7ebdf822d
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
We identify GPRC5A as a marker for cyst-lining collecting duct cells that exhibits increased transcription factor binding motif availability for NF-κB, TEAD, CREB and retinoic acid receptors.

summary:
In Homo sapiens, GPRC5A is identified as a marker for cyst-lining collecting duct cells in autosomal dominant polycystic kidney disease.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:2bbc8116a71db15fa550
claim_id: claim:2bbc8116a71db15fa550
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Subclustering of the PT lineage (PT-1 and PT-2, Fig. 1b ) in control kidneys identified FR-PTC as VCAM1 + PT subpopulation (Fig. 5a ).

summary:
In Homo sapiens, failed-repair proximal tubular cells are identified as a VCAM1-positive proximal tubular cell subpopulation in control kidneys.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:98984eb97df120ae1537
claim_id: claim:98984eb97df120ae1537
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
While PT-3/4 showed lower VCAM1 expression compared to PT-1, they also expressed higher levels of failed-repair signature genes ( CREB5, TPM1, PROM1 [ CD133 ] , TGFB2 , and HAVCR1 , Fig. 5c ) 12 , 21 , suggesting that VCAM1 may not be a sole defining marker of the FR-PTC state.

summary:
In Homo sapiens, proximal tubular cell subtypes PT-3 and PT-4 express lower VCAM1 but higher levels of failed-repair signature genes CREB5, TPM1, PROM1, TGFB2, and HAVCR1 compared to PT-1.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:cdf1201dc29215113dc1
claim_id: claim:cdf1201dc29215113dc1
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal: FIB1 and FIB2 expressed PDGFRB , and they were detected in both ADPKD and control kidneys.
summary:
In Homo sapiens, fibroblast subtypes FIB1 and FIB2 express PDGFRB in both autosomal dominant polycystic kidney disease and control kidneys.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:070b79f4c3b90c07cbe0
claim_id: claim:070b79f4c3b90c07cbe0
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal: In contrast, ACTA2 + myofibroblasts (MyoFIB) were exclusively detected in ADPKD kidneys.
summary:
In Homo sapiens, ACTA2-positive myofibroblasts are exclusively detected in autosomal dominant polycystic kidney disease kidneys.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:3a0cdaa5c36cff414ffa
claim_id: claim:3a0cdaa5c36cff414ffa
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
PKD-FIB expressed IL6 and FGF14 at high levels (Fig. 6b ), suggesting this subset as the major source of IL6 in ADPKD kidneys.

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific fibroblast subtype (PKD-FIB) expresses IL6 and FGF14 at high levels in ADPKD kidneys.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:08d6af70be3d193a342b
claim_id: claim:08d6af70be3d193a342b
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
summary: In Homo sapiens, tubular cells express markers SLC12A1, SLC34A1, and LRP2.
span_literal:
Two uncharacterized clusters (Unknown1 and Unknown2), expressed tubular cell markers ( SLC12A1 , SLC34A1 , and LRP2 ) that were detected in both ADPKD and control kidneys, most likely residual doublets despite our use of DoubletFinder 27 .


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:afa90025e54bc0b532cf
claim_id: claim:afa90025e54bc0b532cf
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
PKD-CNT (cluster5) and PKD-CDC1 (cluster0, Supplementary Fig. 13 ) differentially expressed MET , and PKD-CDC2 (cluster4) differentially expressed LCN2 .

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific connecting tubular cells and ADPKD-specific collecting duct cells 1 differentially express MET, while ADPKD-specific collecting duct cells 2 differentially express LCN2.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:f821237a84c3e774bccc
claim_id: claim:f821237a84c3e774bccc
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
PKD-CNT (cluster5) and PKD-CDC1 (cluster0, Supplementary Fig. 13 ) differentially expressed MET , and PKD-CDC2 (cluster4) differentially expressed LCN2 .

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific collecting duct cells 1 differentially express MET.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:251bb0e4ada9c3ef09ee
claim_id: claim:251bb0e4ada9c3ef09ee
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
PKD-CNT (cluster5) and PKD-CDC1 (cluster0, Supplementary Fig. 13 ) differentially expressed MET , and PKD-CDC2 (cluster4) differentially expressed LCN2 .

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific collecting duct cells 2 differentially express LCN2.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:26aba90bd604cd22d65a
claim_id: claim:26aba90bd604cd22d65a
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Interestingly, ADPKD subclusters upregulated the expression of CFTR (Fig. 7b and Supplementary Fig. 14 ), which encodes a chloride ion channel thought to be involved in cyst fluid accumulation 32 .

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease collecting duct subclusters upregulate expression of CFTR.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:c8ecc966d6b405bc2d17
claim_id: claim:c8ecc966d6b405bc2d17
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Among the differentially expressed genes among CNT_PC subtypes, we identified GPRC5A as one of the most differentially upregulated genes in PKD-CDC1 cluster ( P adj . < 1.0 × 10 −300 , Log-fold change = 1.62) as well as PKD-CDC2 cluster ( P adj . < 2.0 × 10 −90 , Log-fold change = 1.01, Fig. 7f , Supplementary Data 15 ).

summary:
In Homo sapiens, GPRC5A is one of the most differentially upregulated genes in autosomal dominant polycystic kidney disease-specific collecting duct cell 1 and autosomal dominant polycystic kidney disease-specific collecting duct cell 2 clusters.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:57f111074819e9ffae41
claim_id: claim:57f111074819e9ffae41
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Among the differentially expressed genes among CNT_PC subtypes, we identified GPRC5A as one of the most differentially upregulated genes in PKD-CDC1 cluster ( P adj . < 1.0 × 10 −300 , Log-fold change = 1.62) as well as PKD-CDC2 cluster ( P adj . < 2.0 × 10 −90 , Log-fold change = 1.01, Fig. 7f , Supplementary Data 15 ).

summary:
In Homo sapiens, GPRC5A is one of the most differentially upregulated genes in autosomal dominant polycystic kidney disease-specific collecting duct cell 2 cluster.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:a06448c75eaf4e7b14ba
claim_id: claim:a06448c75eaf4e7b14ba
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Immunofluorescence studies validated GPRC5A expression in CDH1 + cyst-lining cells (Fig. 7g , left), while its expression was faint in CDH1 + tubular cells in control kidneys (Fig. 7g , right).

summary:
In Homo sapiens, GPRC5A is expressed in CDH1-positive cyst-lining cells in autosomal dominant polycystic kidney disease kidneys.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:ab15e3a873747f95cef8
claim_id: claim:ab15e3a873747f95cef8
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
This subtype showed higher gene activity of GPRC5A and CD44 compared to other subpopulations (Fig. 8b ), suggesting that they represent the combined PKD-CDC1 and PKD-CDC2 subclusters previously identified in snRNA-seq data.

summary:
In Homo sapiens, the autosomal dominant polycystic kidney disease-specific collecting duct cell subtype shows higher gene activity of GPRC5A and CD44 compared to other subpopulations.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:01d3cf94860c8be89750
claim_id: claim:01d3cf94860c8be89750
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal: We identified a GPRC5A + CDH1 + PC lineage (PKD-CDC1) in cyst-lining cells (Fig. 7f, g ).
summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific collecting duct cell 1 of the principal cell lineage is marked by GPRC5A and CDH1 expression in cyst-lining cells.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:083ae8014e36abb99a13
claim_id: claim:083ae8014e36abb99a13
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
This subpopulation also differentially expresses MET , which mediated HGF-dependent mTORC activation in a mouse model of ADPKD 30 .

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific collecting duct cell 1 differentially expresses MET.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:485146367898fd170c13
claim_id: claim:485146367898fd170c13
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Another PC subpopulation (PKD-CDC2) expresses LCN2 that was shown to be expressed in cyst cells of a mouse model and human samples 31 .

summary:
In Homo sapiens, autosomal dominant polycystic kidney disease-specific collecting duct cell 2 expresses LCN2.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:7deb7b055b5763751eaf
claim_id: claim:7deb7b055b5763751eaf
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Here, we identified two fibroblast subtypes predominant in ADPKD kidneys: ACTA2 + myofibroblasts and FGF14 + IL6 + fibroblasts (Fig. 6 ).

summary:
In Homo sapiens, myofibroblasts in autosomal dominant polycystic kidney disease kidneys are marked by ACTA2 expression.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:39ee0fc833255d9d06b3
claim_id: claim:39ee0fc833255d9d06b3
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Here, we identified two fibroblast subtypes predominant in ADPKD kidneys: ACTA2 + myofibroblasts and FGF14 + IL6 + fibroblasts (Fig. 6 ).

summary:
In Homo sapiens, a fibroblast subtype in autosomal dominant polycystic kidney disease kidneys is marked by FGF14 and IL6 expression.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:d1a794e02e8ea6ea0b1f
claim_id: claim:d1a794e02e8ea6ea0b1f
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
Interestingly, we found the latter fibroblast subtype expressed IL6 at the highest level among all ADPKD kidney cell types (Fig. 4 , Supplementary Fig. 12a ), suggesting a role in the inflammatory microenvironment.

summary:
In Homo sapiens, the FGF14-positive IL6-positive fibroblast subtype expresses IL6 at the highest level among all autosomal dominant polycystic kidney disease kidney cell types.


claim_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943:claim:1ac06fb2d0c11f4cd41d
claim_id: claim:1ac06fb2d0c11f4cd41d
paper_key: hca:0120_10.1038_s41467-022-34255-z_c90043e943
span_literal:
PT-3 strongly expressed some FR-PTC marker genes ( CREB5, TPM1, PROM1 [ CD133 ] , TGFB2 ) but did not express VCAM1 , suggesting that this cell state may be transitioning either toward or away from VCAM1 + cell states.

summary:
In Homo sapiens, proximal tubular cell subtype PT-3 strongly expresses failed-repair proximal tubular cell marker genes CREB5, TPM1, PROM1, and TGFB2 but does not express VCAM1.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:4159615075a7ae999b51
claim_id: claim:4159615075a7ae999b51
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
Cluster 1 shows a basal cell state with expression of HOPX , IGFBP5, and LAMB3 ; and cluster 8 a more mature cell state with expression of KRT1 , KRT8 , LAT (Linker for Activation of T cells) and PTGER both required for TCR (T-cell antigen receptor) signalling

summary:
In Homo sapiens gingiva, basal epithelial cells express HOPX, IGFBP5, and LAMB3, while more mature epithelial cells express KRT1, KRT8, LAT, and PTGER.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:e807dd79b4626db426a3
claim_id: claim:e807dd79b4626db426a3
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
Cluster 1 shows a basal cell state with expression of HOPX , IGFBP5, and LAMB3 ; and cluster 8 a more mature cell state with expression of KRT1 , KRT8 , LAT (Linker for Activation of T cells) and PTGER both required for TCR (T-cell antigen receptor) signalling

summary:
In Homo sapiens gingiva, mature epithelial cells express KRT1, KRT8, LAT (Linker for Activation of T cells), and PTGER.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:3a620f092664435b9f60
claim_id: claim:3a620f092664435b9f60
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
summary: In Homo sapiens gingiva, proliferating basal cells are identified by expression of MKI67 and TOP2A.
span_literal:
Proliferating basal cells were identified in cluster 12 by expression of canonical marker genes of proliferating cells such as MKI67 and TOP2A


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:68656f5d7a7578e5aed6
claim_id: claim:68656f5d7a7578e5aed6
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
two endothelial (clusters 9 and 15) in which cluster 9 specifically expresses CLDN5 and EMCN and cluster 15 shows high expression of genes involved in the regulation of angiogenesis such as KDR , TIE1 , and SOX18

summary:
In Homo sapiens gingiva, endothelial cell cluster 9 expresses CLDN5 and EMCN, while endothelial cell cluster 15 expresses KDR, TIE1, and SOX18.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:7bcdbd8dc1f246a9383b
claim_id: claim:7bcdbd8dc1f246a9383b
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
B cells are shown in three distinct populations (clusters 0, 5, and 7) with clusters 0 and 5 expressing MZB1 , DERL3 , and IGHG4 characteristic of follicular and IgG plasma B cells respectively, and cluster 7 expressing MS4A1 and CD37 corresponding to memory B cells

summary:
In Homo sapiens gingiva, follicular and IgG plasma B cells express MZB1, DERL3, and IGHG4, while memory B cells express MS4A1 and CD37.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:ebbf5fb8d1998f19bff1
claim_id: claim:ebbf5fb8d1998f19bff1
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
summary: In Homo sapiens gingiva, dendritic cells of myeloid origin express CLEC9A and IRF8.
span_literal:
Dendritic cells of myeloid origin with high expression of CLEC9A and IRF8 are found in clusters 13 and 14


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:ca8aca91cbf7a889d875
claim_id: claim:ca8aca91cbf7a889d875
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
summary: In Homo sapiens gingiva, macrophages express LYZ and AIF1.
span_literal:
Macrophages are found in two populations (clusters 4 and 11) sharing high expression of LYZ and AIF1


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:eb36b9e1f3071e46cf54
claim_id: claim:eb36b9e1f3071e46cf54
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
one of the fibroblast-like populations (S0) GO enrichment included ‘upregulation of fibroblast proliferation’ with marked expression of PDGFRA , WNT5A, and IGF1

summary:
In Homo sapiens gingiva, fibroblast-like population S0 shows marked expression of PDGFRA, WNT5A, and IGF1.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:aab5f9f4375e36692bc5
claim_id: claim:aab5f9f4375e36692bc5
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
Another fibroblast-like population (S2) showed enrichment for genes involved in the negative regulation of Wnt signalling ( GREM1 , SFRP1 , APCDD1, and DKK3 )

summary:
In Homo sapiens gingiva, fibroblast-like population S2 shows enrichment for GREM1, SFRP1, APCDD1, and DKK3.


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:366729f069c4ab2dc51a
claim_id: claim:366729f069c4ab2dc51a
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
Highly ranked S5 markers included ILR1 , IFNγR1, and a member of the TNF-receptor superfamily – TNFRS11B (osteoprotegerin) which is a negative regulator of bone resorption and thus a key regulator of osteoclast activity

summary:
In Homo sapiens gingiva, fibroblast-like population S5 is marked by ILR1, IFNGR1, and TNFRSF11B (osteoprotegerin).


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:901167936060b4e5ae52
claim_id: claim:901167936060b4e5ae52
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal:
pro-inflammatory cluster S6, and it included the expression of the major histocompatibility complex (MHC) class II invariant chain ( CD74 ) and AREG

summary:
In Homo sapiens gingiva, pro-inflammatory fibroblast-like population S6 expresses CD74 (major histocompatibility complex class II invariant chain) and AREG (amphiregulin).


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:79be3b73346da7f037b6
claim_id: claim:79be3b73346da7f037b6
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
summary: In Homo sapiens gingiva, mature basal epithelial cell population E1 expresses DDR1 and COL17A1.
span_literal:
E1 indicated a more mature basal cell state with expression of DDR1 known as a cell surface receptor for fibrillar collagen, and COL17A1


claim_key: hca:0121_10.7554_elife.62810_069377f2ec:claim:82fd8962a02579a41017
claim_id: claim:82fd8962a02579a41017
paper_key: hca:0121_10.7554_elife.62810_069377f2ec
span_literal: Cycling basal cells were identified in E5 by expression of MKI67 and AURKB
summary:
In Homo sapiens gingiva, cycling basal cells (population E5) are identified by expression of MKI67 and AURKB.


claim_key: hca:0122_10.1038_s41467-020-18512-7_3e94374231:claim:b6bd1fcc0ee1bd2e0dae
claim_id: claim:b6bd1fcc0ee1bd2e0dae
paper_key: hca:0122_10.1038_s41467-020-18512-7_3e94374231
span_literal:
S100A13 was proposed as a marker of human odontoblasts. This gene is highly overexpressed in one of the subclusters, which is on t-SNE located in the close proximity to dental pulp. S100A13 was proved to be expressed in odontoblasts by immunohistochemistry.

summary:
In Homo sapiens, S100A13 is a marker of odontoblasts, as confirmed by immunohistochemistry in human teeth.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:3de43cb76e4a1ede4401
claim_id: claim:3de43cb76e4a1ede4401
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
FB3 and FB4 were defined by expression of GGT5 and EMILIN1 , markers recently reported in healthy kidney biopsy to represent interstitial fibroblasts

summary:
In Homo sapiens, interstitial fibroblast subtypes FB3 and FB4 are defined by expression of GGT5 and EMILIN1 in kidney.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:def254491c0f67644c30
claim_id: claim:def254491c0f67644c30
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
summary: In Homo sapiens, myofibroblast subtype FB4 uniquely expresses the marker POSTN in kidney.
span_literal:
FB4 uniquely expressed POSTN , another mFB marker recently defined in a cell subpopulation in human kidneys expressing the most ECM genes


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:3eed90ce5ed54d823eab
claim_id: claim:3eed90ce5ed54d823eab
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
FB1 and FB2 expressed the secretory factors CFD , SFRP2 and SFRP4 in addition to genes implicated in promoting cell migration such as MFAP5 , S100A4 and S100A10

summary:
In Homo sapiens, fibroblast subtypes FB1 and FB2 express the secretory factors CFD, SFRP2, and SFRP4 as well as migration-associated genes MFAP5, S100A4, and S100A10.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:4e38ebe87b9e969f544a
claim_id: claim:4e38ebe87b9e969f544a
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal: The infiltrating FB1 cells uniquely expressed FBN1 , IFI27 , WISP2 and PLA2G2A
summary:
In Homo sapiens, infiltrating fibroblast subtype FB1 uniquely expresses FBN1, IFI27, WISP2, and PLA2G2A.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:2f240dc0ef99c1a17fc3
claim_id: claim:2f240dc0ef99c1a17fc3
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal: The pericytes were characterized by PDGFRA -negative, PDGFRB -high, and RGS5 -high signature
summary:
In Homo sapiens, pericytes are characterized by negative PDGFRA expression and high PDGFRB and RGS5 expression.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:bf3f841eb05fc3a24c64
claim_id: claim:bf3f841eb05fc3a24c64
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
summary: In Homo sapiens, proximal tubular cells are defined by expression of MIOX, ANPEP, and SLC13A1.
span_literal:
A single proximal tubular (PT) cell cluster was defined by expression of MIOX , ANPEP , and SLC13A1 genes


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:397c75b8b5b342c9cc6d
claim_id: claim:397c75b8b5b342c9cc6d
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
summary: In Homo sapiens, tubular progenitor cells express PROM1, CD24, and VIM.
span_literal:
Tubular progenitor (PG) cells expressing PROM1 , CD24 , and VIM , however, separated into a major (PG1) and a minor (PG2) population.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:78576f3e37d33d8b081a
claim_id: claim:78576f3e37d33d8b081a
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
We note that PGs also expressed CDH2 (N-cadherin), a known marker for epithelial-mesenchymal transition (EMT)

summary:
In Homo sapiens, tubular progenitor cells express CDH2 (N-cadherin), a known marker for epithelial-mesenchymal transition.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:24fb8048c4e7e53a6951
claim_id: claim:24fb8048c4e7e53a6951
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
Furthermore, PG1 and PG2 are characterized by expression of injury markers HAVCR1 , LCN2 , and MYC , which are absent in PT

summary:
In Homo sapiens, tubular progenitor cell subtypes PG1 and PG2 are characterized by expression of injury markers HAVCR1, LCN2, and MYC, which are absent in proximal tubular cells.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:06cd3ad4b42462a79162
claim_id: claim:06cd3ad4b42462a79162
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
summary: In Homo sapiens kidney, loop of Henle cells are identified by unique expression of UMOD.
span_literal:
The other epithelial cells of the kidney such as LH, CD, and IC-A were identified by unique expression of marker genes UMOD , AQP2 , and ATP6V0D2 , respectively.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:53fbf27269850e642676
claim_id: claim:53fbf27269850e642676
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
Further investigation of endothelial cell types revealed four distinct subtypes; peritubular capillaries (PTC1-3) and descending vasa recta (DVR), primarily based on the distinct expression for PLVAP , AQP1 , and SLC14A

summary:
In Homo sapiens, endothelial cell subtypes including peritubular capillaries and descending vasa recta are distinguished by expression of PLVAP, AQP1, and SLC14A.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:5e88716993aa3f6989e7
claim_id: claim:5e88716993aa3f6989e7
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal: All EC subclusters shared expression of canonical markers such as PECAM1 and CDH5
summary:
In Homo sapiens, all endothelial cell subclusters share expression of canonical markers PECAM1 and CDH5.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:173eba6768c135bbc772
claim_id: claim:173eba6768c135bbc772
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
The PTC2 subpopulation, mostly composed of AK2 cells, was characterized by the unique expression of the structurally and functionally related cytokines CXCL9 , CXCL10 , and CXCL11

summary:
In Homo sapiens, peritubular capillary endothelial cell subpopulation PTC2 is characterized by unique expression of CXCL9, CXCL10, and CXCL11.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:a40ea6799693ca65f743
claim_id: claim:a40ea6799693ca65f743
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
summary: In Homo sapiens, activated T cells mostly express the receptor CXCR3.
span_literal:
These cytokines act as chemoattractants during inflammation through binding to the receptor CXCR3 mostly expressed by activated T cells


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:51cb887c26ab30cfa2a0
claim_id: claim:51cb887c26ab30cfa2a0
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
MACs expressed MS4A4A , STAB1 and SEPP1 typically considered as gene signatures of “alternatively activated” M2 macrophages

summary:
In Homo sapiens, alternatively activated M2 macrophages express MS4A4A, STAB1, and SEPP1 as gene signatures.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:dc4e1b88e610f7b08b59
claim_id: claim:dc4e1b88e610f7b08b59
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
Our migratory FB1 subpopulation showed high expression of MFAP5 , CD34 , THY1 , SLPI , and PLA2G2A , qualifying as MFAP5 hi FBs found in lungs.

summary:
In Homo sapiens, migratory fibroblast subtype FB1 shows high expression of MFAP5, CD34, THY1, SLPI, and PLA2G2A.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:4bf114f242c76e92cfa7
claim_id: claim:4bf114f242c76e92cfa7
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
migratory FB1 subpopulation expressed fibronectin ( FBN1 ), interferon-alpha-inducible protein 27 ( IFI27 ), WNT1-inducible signaling pathway protein 2 ( WISP2 ), and complement-decay-accelerating factor ( CD55

summary:
In Homo sapiens, migratory fibroblast subtype FB1 uniquely expresses fibrillin 1 (FBN1), interferon-alpha-inducible protein 27 (IFI27), WNT1-inducible signaling pathway protein 2 (WISP2), and complement-decay-accelerating factor (CD55).


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:73dc7a44620815d41a7a
claim_id: claim:73dc7a44620815d41a7a
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
migratory FB1 identified in the AK1 biopsy were differentiated from the non-migratory FB4 subpopulation by S100A4 expression in the migratory FBs

summary:
In Homo sapiens, migratory fibroblast subtype FB1 is differentiated from non-migratory fibroblast subtype FB4 by S100A4 expression.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:335f03ddef61b7844096
claim_id: claim:335f03ddef61b7844096
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal: NOTCH3 + RGS5 + PDGFRA - pericytes
summary:
In Homo sapiens, myofibroblast-generating pericytes are NOTCH3-positive, RGS5-positive, and PDGFRA-negative, while myofibroblast-generating fibroblasts include MEG3-positive PDGFRA-positive fibroblasts and COLEC11-positive CXCL12-positive fibroblasts.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:c11b62eeb3f16f32110f
claim_id: claim:c11b62eeb3f16f32110f
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
span_literal:
FB4 uniquely expressed POSTN , another mFB marker recently defined in a cell subpopulation in human kidneys expressing the most ECM genes

summary:
In Homo sapiens, fibroblast subtype FB4 uniquely expresses POSTN, a myofibroblast marker, in kidney.


claim_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3:claim:fb956abb5cffebd2281f
claim_id: claim:fb956abb5cffebd2281f
paper_key: hca:0123_10.1371_journal.pone.0267704_5a8157f0f3
summary: In Homo sapiens, fibroblast subtype FB4 uniquely expresses TNC, COL4A1, COL18A1, and TGM2.
span_literal:
Furthermore, FB4 cells uniquely expressed TNC , COL4A1 , COL18A1 , and TGM2 , genes involved in beta-1 integrin cell surface interactions and cell adhesion to the extracellular matrix.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:2929b924c4c9815c78c2
claim_id: claim:2929b924c4c9815c78c2
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Skin T cells consist of the three subtypes: cytotoxic (Tc) expressing CD8A/B , helper (Th) expressing CD4 , CD40LG and regulatory (Treg) expressing FOXP3 , TIGIT , CTLA4

summary:
In Homo sapiens skin, cytotoxic T cells express CD8A and CD8B, helper T cells express CD4 and CD40LG, and regulatory T cells express FOXP3, TIGIT, and CTLA4.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:caf2dc59c8edf5e2bbd2
claim_id: claim:caf2dc59c8edf5e2bbd2
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
We identified 4 clusters of innate lymphocytes that were CD161 ( KLRB1 ) + CD3 ( CD3D/CD3G ) - , consisting of ILC1/3, ILC2, ILC1/Natural Killer (NK) and NK ( KLRD1 + , GNLY + , PRF1 + , GZMB + and FCGR3A + ) cells

summary:
In Homo sapiens skin, innate lymphocytes are KLRB1 positive and CD3D/CD3G negative, and natural killer cells express KLRD1, GNLY, PRF1, GZMB, and FCGR3A.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:a1f313a5e77a1b53e3af
claim_id: claim:a1f313a5e77a1b53e3af
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
summary: In Homo sapiens skin, innate lymphoid cell 2 expresses IL7R, PTGDR2, and GATA3.
span_literal:
ILC2 ( IL7R , PTGDR2 , GATA3 ) has the most distinct signature in our data and in existing literature


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:1ee2b78149819496ad1a
claim_id: claim:1ee2b78149819496ad1a
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Mac1 shows higher expression of complement transcripts ( C1QB , C1QC ) and scavenger receptors ( CD163 , MARCO ), whereas Mac2 is characterized by the expression of F13A1 and transcription factors associated with alternative activation and suppression of immune responses ( NR4A1 , NR4A2 , KLF4 )

summary:
In Homo sapiens skin, macrophage 1 shows higher expression of C1QB, C1QC, CD163, and MARCO, whereas macrophage 2 is characterized by expression of F13A1, NR4A1, NR4A2, and KLF4.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:b9e6a4082dfdccd4631a
claim_id: claim:b9e6a4082dfdccd4631a
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
The clusters at the convergence of these branches (moDC3, LC4 and migratory DC (Mig. DC)) express transcripts associated with DC maturation ( CD83 , CCR7 , LAMP3 , CD40 , CD86 ), immunoregulation ( CD274 , IDO1 , CD200 , PDCD1LG2 , SOCS1 )

summary:
In Homo sapiens skin, migratory dendritic cells express dendritic cell maturation transcripts CD83, CCR7, LAMP3, CD40, CD86, and immunoregulation transcripts CD274, IDO1, CD200, PDCD1LG2, and SOCS1.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:5bdf521085ffa2c84e17
claim_id: claim:5bdf521085ffa2c84e17
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Undifferentiated keratinocytes transcribe basal epidermal proteins ( KRT5 , KRT14 ) and are abundant in the CD49f hi FACS gate

summary:
In Homo sapiens skin, undifferentiated keratinocytes express basal epidermal proteins KRT5 and KRT14.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:d4d18452d6407a4100fe
claim_id: claim:d4d18452d6407a4100fe
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Proliferating keratinocytes ( CDK1 + , PCNA + ) have lower expression of suprabasal cell transcripts e.g. KRT1 , KRT10 that characterize differentiated keratinocytes

summary:
In Homo sapiens skin, proliferating keratinocytes express CDK1 and PCNA, while differentiated keratinocytes are characterized by KRT1 and KRT10.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:b58d959ae9c6cd78f73a
claim_id: claim:b58d959ae9c6cd78f73a
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Proliferating keratinocytes ( CDK1 + , PCNA + ) have lower expression of suprabasal cell transcripts e.g. KRT1 , KRT10 that characterize differentiated keratinocytes

summary:
In Homo sapiens skin, differentiated keratinocytes are characterized by expression of KRT1 and KRT10.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:beeeff2356f4040033b3
claim_id: claim:beeeff2356f4040033b3
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Inflammatory differentiated keratinocytes co-express lower levels of undifferentiated ( TP63 , ITGA6 ) and differentiated ( KRT1 , KRT10 ) transcripts but additionally express ICAM1 , TNF and CCL20

summary:
In Homo sapiens skin, inflammatory differentiated keratinocytes express ICAM1, TNF, and CCL20, with lower levels of TP63, ITGA6, KRT1, and KRT10.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:42141d578cc6e2ed68d2
claim_id: claim:42141d578cc6e2ed68d2
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Endothelial cells in the healthy adult dermis comprise vascular endothelium ( PECAM1 , EMCN ) and lymphatic endothelium ( LYVE1 , PDPN )

summary:
In Homo sapiens dermis, vascular endothelial cells express PECAM1 and EMCN, while lymphatic endothelial cells express LYVE1 and PDPN.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:e095c693dac490502a4b
claim_id: claim:e095c693dac490502a4b
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
VE3, which forms ~2% of endothelial cells, is characterized by gamma synuclein ( SNCG ) and high expression of the venular capillary marker ACKR1

summary:
In Homo sapiens skin, vascular endothelial cell 3 is characterized by gamma synuclein (SNCG) and high expression of ACKR1.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:ad4d1feaca30341ce058
claim_id: claim:ad4d1feaca30341ce058
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
summary: In Homo sapiens skin, vascular endothelial cell 3 co-expresses IL6, IL33, SELE, and ICAM1.
span_literal:
In addition, VE3 co-express inflammatory cytokines, chemokines and leukocyte adhesion molecules including IL6 , IL33 , SELE and ICAM1


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:51b7302ebcbd521d306a
claim_id: claim:51b7302ebcbd521d306a
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Three fibroblast subsets expressing extracellular matrix (ECM)-related genes such as MMP2 , COL1A1 , COL1A2 and NT5E (encodes CD73) are present in healthy human skin, dominated by Fb1 fibroblasts with minor populations of Fb2 and Fb3 fibroblasts

summary:
In Homo sapiens skin, fibroblast subsets express extracellular matrix-related genes MMP2, COL1A1, COL1A2, and NT5E.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:21103f943bed194bb89e
claim_id: claim:21103f943bed194bb89e
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Notably, LE1 cells express higher levels of the chemoattractant CCL21 , which mediates dendritic cell (DC) migration into skin draining lymph nodes, as well as angiogenesis factors CAVIN2 and CCND1 , further supporting their function as initial afferent lymphatics

summary:
In Homo sapiens skin, lymphatic endothelial cell 1 expresses higher levels of CCL21, CAVIN2, and CCND1.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:4e3fa6814384226e276f
claim_id: claim:4e3fa6814384226e276f
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
These cells express genes characteristic of activated and pathogenic Th17 cells ( KLRB1 , RBPJ and CXCL13 )

summary:
In Homo sapiens skin, Tc17/Th17 cells express genes characteristic of activated and pathogenic T helper 17 cells including KLRB1, RBPJ, and CXCL13.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:6d33ed2317a8d449202b
claim_id: claim:6d33ed2317a8d449202b
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
In atopic dermatitis (AD), cytotoxic T cells expressing IL13 , IL22 and IFNG (Tc IL13/IL22) and in psoriasis, T cells expressing IL17A , IL17F , IFNG , IL22 and IL26 (Tc17/Th17) are found in both lesional and non-lesional skin, but are significantly enriched in lesional skin

summary:
In Homo sapiens atopic dermatitis skin, cytotoxic T cells (Tc IL13/IL22) express IL13, IL22, and IFNG.


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:7fc9b462968daf34d06b
claim_id: claim:7fc9b462968daf34d06b
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
span_literal:
Tc IL13/IL22 cells are dominant in the dermis of AD lesional skin ( Fig. 2D ) and express amphiregulin ( AREG ), a member of the epidermal growth factor family

summary:
In Homo sapiens atopic dermatitis skin, cytotoxic T cell IL13/IL22 cells express amphiregulin (AREG).


claim_key: hca:0124_10.1126_science.aba6500_a77c502bf7:claim:cab23c59436fdcc38ba6
claim_id: claim:cab23c59436fdcc38ba6
paper_key: hca:0124_10.1126_science.aba6500_a77c502bf7
summary: In Homo sapiens dermis, dermal regulatory T cells show high expression of SELL (CD62L).
span_literal:
Dermal Tregs show high mRNA and protein expression of the circulating central memory T cells marker CD62L ( SELL )


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:9fa8d78a7bf803377ee7
claim_id: claim:9fa8d78a7bf803377ee7
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Cluster 3 genes include immune cell-specific markers such as CD3D and CD79A , indicating a higher proportion of immune cells in hip skin

summary:
In Homo sapiens, CD3D and CD79A are immune cell-specific markers indicating a higher proportion of immune cells in hip skin.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:3ec4727fd3de89342a48
claim_id: claim:3ec4727fd3de89342a48
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
as well as melanocyte markers MLANA , TYR , and TYRP1 and Langerhans cell markers CD1A and CD207 (langerin), corresponding to cell types that are more abundant in non-palmoplantar skin.

summary:
In Homo sapiens, MLANA, TYR, and TYRP1 are markers of melanocytes that are more abundant in non-palmoplantar skin.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:e925b22565347569ed84
claim_id: claim:e925b22565347569ed84
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
as well as melanocyte markers MLANA , TYR , and TYRP1 and Langerhans cell markers CD1A and CD207 (langerin), corresponding to cell types that are more abundant in non-palmoplantar skin.

summary:
In Homo sapiens, CD1A and CD207 (langerin) are markers of Langerhans cells that are more abundant in non-palmoplantar skin.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:3d8e44a9f3819ec0a86f
claim_id: claim:3d8e44a9f3819ec0a86f
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Although this cluster was annotated based on high expression of traditional melanocyte markers, such as KIT and MLANA, these markers were expressed only in a subset of the cluster.

summary:
In Homo sapiens, KIT and MLANA are traditional melanocyte markers expressed in a subset of the melanocyte/melanocyte-like cluster.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:dab3529d28e25a1937d9
claim_id: claim:dab3529d28e25a1937d9
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
However, these two clusters share expression of markers such as WIF1 , MMP2 , SFRP2 , and DPP4 , suggesting a shared role in maintaining dermal and extracellular matrix homeostasis

summary:
In Homo sapiens, fibroblast II and fibroblast III share expression of WIF1, MMP2, SFRP2, and DPP4, suggesting a shared role in maintaining dermal and extracellular matrix homeostasis.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:790fa3577172dc6bdf99
claim_id: claim:790fa3577172dc6bdf99
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
However, these two clusters share expression of markers such as WIF1 , MMP2 , SFRP2 , and DPP4 , suggesting a shared role in maintaining dermal and extracellular matrix homeostasis

summary:
In Homo sapiens, fibroblast III shares expression of WIF1, MMP2, SFRP2, and DPP4 with fibroblast II, suggesting a shared role in maintaining dermal and extracellular matrix homeostasis.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:12c1f461fc784125a1ab
claim_id: claim:12c1f461fc784125a1ab
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
The palmo plantar-specific fibroblast II also expressed ANGPTL7 and PRG4 , markers of two previously identified minor fibroblast populations

summary:
In Homo sapiens, the palmoplantar-specific fibroblast II expressed ANGPTL7 and PRG4, markers of two previously identified minor fibroblast populations.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:10be243c8f16e64a5d99
claim_id: claim:10be243c8f16e64a5d99
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Fibroblast I is marked by upregulation of CXCL12 , APOE , FMO1 , and LSP1 , pointing to a role in immune surveillance and promotion of inflammation

summary:
In Homo sapiens, fibroblast I is marked by upregulation of CXCL12, APOE, FMO1, and LSP1, pointing to a role in immune surveillance and promotion of inflammation.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:45e50d1962c3f878102c
claim_id: claim:45e50d1962c3f878102c
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Fibroblast IV was marked by APOD , C2orf40 , ITGA6 , CLDN1, and TM4SF1 , overlapping with a specialized fibroblast population previously identified in single-cell analysis of healthy human skin

summary:
In Homo sapiens, fibroblast IV was marked by APOD, C2orf40, ITGA6, CLDN1, and TM4SF1, overlapping with a specialized fibroblast population previously identified in single-cell analysis of healthy human skin.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:9f75f834392ab0972139
claim_id: claim:9f75f834392ab0972139
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
and one cluster (stressed/adnexae) marked by higher expression of stress-response genes such as KRT6B , as well as genes expressed in the pilosebaceous units and eccrine glands, i.e., MGST1

summary:
In Homo sapiens, the stressed/adnexae keratinocyte cluster is marked by higher expression of KRT6B and MGST1.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:f1d301f4395e6529d87e
claim_id: claim:f1d301f4395e6529d87e
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
As expected, KRT9 , a well-known marker of suprabasal keratinocytes in palmoplantar skin, 4 , 22 , 23 is strongly expressed in the differentiated keratinocytes of the palm and sole

summary:
In Homo sapiens, KRT9 is a well-known marker of suprabasal keratinocytes in palmoplantar skin, strongly expressed in differentiated keratinocytes of the palm and sole.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:63ebac56e8fb5193ebd9
claim_id: claim:63ebac56e8fb5193ebd9
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal: Spinous II, which is enriched in the palm, is marked by high expression of FOS and GADD45B
summary:
In Homo sapiens, spinous II keratinocytes, enriched in the palm, are marked by high expression of FOS and GADD45B.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:4af3ddbba853711a7734
claim_id: claim:4af3ddbba853711a7734
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
spinous I, enriched in the sole, lacks FOS expression but shows expression of GRHL3 , FOSL1 , and SOX9

summary:
In Homo sapiens, spinous I keratinocytes, enriched in the sole, lack FOS expression but show expression of GRHL3, FOSL1, and SOX9.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:953537e7ae1f844adab9
claim_id: claim:953537e7ae1f844adab9
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Fibroblast I, which is found in both hip and palmoplantar skin, matches a previously described major fibroblast population defined by FMO1 / LSP1 expression.

summary:
In Homo sapiens, fibroblast I matches a previously described major fibroblast population defined by FMO1 and LSP1 expression.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:6e19406f472bdbffab94
claim_id: claim:6e19406f472bdbffab94
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Fibroblasts II and III are both marked by SFRP2 and DPP4 , matching a second major fibroblast population in human skin that is implicated in matrix deposition and extracellular matrix homeostasis.

summary:
In Homo sapiens, fibroblast II and fibroblast III are both marked by SFRP2 and DPP4, matching a major fibroblast population implicated in matrix deposition and extracellular matrix homeostasis.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:cadc369e06d8c3979cdb
claim_id: claim:cadc369e06d8c3979cdb
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Fibroblasts II and III are both marked by SFRP2 and DPP4 , matching a second major fibroblast population in human skin that is implicated in matrix deposition and extracellular matrix homeostasis.

summary:
In Homo sapiens, fibroblast III is marked by SFRP2 and DPP4, matching a major fibroblast population implicated in matrix deposition and extracellular matrix homeostasis.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:4f70a2537c599fc564da
claim_id: claim:4f70a2537c599fc564da
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
We note that the palmoplantar fibroblast II shares certain key markers, namely ANGPTL7 and PRG4 , with two other previously identified minor fibroblast populations

summary:
In Homo sapiens, the palmoplantar fibroblast II shares key markers ANGPTL7 and PRG4 with two previously identified minor fibroblast populations.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:8fd75e192b0841363964
claim_id: claim:8fd75e192b0841363964
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
The final cluster, fibroblast IV, is marked by expression of ANGPTL7 and C2orf40 , matching a minor, specialized population of fibroblasts

summary:
In Homo sapiens, fibroblast IV is marked by expression of ANGPTL7 and C2orf40, matching a minor, specialized population of fibroblasts.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:1d3df954adaf65e4536b
claim_id: claim:1d3df954adaf65e4536b
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
This population is also defined by exclusive expression of ITGA6 and ITGB4 , which have been shown to be expressed specifically in Schwann cells and perineural fibroblasts in the dermis

summary:
In Homo sapiens, fibroblast IV is defined by exclusive expression of ITGA6 and ITGB4, which are expressed specifically in Schwann cells and perineural fibroblasts in the dermis.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:c1584bf889e688125103
claim_id: claim:c1584bf889e688125103
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
Cluster 3 is marked by specific immune cell markers, such as CD3D , CD79A , and CD207 , suggesting that hip skin contains a higher fraction of immune cells than palmoplantar skin.

summary:
In Homo sapiens, immune cells in hip skin are marked by CD3D, CD79A, and CD207, suggesting a higher fraction of immune cells than in palmoplantar skin.


claim_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65:claim:3ebcd20bfb039ab657f5
claim_id: claim:3ebcd20bfb039ab657f5
paper_key: hca:0125_10.1016_j.celrep.2023.111994_fd20125b65
span_literal:
CCL27 , encoding a T cell activating protein and one of the top upregulated genes in non-palmoplantar skin in the bulk RNA-seq analysis, is selectively expressed in all hip keratinocytes

summary:
In Homo sapiens, CCL27, encoding a T cell activating protein, is selectively expressed in all hip keratinocytes.


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:9227020c6387c01ebe95
claim_id: claim:9227020c6387c01ebe95
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
We used smoothed expression of these and other common T-cell subset markers ( Methods , Supplementary Table 6 ) to classify the cells into naive ( CCR7+CD45RA+ ), central memory (CM, CCR7+CD45RO+ ), effector memory (EM, CCR7−CD45RO+ ), terminally differentiated effector memory re-expressing CD45RA (EMRA, CCR7 − CD45RA +), and regulatory T-cells ( FOXP3 +)

summary:
In Homo sapiens, naive T cells are classified by positive expression of CCR7 and CD45RA (PTPRC isoform).


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:4c6fd640780f499574dc
claim_id: claim:4c6fd640780f499574dc
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
We used smoothed expression of these and other common T-cell subset markers ( Methods , Supplementary Table 6 ) to classify the cells into naive ( CCR7+CD45RA+ ), central memory (CM, CCR7+CD45RO+ ), effector memory (EM, CCR7−CD45RO+ ), terminally differentiated effector memory re-expressing CD45RA (EMRA, CCR7 − CD45RA +), and regulatory T-cells ( FOXP3 +)

summary:
In Homo sapiens, central memory T cells are classified by positive expression of CCR7 and CD45RO (PTPRC isoform).


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:482532787ca36a8ac1db
claim_id: claim:482532787ca36a8ac1db
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
We used smoothed expression of these and other common T-cell subset markers ( Methods , Supplementary Table 6 ) to classify the cells into naive ( CCR7+CD45RA+ ), central memory (CM, CCR7+CD45RO+ ), effector memory (EM, CCR7−CD45RO+ ), terminally differentiated effector memory re-expressing CD45RA (EMRA, CCR7 − CD45RA +), and regulatory T-cells ( FOXP3 +)

summary:
In Homo sapiens, effector memory T cells are classified by negative expression of CCR7 and positive expression of CD45RO (PTPRC isoform).


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:a1132e6693e31e24683b
claim_id: claim:a1132e6693e31e24683b
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
summary:
In Homo sapiens, terminally differentiated effector memory T cells re-expressing CD45RA are classified by negative expression of CCR7 and positive expression of CD45RA (PTPRC isoform).


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:1c04841e4a64782efc0b
claim_id: claim:1c04841e4a64782efc0b
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
We further distinguished CD4+ cytotoxic cells (CD4+ CTLs, NKG7 +), prevalent in our dataset, from other EMs with a more typical helper phenotype

summary:
In Homo sapiens, CD4-positive cytotoxic T lymphocytes are distinguished from effector memory T cells by positive expression of NKG7.


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:73b5cf0511cbb8680cd2
claim_id: claim:73b5cf0511cbb8680cd2
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
summary: In Homo sapiens, regulatory T cells express classic markers IL2RA (CD25) and CTLA4.
span_literal:
We also observed other classic markers of T-regs among the top differentially expressed genes including IL2RA (CD25) and CTLA4


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:c9ef2bba0434763a62ec
claim_id: claim:c9ef2bba0434763a62ec
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
Tisa-cel responders had more cells from the cluster expressing CM markers CCR7 and LEF1 (two-tailed t-test p=0.0057, Fig. 4c , d ), and expressed the transcription factor STAT1.

summary:
In Homo sapiens, central memory T cells express the markers CCR7, LEF1, and the transcription factor STAT1.


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:d72ee525a247e0eb7554
claim_id: claim:d72ee525a247e0eb7554
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
Their cells were distinguished by high expression of KLRG1 and lack of L-selectin ( SELL) , a phenotype attributed to short-lived effector cells (SLECs)

summary:
In Homo sapiens, short-lived effector cells are distinguished by high expression of KLRG1 and negative expression of SELL (L-selectin).


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:0a97dc1c31c942ddc77f
claim_id: claim:0a97dc1c31c942ddc77f
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
Conventional T-cells were classified by differentiation state as Naive ( CCR7 + CD45RA +), CM ( CCR7 + CD45RA −), EM ( CCR7 − CD45RA −), and TEMRA ( CCR7 − CD45RA +).

summary:
In Homo sapiens, naive T cells are classified as CCR7-positive and CD45RA-positive, central memory T cells as CCR7-positive and CD45RA-negative, effector memory T cells as CCR7-negative and CD45RA-negative, and terminally differentiated effector memory T cells re-expressing CD45RA as CCR7-negative and CD45RA-positive.


claim_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71:claim:85c5eaae7245aeadb310
claim_id: claim:85c5eaae7245aeadb310
paper_key: hca:0126_10.1038_s41591-022-01959-0_cbdd92bc71
span_literal:
We further distinguished two additional T-cell subsets: T-regs ( FOXP3 +) and CD4+ CTLs ( CD4+NKG7 +).

summary:
In Homo sapiens, regulatory T cells are marked by positive expression of FOXP3, and CD4-positive cytotoxic T lymphocytes are marked by positive expression of NKG7.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:924990278fcede105a36
claim_id: claim:924990278fcede105a36
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
ASCs resembled colonic stem and progenitor cells, expressed genes indicative of WNT pathway activation ( LGR5 , OLFM4 , ASCL2 , AXIN2 , RNF43 , and EPHB2 )

summary:
In Homo sapiens, adenoma-specific cells express LGR5, OLFM4, ASCL2, AXIN2, RNF43, and EPHB2, indicative of WNT pathway activation, resembling colonic stem and progenitor cells.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:2969dec93e89ebed1eab
claim_id: claim:2969dec93e89ebed1eab
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
SSCs highly expressed genes not normally observed in the colon ( MUC5AC , AQP5 , TACSTD2 [TROP2], TFF2 , MUC17 , and MSLN ) but rather found in other endodermal organs, most notably, the gastric epithelium

summary:
In Homo sapiens, serrated-specific cells highly express MUC5AC, AQP5, TACSTD2, TFF2, MUC17, and MSLN, genes normally found in the gastric epithelium rather than the colon.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:2b7a1c94edaa1ee0f6bc
claim_id: claim:2b7a1c94edaa1ee0f6bc
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
SSCs also expressed functional goblet cell genes, including TFF3 and MUC2 , but surprisingly without the master secretory cell TF ATOH1 and the ATOH1 regulon, suggesting SSCs harbor a mixed cellular identity

summary:
In Homo sapiens, serrated-specific cells express the goblet cell genes TFF3 and MUC2 but lack expression of the master secretory cell transcription factor ATOH1.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:239d622547742caca013
claim_id: claim:239d622547742caca013
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
CDX2 was expressed in most colonic cell types, including ASCs; however, it was downregulated in SSCs, supporting a loss of regional identity in these cells

summary:
In Homo sapiens, CDX2 is expressed in adenoma-specific cells but is downregulated in serrated-specific cells, supporting a loss of regional identity.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:0b58af4af7b663284ae8
claim_id: claim:0b58af4af7b663284ae8
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Stem cell markers, OLFM4 and SOX9, were abundant in ADs but were significantly reduced in HPs and SSLs

summary:
In Homo sapiens, the stem cell markers OLFM4 and SOX9 are abundant in conventional adenomas but significantly reduced in hyperplastic polyps and sessile serrated lesions.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:569a9ac8f1995b15e15c
claim_id: claim:569a9ac8f1995b15e15c
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Stem cell markers, OLFM4 and SOX9, were abundant in ADs but were significantly reduced in HPs and SSLs

summary:
In Homo sapiens, the stem cell markers OLFM4 and SOX9 are significantly reduced in hyperplastic polyps compared to conventional adenomas.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:1072b9291eb4719d5d96
claim_id: claim:1072b9291eb4719d5d96
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Stem cell markers, OLFM4 and SOX9, were abundant in ADs but were significantly reduced in HPs and SSLs

summary:
In Homo sapiens, the stem cell markers OLFM4 and SOX9 are significantly reduced in sessile serrated lesions compared to conventional adenomas.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:b8200ab69ba897047f62
claim_id: claim:b8200ab69ba897047f62
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal: MUC5AC, a marker of SSCs, was highly expressed in HPs and SSLs but not in normal biopsies and ADs
summary:
In Homo sapiens, MUC5AC, a marker of serrated-specific cells, is highly expressed in hyperplastic polyps and sessile serrated lesions but not in normal biopsies and conventional adenomas.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:372fbe4972d8a7af5d10
claim_id: claim:372fbe4972d8a7af5d10
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Positive MUC5AC and MSLN expression, coupled to loss of CDX2 expression, distinguished metaplastic cells from LGR5 /β-catenin-expressing proliferative stem cells within the same tumor

summary:
In Homo sapiens, positive MUC5AC and MSLN expression coupled to loss of CDX2 expression distinguishes metaplastic cells from LGR5-expressing proliferative stem cells within microsatellite unstable colorectal cancer.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:e7f15efb0a9c854d10e2
claim_id: claim:e7f15efb0a9c854d10e2
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Positive MUC5AC and MSLN expression, coupled to loss of CDX2 expression, distinguished metaplastic cells from LGR5 /β-catenin-expressing proliferative stem cells within the same tumor

summary:
In Homo sapiens, LGR5 expression marks proliferative stem cells, distinguishing them from metaplastic cells within microsatellite unstable colorectal cancer.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:3a44b419c28bde421411
claim_id: claim:3a44b419c28bde421411
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Nuclear CDX2 was detected in the normal colon and in ADs but was decreased in HPs and absent in SSLs

summary:
In Homo sapiens, CDX2 protein is detected in conventional adenomas but is decreased in hyperplastic polyps and absent in sessile serrated lesions.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:a7e7dee5f3a3e4a7107a
claim_id: claim:a7e7dee5f3a3e4a7107a
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
Stem cell markers (OLFM4, SOX9) were expressed throughout MSS CRCs, and they uniformly lacked MUC5AC expression

summary:
In Homo sapiens, microsatellite stable colorectal cancers express the stem cell markers OLFM4 and SOX9 throughout and uniformly lack MUC5AC expression.


claim_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b:claim:05495d083dcb8db37999
claim_id: claim:05495d083dcb8db37999
paper_key: hca:0127_10.1016_j.cell.2021.11.031_38bd899f1b
span_literal:
SOX9 was generally overexpressed in MSI-H CRCs, suggesting all malignant cells gained some level of stemness

summary:
In Homo sapiens, SOX9 is generally overexpressed in microsatellite instability-high colorectal cancers, suggesting malignant cells gained stemness.


claim_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1:claim:bae47c492050bd81de58
claim_id: claim:bae47c492050bd81de58
paper_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1
summary: In Homo sapiens, endothelial cells are defined by expression of CDH5, KDR, FLT1, and ESAM.
span_literal:
The endothelial cluster was defined by a gene set expected to be present in ECs, including CDH5, KDR, FLT1, and ESAM


claim_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1:claim:715dcefdcbeefe215477
claim_id: claim:715dcefdcbeefe215477
paper_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1
span_literal:
This analysis also revealed EC heterogeneity in the form of sub-clusters, including a lymphatic EC cluster apparent in the lung (cluster 5) and intestine (cluster 2) as defined by PROX1 expression

summary:
In Homo sapiens, lymphatic endothelial cells in the lung and intestine are defined by PROX1 expression.


claim_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1:claim:372cc88eb83d2740c446
claim_id: claim:372cc88eb83d2740c446
paper_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1
span_literal:
Three EC-specific organ-enriched genes were selected from lung (CA4, ADRB1, VIRP1), intestine (MEOX1, NKX2.3, FABP4) and kidney (CRHBP, IRX3, IRX5) for validation by multiplexed FISH or immunofluorescence

summary:
In Homo sapiens, lung endothelial cells are enriched for CA4, ADRB1, and VIPR1 relative to intestine and kidney endothelial cells. In Homo sapiens, intestinal endothelial cells are enriched for MEOX1, NKX2.3, and FABP4 relative to lung and kidney endothelial cells. In Homo sapiens, kidney endothelial cells are enriched for CRHBP, IRX3, and IRX5 relative to lung and intestine endothelial cells.


claim_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1:claim:77b6932018463ebe993f
claim_id: claim:77b6932018463ebe993f
paper_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1
span_literal: EC genes (CD31, CDH5, KDR
summary:
In Homo sapiens, endothelial cells are highly enriched for CD31, CDH5, and KDR, while mesenchymal cells express PDGFRa, epithelial cells express EPCAM, and immune cells express CD45.


claim_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1:claim:6fe974bdedea1b682058
claim_id: claim:6fe974bdedea1b682058
paper_key: hca:0128_10.1016_j.devcel.2020.07.023_7908e44bb1
span_literal:
Right: TMM normalized expression of representative organ-specific EC enriched gene candidates in human lung (pink: CA4, ADRB1, VIRP1), intestine (blue: MEOX1, NKX2.3, FABP4), and kidney (yellow: CRHBP, IRX5, IRX3) are shown across all primary samples.

summary:
In Homo sapiens, lung endothelial cells are enriched for CA4, ADRB1, and VIPR1 as organ-specific markers. In Homo sapiens, intestinal endothelial cells are enriched for MEOX1, NKX2.3, and FABP4 as organ-specific markers. In Homo sapiens, kidney endothelial cells are enriched for CRHBP, IRX5, and IRX3 as organ-specific markers.


claim_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c:claim:685c0b872f9c1cd37877
claim_id: claim:685c0b872f9c1cd37877
paper_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c
summary: In Homo sapiens, DNAAF3 is a marker gene of ciliated cells in the airway epithelium.
span_literal:
expressing typical human airway cell type marker genes (DNAAF3, ciliated cells; KRT5, basal cells; and SCGB1A1 and MUC5B, secretory cells; Figure 2 C; Figure S2 C)


claim_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c:claim:8a981e8e70c1efb71a62
claim_id: claim:8a981e8e70c1efb71a62
paper_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c
span_literal:
expressing typical human airway cell type marker genes (DNAAF3, ciliated cells; KRT5, basal cells; and SCGB1A1 and MUC5B, secretory cells; Figure 2 C; Figure S2 C)

summary:
In Homo sapiens, SCGB1A1 is a marker gene of secretory cells in the airway epithelium. In Homo sapiens, MUC5B is a marker gene of secretory cells in the airway epithelium.


claim_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c:claim:5512c3db214dcfa43cad
claim_id: claim:5512c3db214dcfa43cad
paper_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c
summary: In Homo sapiens, keratin 5 (KRT5) is a marker of airway basal stem cells.
span_literal:
We then assessed the number of ABSCs, the key stem cell type orchestrating the repair response by proliferation, by IF for keratin 5 (KRT5).


claim_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c:claim:4a560915287e9a16846a
claim_id: claim:4a560915287e9a16846a
paper_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c
summary: In Homo sapiens, MUC5AC is a marker of mucus cells in the airway epithelium.
span_literal:
We found that CS exposure alone showed a trend toward a decrease in the number of ciliated cells (p = 0.06) marked by the presence of acetylated β-tubulin and significantly increased the number of Muc5AC-expressing mucus cells (p < 0.001)


claim_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c:claim:b0128f07dde4213f2df7
claim_id: claim:b0128f07dde4213f2df7
paper_key: hca:0129_10.1016_j.stem.2020.11.010_32cb10758c
span_literal:
We detected SARS-CoV-2 transcripts in all major cell types and found the proportion of infected cells to be highest in FOXN4+ cells

summary:
In Homo sapiens, FOXN4 is a positive marker of FOXN4-positive cells, which showed the highest proportion of SARS-CoV-2 infection.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:df81bbfa3d862b58c940
claim_id: claim:df81bbfa3d862b58c940
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal:
Monocytes clustered separately from macrophages based on the absence of macrophage markers ( CD68 , MSR1 , MRC1 ) and presence of monocyte markers ( IL1RN , FCN1 , LILRA5

summary:
In Homo sapiens, monocytes are characterized by the absence of macrophage markers CD68, MSR1, and MRC1, and the presence of monocyte markers IL1RN, FCN1, and LILRA5.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:1c64a04cd9618d4ef99a
claim_id: claim:1c64a04cd9618d4ef99a
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal:
Based on CSF1R, CSF3R and SPP1 , 3 monocyte-derived macrophages could further be delineated, including CCL2 high , CCL18 high and RGS1 high macrophages

summary:
In Homo sapiens, monocyte-derived macrophages are delineated based on expression of CSF1R, CSF3R, and SPP1.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:c888730fdf361734728f
claim_id: claim:c888730fdf361734728f
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal:
The latter two populations were characterized by high expression of resident markers ( FABP4 , PPARG ), anti-inflammatory ( CCL18 , CCL22 ) and antigen-presentation relevant MHC-I/II genes.

summary:
In Homo sapiens, alveolar macrophages are characterized by high expression of resident markers FABP4 and PPARG, and anti-inflammatory genes CCL18 and CCL22.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:ff99eee6e2e8a90ec68c
claim_id: claim:ff99eee6e2e8a90ec68c
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal: cluster 3 expressed IFN-induced genes and calgranulins ( S100A8/9 , S100A9 and S100A12
summary:
In Homo sapiens, inflammatory mature neutrophil cluster 3 expresses calgranulins S100A8/9, S100A9, and S100A12, while inflammatory mature neutrophil cluster 4 expresses IL1B, CXCL8, CCL3, and CCL4.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:72fb3f6d85392218ec9d
claim_id: claim:72fb3f6d85392218ec9d
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal: cluster 4 expressed high levels of cytokines ( IL1B ) and chemokines ( CXCL8, CCL3 , CCL4
summary:
In Homo sapiens, inflammatory mature neutrophil cluster 4 expresses high levels of cytokines IL1B and chemokines CXCL8, CCL3, and CCL4.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:eab4607b3912b590b9fb
claim_id: claim:eab4607b3912b590b9fb
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal:
The former were characterized by a unique CD27 – /IGHD + (IgD)/IGHM + (IgM) signature and give rise to the latter by migrating through the germinal center to form CD27 + /IGHD – (IgD)/IGHM – (IgM) memory B-cells

summary:
In Homo sapiens, mature-naïve follicular B-cells are characterized by a CD27-negative, IGHD-positive, and IGHM-positive signature, while memory B-cells are CD27-positive, IGHD-negative, and IGHM-negative.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:769aa733762fd73c0aa7
claim_id: claim:769aa733762fd73c0aa7
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal:
The former were characterized by a unique CD27 – /IGHD + (IgD)/IGHM + (IgM) signature and give rise to the latter by migrating through the germinal center to form CD27 + /IGHD – (IgD)/IGHM – (IgM) memory B-cells

summary:
In Homo sapiens, memory B-cells are characterized by a CD27-positive, IGHD-negative, and IGHM-negative signature.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:e2830525d2712f024eb5
claim_id: claim:e2830525d2712f024eb5
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
summary: In Homo sapiens, plasma cells express IGHA1, IGHG1, and JCHAIN.
span_literal:
Memory B-cells then further differentiate into antibody-secreting plasma cells ( IGHA1 , IGHG1 , JCHAIN ), which themselves can be further classified into short-lived and long-lived plasma cells.


claim_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a:claim:6e1090e273d85d6bff26
claim_id: claim:6e1090e273d85d6bff26
paper_key: hca:0130_10.1038_s41422-020-00455-9_6ab85d317a
span_literal:
A first subcluster of ‘active’ plasma cells expressed high levels of PRDM1 (Blimp-1) and XBP1 , indicating high antibody-secretion capacity, while a second cluster referred to as ‘terminal’ plasma cells was enriched for CCL2 and CCL5

summary:
In Homo sapiens, active plasma cells express high levels of PRDM1 and XBP1, while terminal plasma cells are enriched for CCL2 and CCL5.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:87f5588fc07e05482250
claim_id: claim:87f5588fc07e05482250
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Three KRT5 -expressing basal cell populations were distinguished from one another by expression of genes involved in proliferation (Supplementary Fig. 1c ), differentiation ( IL33 and TP63 ), or a squamous metaplastic response to injury or stress (e.g. KRT14 and KRT13 12 , 13 , Supplementary Fig. 2 ).

summary:
In Homo sapiens tracheal epithelium, basal cell populations express KRT5, and are distinguished by IL33, TP63, KRT14, and KRT13.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:d0ebaa833e14951ea2f5
claim_id: claim:d0ebaa833e14951ea2f5
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal: we also identified a cluster characterized by high KRT8 expression (Fig. 1 c, e, f).
summary:
In Homo sapiens tracheal epithelium, a KRT8-high cell cluster is characterized by high KRT8 expression.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:b2084df3d61be4b8b4ad
claim_id: claim:b2084df3d61be4b8b4ad
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
We also identified low abundance clusters containing cells expressing markers diagnostic for pulmonary neuroendocrine cells (PNECs and ASCL1 ) 16 , ionocytes ( FOXI1 ) 17 , 18 , or tuft cells ( POU2F3 ) 19 .

summary:
In Homo sapiens tracheal epithelium, pulmonary neuroendocrine cells are marked by ASCL1, ionocytes are marked by FOXI1, and tuft cells are marked by POU2F3.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:e0e5331adaf1a9334285
claim_id: claim:e0e5331adaf1a9334285
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
One of these SMG clusters highly expressed basal cell markers (e.g. KRT5 and KRT14 ), whereas the other exhibited mucus secretory character, including high MUC5B expression, which we confirmed with IF (Fig. 1h , Supplementary Fig. 1 f).

summary:
In Homo sapiens tracheal epithelium, submucosal gland basal cells highly express KRT5 and KRT14, whereas submucosal gland mucus secretory cells highly express MUC5B.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:00c5ec624e089c09825f
claim_id: claim:00c5ec624e089c09825f
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
FISH distinguishes rare cell mRNA markers: left, PNECs ( GRP , green) and ionocytes ( CLCNKA/B , magenta); right, ionocytes ( CFTR , magenta) and tuft-like cells ( POU2F3 , green).

summary:
In Homo sapiens tracheal epithelium, pulmonary neuroendocrine cells are marked by GRP, ionocytes are marked by CLCNKA/B and CFTR, and tuft-like cells are marked by POU2F3.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:72801884391bdce0ba0d
claim_id: claim:72801884391bdce0ba0d
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Subclustering of this population revealed three SMG basal cell states, united by KRT14 expression (Fig. 4 d, e, Supplementary Fig. 6 e, f).

summary:
In Homo sapiens tracheal epithelium, submucosal gland basal cell states are united by KRT14 expression.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:b4b3a64d07518487379e
claim_id: claim:b4b3a64d07518487379e
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
The smallest cluster uniquely expressed 34 muscle contraction/development genes (e.g. ACTA2 and MYLK ) (Supplementary Fig. 6 f), reflecting murine myoepithelial cells 41 , 42 .

summary:
In Homo sapiens tracheal epithelium, the myoepithelial cell cluster uniquely expresses ACTA2 and MYLK.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:fc6879fc26395a263e4d
claim_id: claim:fc6879fc26395a263e4d
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Our ACTA2 + SMG population was MKI67 − and poorly expressed KRT5 , suggesting it represents a quiescent myoepithelial population.

summary:
In Homo sapiens tracheal epithelium, the myoepithelial cell population is ACTA2-positive, MKI67-negative, and poorly expresses KRT5.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:15fc26b01054b78e2adb
claim_id: claim:15fc26b01054b78e2adb
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
The early ciliating state was enriched for genes involved in basal body assembly 45 ( DEUP1 , STIL , and PLK4 ) (Fig. 5d ) and also contained known early transcriptional drivers of ciliogenesis ( MCIDAS , MYB , and TP73 ) 46 , 47 (Fig. 5f ).

summary:
In Homo sapiens airway epithelium, the early ciliating cell state is enriched for DEUP1, STIL, PLK4, MCIDAS, MYB, and TP73.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:464126584b64fd185ffb
claim_id: claim:464126584b64fd185ffb
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
These TFs were downregulated in the final ciliary state, which displayed the highest expression of the ciliogenesis and ciliary maintenance TF, FOXJ1 52 (Fig. 5f ).

summary:
In Homo sapiens airway epithelium, the mature ciliated cell state displays the highest expression of FOXJ1.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:f3d8b6de28abbec24c1f
claim_id: claim:f3d8b6de28abbec24c1f
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Similar to the recently reported deuterosomal ciliated cell state, our early ciliating state exclusively expressed the forkhead box N4 gene ( FOXN4 ) 18 , 32 .

summary:
In Homo sapiens airway epithelium, the early ciliating cell state exclusively expresses FOXN4 (forkhead box N4).


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:3764e305d3fbcd8e258c
claim_id: claim:3764e305d3fbcd8e258c
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
summary: In Homo sapiens, ionocytes highly express CFTR and other chloride channel genes.
span_literal:
Human ionocytes highly expressed genes involved in energy production, cholesterol biosynthesis, and CFTR 17 , 18 , in addition to several other chloride channel genes (Fig. 7b , c).


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:bf9754a990e479e7e262
claim_id: claim:bf9754a990e479e7e262
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Despite characteristic POU2F3 and ASCL2 expression in our human tuft cell population, many diagnostic markers in mice (e.g., GNAT3 and TRPM5 ) were not detected in our tuft population, while other murine markers were observed ( HCK and LRMP ) 17 (Fig. 7 b, Supplementary Fig. 9a ).

summary:
In Homo sapiens, tuft-like cells characteristically express POU2F3, ASCL2, HCK, and LRMP, but do not express GNAT3 or TRPM5.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:655de7386cede8692b19
claim_id: claim:655de7386cede8692b19
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Moreover, ionocyte marker, FOXI1 59 , reported to be sufficient to produce CFTR high ionocytes 17 , 18 , was expressed by roughly half of POU2F3 + tuft-like cells (Fig. 7c ).

summary:
In Homo sapiens, FOXI1 is a marker of ionocytes and is also expressed by roughly half of POU2F3-positive tuft-like cells.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:c51cce50aedfca6364f1
claim_id: claim:c51cce50aedfca6364f1
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Distinct TF profiles were observed in these two cell types, including high expression of CREB3L1 and SPDEF on the surface, whereas SMG cells uniquely expressed SOX9 , as well as known lacrimal gland TFs, FOXC1 and BARX2 34 , 35 (Fig. 4a ).

summary:
In Homo sapiens tracheal epithelium, surface mucus secretory cells highly express CREB3L1 and SPDEF, whereas submucosal gland mucus secretory cells uniquely express SOX9, FOXC1, and BARX2.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:9db7a392f5538c788ce2
claim_id: claim:9db7a392f5538c788ce2
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Distinct TF profiles were observed in these two cell types, including high expression of CREB3L1 and SPDEF on the surface, whereas SMG cells uniquely expressed SOX9 , as well as known lacrimal gland TFs, FOXC1 and BARX2 34 , 35 (Fig. 4a ).

summary:
In Homo sapiens tracheal epithelium, submucosal gland mucus secretory cells uniquely express SOX9, FOXC1, and BARX2 compared to surface mucus secretory cells.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:5de45d22c7bf741d03e5
claim_id: claim:5de45d22c7bf741d03e5
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Consistent with KRT8 being a differentiating epithelial cell marker 15 , KRT8 + cells localized to the mid-to-upper epithelium, above KRT5 + basal cells and often reaching the airway surface as shown by IF (Fig. 1f ).

summary:
In Homo sapiens tracheal epithelium, KRT8 is a marker of differentiating epithelial cells, and KRT5 is a marker of basal cells.


claim_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b:claim:6c6c74756e86173d69e3
claim_id: claim:6c6c74756e86173d69e3
paper_key: hca:0132_10.1038_s41467-020-16239-z_001d78a35b
span_literal:
Our broad clustering identified a population of cells expressing a signature characteristic of SMG basal cells ( KRT14 , CAV2 , IFITM3 , and ACTN1 ) (Fig. 1b , Supplementary Figs. 2b and 6e ) 2 , 38 – 40 .

summary:
In Homo sapiens tracheal epithelium, submucosal gland basal cells express a characteristic signature including KRT14, CAV2, IFITM3, and ACTN1.


claim_key: hca:0133_10.1038_ng.3678_4247e86a2b:claim:8075440074c87eb2204b
claim_id: claim:8075440074c87eb2204b
paper_key: hca:0133_10.1038_ng.3678_4247e86a2b
span_literal:
most notably a significant ( P =1.6x10 −8 ) clonal RME of KLRB1 (Killer Cell Lectin-Like Receptor) in one clone

summary:
In Homo sapiens, clonal random monoallelic expression of KLRB1 (killer cell lectin-like receptor subfamily B member 1) was detected in an ex vivo expanded CD8-positive T-cell clone.


claim_key: hca:0133_10.1038_ng.3678_4247e86a2b:claim:344a74bf7a4b4ccc4d70
claim_id: claim:344a74bf7a4b4ccc4d70
paper_key: hca:0133_10.1038_ng.3678_4247e86a2b
span_literal:
Additionally, we noted clone-consistent aRME for CD7 (T-cell antigen) in two clones with opposite alleles expressed.

summary:
In Homo sapiens, clone-consistent autosomal random monoallelic expression of CD7 (T-cell antigen) was observed in CD8-positive T-cell clones.


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:39db1d6051ccc1101f98
claim_id: claim:39db1d6051ccc1101f98
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
summary: In Homo sapiens, B cells are marked by CD19 and CD20 protein expression.
span_literal:
Cell clusters were annotated using the expression of marker proteins: CD19 and CD20 for B cells, CD16 and CD56 for NK cells, CD14 and CD11c for CD14 + monocytes, CD3 and CD4 for CD4 + T cells, CD3 and CD8a for CD8 + T cells, and CD45RA and CD45RO for naïve and memory T cells, respectively


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:5719559e95814d640158
claim_id: claim:5719559e95814d640158
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
summary: In Homo sapiens, memory T cells including T helper 17 cells express CD45RO, CCR6, and CD161.
span_literal:
CD45RO + CCR6 + CD161 + (cluster 3; memory cells including Th17 cells), CD45RO + CXCR5 + (cluster 1; memory cells including Tfh cells), and CD45RO + CD57 + CCR5 + CCR7 cells + (cluster 4; other memory cells)


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:dec2e2e10335771288f3
claim_id: claim:dec2e2e10335771288f3
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal:
Cluster 3 cells ( Figures 2D,E ) expressed chemokine receptor CCR6 (indicating tissue-specific homing properties) and C-type lectin receptor CD161 ( KLRB1 ) and CD127 ( IL7R ) on their surface constituted ~9.9% of CD4 + T cells

summary:
In Homo sapiens, CD4-positive memory T cell cluster 3 expresses CCR6, KLRB1 (CD161), and IL7R (CD127).


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:ddb3e02b737abf675c45
claim_id: claim:ddb3e02b737abf675c45
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal:
Cluster 0 cells expressed genes associated with age-associated B cells (ABC) ( 38 – 40 ) and DN2 cells ( 41 ) (e.g., TLR7, PRDM1, TGAX/ CD11c and TBX2 1/T-bet).

summary:
In Homo sapiens, activated B cell cluster 0 expresses genes associated with age-associated B cells and double negative 2 cells, including TLR7, PRDM1, ITGAX (CD11c), and TBX21 (T-bet).


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:fb8e67daec530e2edf27
claim_id: claim:fb8e67daec530e2edf27
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal:
Distinct from ABCs and DN2 cells, they retained follicular ( CXCR5) and conventional memory ( CD27) markers.

summary:
In Homo sapiens, activated B cell cluster 0 retains follicular marker CXCR5 and conventional memory marker CD27, distinguishing them from age-associated B cells and double negative 2 cells.


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:45ba6341401a3f2d4557
claim_id: claim:45ba6341401a3f2d4557
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal:
Cluster 3 cells expressed additional markers associated with DN2 cells, such as FCRL5 and TRAF5 , but lacked the expression of TLR7, ITGAX , and TBX21 .

summary:
In Homo sapiens, activated B cell cluster 3 expresses FCRL5 and TRAF5 but lacks expression of TLR7, ITGAX, and TBX21.


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:487b4f372d812667477b
claim_id: claim:487b4f372d812667477b
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal:
clusters 2, 3, and 6 cells were mostly from the baseline condition and enriched for KLF2 , which encodes a transcription factor important for NK cell survival

summary:
In Homo sapiens, resting natural killer cells are enriched for KLF2, a transcription factor important for natural killer cell survival.


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:91f106ec7ceb2db2e3b6
claim_id: claim:91f106ec7ceb2db2e3b6
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal: CD161 + CCR6 + cells (cluster 5; MAIT, mucosal-associated invariant T cells, ~7.9% of CD8+ T cells)
summary:
In Homo sapiens, mucosal-associated invariant T cells among CD8-positive T cells are marked by CD161 and CCR6 expression.


claim_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e:claim:e9caa466eea6a08b052b
claim_id: claim:e9caa466eea6a08b052b
paper_key: hca:0134_10.3389_fimmu.2021.636720_9a958ecc4e
span_literal:
late stage activated B cells expressed molecules that have been expressed in B cells associated with aging and auto-immune diseases ( TLR7, PRDM1, ITGAX /CD11c, TBX21 /T-bet)

summary:
In Homo sapiens, late stage activated B cells express TLR7, PRDM1, ITGAX (CD11c), and TBX21 (T-bet), molecules associated with age-associated B cells and autoimmune disease-associated B cells.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:eef4d959389272ff6753
claim_id: claim:eef4d959389272ff6753
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
summary: In Homo sapiens, naïve B cells are marked by LAIR1 and TCL1A.
span_literal:
We recovered 3,175 single-cell transcriptomes spanning a functional differentiation trajectory from naïve (n=166 cells; LAIR1 , TCL1A ) to activated B cells (n=1,032; BANK1 , BLK ) and plasma cells (n=1,977; SDC1 , CD38 , PRDM1 ) across 28 patients


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:6bc638e7cca1f87f41d7
claim_id: claim:6bc638e7cca1f87f41d7
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
CD8 + T cells, with high expression of TOX (n=5,474) (TOX + CD8 + T cells), a marker associated with and required for T cell dysfunction

summary:
In Homo sapiens, TOX-positive CD8-positive T cells are characterized by high expression of TOX, a marker associated with T cell dysfunction.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:b4c82f294d10744f4df8
claim_id: claim:b4c82f294d10744f4df8
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
effector memory T cells characterized by expression of TCF7 (n=3,675) (TCF7 + CD8 + T cells), a marker of progenitor-like function

summary:
In Homo sapiens, TCF7-positive CD8-positive T cells (effector memory T cells) are characterized by expression of TCF7, a marker of progenitor-like function.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:7df7b95f6680b8dded36
claim_id: claim:7df7b95f6680b8dded36
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
MG1 was characterized by significantly higher expression of SPP1 (encoding for osteopontin; an indicator for a pro-tumor phenotype

summary:
In Homo sapiens, microglia subpopulation 1 is characterized by significantly higher expression of SPP1, encoding for osteopontin.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:f47ff14bcbf3193453e4
claim_id: claim:f47ff14bcbf3193453e4
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
summary: In Homo sapiens, FTL-positive monocyte-derived macrophage cluster 2 is marked by expression of FTL.
span_literal:
Among the most strongly differentially expressed genes (DEGs) between the two MDM clusters was FTL (in MDM-c2); we thus labeled MDM-c2 as FTL + MDM, and the remainder MDM-c1.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:90650b5b49dcea5891e5
claim_id: claim:90650b5b49dcea5891e5
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
summary: In Homo sapiens, TOX-positive CD8-positive T cells co-express TOX, HAVCR2, and ENTPD1.
span_literal:
TOX + CD8 + T cells co-expressing TOX and multiple co-inhibitory receptors including HAVCR2 and ENTPD1


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:5fc3680a78d9557fc1b1
claim_id: claim:5fc3680a78d9557fc1b1
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
summary: In Homo sapiens, TCF7-positive CD8-positive T cells express high levels of IL7R, CD69, and CCL5.
span_literal:
TCF7 + CD8 + T cells with low levels of inhibitory receptors and high levels of IL7R , CD69 and CCL5


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:f01d27c3fb07586e9d90
claim_id: claim:f01d27c3fb07586e9d90
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
summary: In Homo sapiens, TCF7-positive CD8-positive T cells have low expression of PDCD1 and HAVCR2.
span_literal:
TCF7 + CD8 + T cells expressed markers consistent with a naïve or memory phenotype as well as effector molecules, and had low expression of immune checkpoints, such as PDCD1 /PD1 and HAVCR2 /TIM3


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:56ed2f297c7fd39ff943
claim_id: claim:56ed2f297c7fd39ff943
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
Comparison of clonally expanded (n=2,121) and non-expanded (n=901) CD8 + T cells showed significant enrichment of IL7R , LTB , SELL , and TCF7 in non-expanded T cells, and increased expression of genes associated with cytokine production, cytotoxicity ( IFNG, GZMB ), co-stimulation (TNFRSF9/ 4-1BB), immune checkpoints (e.g., CTLA4 , HAVCR2 ), and terminal differentiation (MIR155UG) ( Dudda et al., 2013 ) in expanded T cells

summary:
In Homo sapiens, non-expanded CD8-positive T cells are enriched for IL7R, LTB, SELL, and TCF7, while clonally expanded CD8-positive T cells show increased expression of IFNG, GZMB, TNFRSF9, CTLA4, HAVCR2, and MIR155HG.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:0b20579852eee195d4ef
claim_id: claim:0b20579852eee195d4ef
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
Comparison of clonally expanded (n=2,121) and non-expanded (n=901) CD8 + T cells showed significant enrichment of IL7R , LTB , SELL , and TCF7 in non-expanded T cells, and increased expression of genes associated with cytokine production, cytotoxicity ( IFNG, GZMB ), co-stimulation (TNFRSF9/ 4-1BB), immune checkpoints (e.g., CTLA4 , HAVCR2 ), and terminal differentiation (MIR155UG) ( Dudda et al., 2013 ) in expanded T cells

summary:
In Homo sapiens, clonally expanded CD8-positive T cells show increased expression of IFNG, GZMB, TNFRSF9, CTLA4, HAVCR2, and MIR155HG compared to non-expanded CD8-positive T cells.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:a4a6c9c461c893408e55
claim_id: claim:a4a6c9c461c893408e55
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
that expressed a gradient of putative pro-tumorigenic MDM features (e.g., CD163L1 , SELENOP , F13A1 , DAB2 , SIGLEC1 )

summary:
In Homo sapiens, monocyte-derived macrophages express putative pro-tumorigenic features including CD163L1, SELENOP, F13A1, DAB2, and SIGLEC1.


claim_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa:claim:60bc4590ff237c8311b3
claim_id: claim:60bc4590ff237c8311b3
paper_key: hca:0135_10.1016_j.cell.2022.06.007_78f5f057fa
span_literal:
MDM-c1 showed higher expression of efferocytosis receptors ( AXL , MERTK ) and several marker genes associated with a pro-tumorigenic macrophage program, such as CD163

summary:
In Homo sapiens, monocyte-derived macrophage cluster 1 shows higher expression of AXL, MERTK, and CD163 compared to FTL-positive monocyte-derived macrophages.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:0fa4cb480ee1560c958b
claim_id: claim:0fa4cb480ee1560c958b
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
summary: In Homo sapiens retinoblastoma tumors, cone precursors show high expression of Arrestin 3 (ARR3).
span_literal:
Detailed ridge-plots showed high expression of cone Arrestin 3 ( ARR3 ) in the predicted cone clusters 0-9, 11, 12 and 14


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:c59ae95fa3f0f0b0aab1
claim_id: claim:c59ae95fa3f0f0b0aab1
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal:
Cone Arrestin 3 has been shown to be expressed in human cone precursors that enter the cell cycle in retinoblastoma.

summary:
In Homo sapiens, Arrestin 3 is expressed in cone precursors that enter the cell cycle in retinoblastoma.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:f5c2ca03a887ca3b6aeb
claim_id: claim:f5c2ca03a887ca3b6aeb
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal:
Furthermore, the Rb cone clusters organized in an apparent cyclic form dictated by the dynamic cell cycle data, expressed other cone precursor markers at a high level including RXRG, THRB, as well as genes involved in the visual cycle ( GNAT2, GNB3, PDE6H ).

summary:
In Homo sapiens retinoblastoma tumors, cone precursors express RXRG, THRB, GNAT2, GNB3, and PDE6H at high levels.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:ad89764b874fec684093
claim_id: claim:ad89764b874fec684093
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
summary: In Homo sapiens retinoblastoma tumors, cone precursors express NRL but lack NR2E3 expression.
span_literal:
The expression of rod precursor markers was variable, with NRL expressed in all cone clusters and NR2E3 absent.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:0805d62110b6ac64bfa6
claim_id: claim:0805d62110b6ac64bfa6
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal:
Although SIX3 and SIX6 are jointly required to maintain the multipotent RPCs, we only observed high expression of SIX6 in the tumor cone clusters

summary:
In Homo sapiens retinoblastoma tumors, cone precursors show high expression of SIX6 but not SIX3, distinguishing them from retinal progenitor cells.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:0722d411ac9276af0f57
claim_id: claim:0722d411ac9276af0f57
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal:
This together with lack of expression of other well-known RPCs markers such as SOX2, SFRP2, HES1 and HES5 , excludes RPCs as cell of origin for retinoblastoma.

summary:
In Homo sapiens retinoblastoma tumors, cone precursors lack expression of retinal progenitor cell markers SOX2, SFRP2, HES1, and HES5, excluding retinal progenitor cells as the cell of origin.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:eba58338af0720c4a94b
claim_id: claim:eba58338af0720c4a94b
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal: SOX4 and SOX11 , markers of neurogenic RPCs, were also expressed in most tumor cone clusters.
summary:
In Homo sapiens retinoblastoma tumors, SOX4 and SOX11, markers of neurogenic retinal progenitor cells, are expressed in most tumor cone precursor clusters.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:962ff6f5588616a5a13b
claim_id: claim:962ff6f5588616a5a13b
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal:
To identify the clusters, we relied on chromatin accessibility peaks of widely used retinal cell type specific markers (for example, ONECUT1 and ONECUT2 for horizontal cells; GNAT2, RXRG for cones, etc.

summary:
In Homo sapiens retina, ONECUT1 and ONECUT2 are markers of horizontal cells, while GNAT2 and RXRG are markers of cone cells.


claim_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2:claim:467ad339c8168bf58b12
claim_id: claim:467ad339c8168bf58b12
paper_key: hca:0136_10.1167_iovs.62.6.18_7e8926eaf2
span_literal:
To identify the clusters, we relied on chromatin accessibility peaks of widely used retinal cell type specific markers (for example, ONECUT1 and ONECUT2 for horizontal cells; GNAT2, RXRG for cones, etc.

summary:
In Homo sapiens retina, GNAT2 and RXRG are markers of cone cells, while ONECUT1 and ONECUT2 are markers of horizontal cells.


claim_key: hca:0137_10.1084_jem.20221350_7ac74dedfd:claim:2ae45c4a32b119d77189
claim_id: claim:2ae45c4a32b119d77189
paper_key: hca:0137_10.1084_jem.20221350_7ac74dedfd
span_literal:
PRRX1 expression was highly enriched and represented as the most abundant fibroblast population as cluster 1

summary:
In Homo sapiens, PRRX1 is highly enriched in the most abundant oral fibroblast population (fibroblast cluster 1) in the anterior palate.


claim_key: hca:0137_10.1084_jem.20221350_7ac74dedfd:claim:087241c2befbc700a2c9
claim_id: claim:087241c2befbc700a2c9
paper_key: hca:0137_10.1084_jem.20221350_7ac74dedfd
span_literal:
GO analysis of differentially upregulated transcripts from this Prx1 + cluster revealed gene enrichment in ossification, chondrogenesis, regeneration and inhibition of Wnt signaling pathway

summary:
In Homo sapiens, the PRRX1-enriched fibroblast cluster 1 from oral mucosa shows gene enrichment in ossification, chondrogenesis, regeneration, and inhibition of Wnt signaling pathway.


claim_key: hca:0137_10.1084_jem.20221350_7ac74dedfd:claim:cc01fcda95d40ebf401b
claim_id: claim:cc01fcda95d40ebf401b
paper_key: hca:0137_10.1084_jem.20221350_7ac74dedfd
span_literal:
The significantly upregulated genes from Prx1 + cluster included WNT16 and SLPI , WIF1 and SFRP2 , and LRP6 and FZD3 , for activation, inhibition, and receptor function of Wnt signaling, respectively

summary:
In Homo sapiens, the PRRX1-enriched fibroblast cluster 1 from oral mucosa has significantly upregulated expression of WNT16, SLPI, WIF1, SFRP2, LRP6, and FZD3.


claim_key: hca:0137_10.1084_jem.20221350_7ac74dedfd:claim:7ed9f0382bc3eeac4977
claim_id: claim:7ed9f0382bc3eeac4977
paper_key: hca:0137_10.1084_jem.20221350_7ac74dedfd
summary: In Homo sapiens, chemotactic fibroblast cluster 3 from oral mucosa co-expresses CCL2 and CXCL1.
span_literal:
Although humans do not express orthologous gene to murine Ly6a , similarly chemotactic fibroblast cluster 3 was found to co-express CCL2 and CXCL1


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:90f77cc08fece2b4d927
claim_id: claim:90f77cc08fece2b4d927
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
Sub-clustering of myeloid cells showed two distinct populations of conventional dendritic cells: cDC1 expressing XCR1 , CADM1 , CLEC9A , BATF3 and IDO1 , and cDC2 expressing CLEC10A and CD86

summary:
In Homo sapiens, conventional dendritic cell type 1 expresses XCR1, CADM1, CLEC9A, BATF3, and IDO1 in the colon.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:2fa1af18d800abe008a0
claim_id: claim:2fa1af18d800abe008a0
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
summary: In Homo sapiens, monocytes express CD14 and CD68 in the colon.
span_literal:
In addition, we identified monocytes expressing CD14 and CD68 , macrophages expressing FCGR3A (gene encoding CD16), LYVE1 + macrophages 16 and plasmacytoid DCs (pDCs) expressing IRF4 and SELL


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:d8ee350a15f6eef4a922
claim_id: claim:d8ee350a15f6eef4a922
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
In the mLN, CD4 + T cells were typically CXCR5 + , ICOS hi follicular helper cells, and SELL + (encodes CD62L), CCR7 + central memory cells

summary:
In Homo sapiens, follicular helper T cells in the mesenteric lymph node are CXCR5-positive and ICOS-high.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:666720d9c903e9322d7d
claim_id: claim:666720d9c903e9322d7d
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
In the mLN, CD4 + T cells were typically CXCR5 + , ICOS hi follicular helper cells, and SELL + (encodes CD62L), CCR7 + central memory cells

summary:
In Homo sapiens, central memory T cells in the mesenteric lymph node are SELL-positive and CCR7-positive.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:eec45cad3ae1d5107fd1
claim_id: claim:eec45cad3ae1d5107fd1
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
In contrast, colonic CD4 + T cells had a more effector phenotype, expressing high levels of the tissue residency marker CD69 17 , falling into the T H 17 ( CCR6 + , IL22 + , CCL20 + ) or T H 1 ( CXCR3 + , IFNG + ) subtypes.

summary:
In Homo sapiens, colonic T helper 17 cells express CCR6, IL22, and CCL20, while T helper 1 cells express CXCR3 and IFNG.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:cabe574f6a7de4ef54a5
claim_id: claim:cabe574f6a7de4ef54a5
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
B cells in the mLN were predominantly CD19 + , MS4A1 + (encodes CD20), CD40 + , TNFRSF13B + (encodes TACI), CD38 − memory or CXCR5 + , TCL1A + , FCER2 + (encodes CD23) follicular B cells

summary:
In Homo sapiens, memory B cells in the mesenteric lymph node are CD19-positive, MS4A1-positive, CD40-positive, TNFRSF13B-positive, and CD38-negative.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:d6fe316a9b1daac37365
claim_id: claim:d6fe316a9b1daac37365
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
B cells in the mLN were predominantly CD19 + , MS4A1 + (encodes CD20), CD40 + , TNFRSF13B + (encodes TACI), CD38 − memory or CXCR5 + , TCL1A + , FCER2 + (encodes CD23) follicular B cells

summary:
In Homo sapiens, follicular B cells in the mesenteric lymph node are CXCR5-positive, TCL1A-positive, and FCER2-positive.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:c23627ee80130e764613
claim_id: claim:c23627ee80130e764613
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
summary: In Homo sapiens, plasma cells in the colon are SDC1-positive and CD38-positive.
span_literal:
In contrast, in the three regions of the colon, the main population of B cells were SDC1 + (encodes CD138), CD38 + , plasma cells.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:ef40f2111bb3a14f5122
claim_id: claim:ef40f2111bb3a14f5122
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
Central T reg cells were defined by highest expression of SELL , while effector T reg cells were characterized by genes associated with the TNFRSF-NF-κB pathway ( TNFRSF9 and TNF )

summary:
In Homo sapiens, central T regulatory cells are defined by highest expression of SELL, while effector T regulatory cells are characterized by TNFRSF9 and TNF.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:173a2c6eefd5dacc9130
claim_id: claim:173a2c6eefd5dacc9130
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
These have characteristics of non-lymphoid tissue T reg cells, including high expression of FOXP3 , PRDM1 , RORA , IL2RG , IL2RA and CTLA4

summary:
In Homo sapiens, non-lymphoid tissue-like T regulatory cells express FOXP3, PRDM1, RORA, IL2RG, IL2RA, and CTLA4.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:f1dd423af55801f64dc7
claim_id: claim:f1dd423af55801f64dc7
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
A fourth population, termed T reg -like cells, lacked the conventional markers of T reg cells - FOXP3 and IL2RA - but clustered more closely with T reg cells than conventional T cells

summary:
In Homo sapiens, T regulatory-like cells lack expression of the conventional T regulatory cell markers FOXP3 and IL2RA.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:d1b4b3c71490c36b6d37
claim_id: claim:d1b4b3c71490c36b6d37
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
These expressed the highest levels of PDCD1 (gene encoding PD-1) among T reg cell populations and, uniquely for this cell type, the transmembrane protein-encoding gene MS4A6A

summary:
In Homo sapiens, T regulatory-like cells express the highest levels of PDCD1 among T regulatory cell populations and uniquely express MS4A6A.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:9fea29ba9834b4ebd0d7
claim_id: claim:9fea29ba9834b4ebd0d7
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
KLRB1 + (also known as CD161) T reg cells were characterized by expression of LAG3 , IL2RA , CTLA4, KLRB1 , ICOS and FOXP3

summary:
In Homo sapiens, KLRB1-positive T regulatory cells in the colon are characterized by expression of LAG3, IL2RA, CTLA4, KLRB1, ICOS, and FOXP3.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:bb9508f6559e58e7c326
claim_id: claim:bb9508f6559e58e7c326
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
The third population exhibited a profile reminiscent of lymphoid tissue T reg cells with expression of SELL , CCR7 , TCR7 , CXCR5 and RGS2 , and were termed Lymphoid Tissue-like T reg (LT-like T reg ) cells

summary:
In Homo sapiens, lymphoid tissue-like T regulatory cells in the colon express SELL, CCR7, TCR7, CXCR5, and RGS2.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:6cd7bc9bb0001c9196f5
claim_id: claim:6cd7bc9bb0001c9196f5
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
Genes expressed at the beginning of pseudospace included SELL , CCR7 and CXCR4 , permitting entry into lymph nodes

summary:
In Homo sapiens, resting central T regulatory cells in the mesenteric lymph node express SELL, CCR7, and CXCR4, permitting entry into lymph nodes.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:4c52ac754129ad0f28ca
claim_id: claim:4c52ac754129ad0f28ca
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
At the end of pseudospace, the most highly expressed genes were FOXP3 , IL2RA, CTLA4 , IL10 and LAG3.

summary:
In Homo sapiens, highly suppressive colonic T regulatory cells express FOXP3, IL2RA, CTLA4, IL10, and LAG3.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:9fefbb7d9039f86e5ec8
claim_id: claim:9fefbb7d9039f86e5ec8
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
These genes encoding suppressive molecules were co-expressed with TNF receptor genes ( TNFRSF4 , TNFRSF18 , TNFRSF1B ) indicating a reliance on the TNFRSF-NF-κB axis.

summary:
In Homo sapiens, colonic T regulatory cells co-express TNFRSF4, TNFRSF18, and TNFRSF1B, indicating reliance on the TNFRSF-NF-κB axis.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:652d15c92966a6f478fb
claim_id: claim:652d15c92966a6f478fb
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
summary: In Homo sapiens, peripheral T regulatory cells in the colon express CXCR3, CXCR6, CCR6, and CCR4.
span_literal:
Chemokine receptor-encoding genes, CXCR3 , CXCR6 , CCR6 and CCR4, were also expressed by T reg cells in the periphery, matching previous reports of T H 1- and T H 17-like T reg cells in the colon


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:f414544e18c8b00d0b1e
claim_id: claim:f414544e18c8b00d0b1e
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
summary: In Homo sapiens, cecal plasma cells are enriched for CCL3 and CCL4 expression.
span_literal:
This analysis revealed CCL3 and CCL4 as highly enriched in cecal plasma cells (log fold change of 0.61 and 0.70 and adjusted P <10 −28 and <10 −9 respectively)


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:2ac82a3c796593884450
claim_id: claim:2ac82a3c796593884450
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
Among the genes more highly expressed by plasma cells in the sigmoid colon was CD27 ( Figure 5a ; log fold change of 0.24; adjusted P <10 −40 ), encoding a member of the TNF receptor family that is expressed by memory B cells and even more highly by plasma cells 29

summary:
In Homo sapiens, plasma cells in the sigmoid colon more highly express CD27 compared to other colon regions.


claim_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d:claim:6c015bd32ef439b664b1
claim_id: claim:6c015bd32ef439b664b1
paper_key: hca:0139_10.1038_s41590-020-0602-z_71058e050d
span_literal:
CCR10 (log fold change of 0.24; adjusted P < 10 −16 ), ITGA4 (log fold change of 0.58; adjusted P < 10 −24 ) and ITGB4 (log fold change 0.57; adjusted P < 10 −108 ) were also more highly expressed by sigmoid colon IgA + plasma cells

summary:
In Homo sapiens, sigmoid colon IgA-positive plasma cells more highly express CCR10, ITGA4, and ITGB4.


claim_key: hca:0140_10.1101_2021.03.01.21252411_572fc1288d:claim:dbd5e82fc6064fca0cb5
claim_id: claim:dbd5e82fc6064fca0cb5
paper_key: hca:0140_10.1101_2021.03.01.21252411_572fc1288d
summary: In Homo sapiens, B cells are identified by the canonical marker MS4A1.
span_literal:
The first method of assignment of cell types to cell clusters was based on their canonical markers: B cells (MS4A1 marker), CD14+ monocytes (CD14 and LYZ), CD4+ T cells (IL7R, CCR7, and CD27), CD8+ T cells (CD8A), DCs (FCER1A, CST3, CD123, and GZMB), erythroid precursors (GYPB and AHSP), FCGR3A+ monocytes (FCGR3A and MS4A7), Neutrophils (JAML and SERPINB), NK cells (GNLY and NKG7), and Platelets (PPBP).


claim_key: hca:0140_10.1101_2021.03.01.21252411_572fc1288d:claim:fcb0d9a63f292764dcb3
claim_id: claim:fcb0d9a63f292764dcb3
paper_key: hca:0140_10.1101_2021.03.01.21252411_572fc1288d
summary:
In Homo sapiens, dendritic cells are identified by the canonical markers FCER1A, CST3, CD123, and GZMB.


claim_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d:claim:cd8e34e45e91f9eaab9b
claim_id: claim:cd8e34e45e91f9eaab9b
paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
span_literal:
The majority of T cells isolated from the human lung demonstrated classic markers of tissue residency, including the expression of CD69 , CD44 , ITGAE , and IL7R , and the lack of expression of SELL (CD62L), S1PR1 , and CCR7

summary:
In Homo sapiens lung, tissue-resident T cells are marked by positive expression of CD69, CD44, ITGAE, and IL7R, and negative expression of SELL (CD62L), S1PR1, and CCR7.


claim_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d:claim:3da63ddde703e4db8928
claim_id: claim:3da63ddde703e4db8928
paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
span_literal:
DEG analysis between the two subsets found that CEACAM6 (CD66c) was highly enriched in the AT2-signaling population

summary:
In Homo sapiens, CEACAM6 (CD66c) is highly enriched in the alveolar epithelial type 2 signaling cell population compared to the alveolar epithelial type 2 bulk population.


claim_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d:claim:adb80124d054de587e34
claim_id: claim:adb80124d054de587e34
paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
span_literal:
In contrast, CD66c − AT2s are enriched in expression of genes relevant to surfactant production driven by ETV5, including SFTPA1, SFTPA2, SFTPC, LAMP3 , and ABCA3.

summary:
In Homo sapiens, CD66c-negative alveolar epithelial type 2 cells are enriched in expression of ETV5, SFTPA1, SFTPA2, SFTPC, LAMP3, and ABCA3.


claim_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d:claim:4d88b4f1c7c536eba0d5
claim_id: claim:4d88b4f1c7c536eba0d5
paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
span_literal:
DEGs demonstrated increased expression of both IFNGR1 and IFNGR2 in CD66c + AT2s along with other IFN response genes

summary:
In Homo sapiens, CD66c-positive alveolar epithelial type 2 cells show increased expression of IFNGR1 and IFNGR2.


claim_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d:claim:bd7f489a174363c0eac4
claim_id: claim:bd7f489a174363c0eac4
paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
span_literal: In contrast to mouse lungs, human lung HHIP is predominantly expressed in the CD66c − AT2s
summary:
In Homo sapiens lung, HHIP is predominantly expressed in CD66c-negative alveolar epithelial type 2 cells.


claim_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d:claim:d75f8cc7ac0c9f3bc1e0
claim_id: claim:d75f8cc7ac0c9f3bc1e0
paper_key: hca:0142_10.1016_j.immuni.2023.01.032_b86bd8b65d
span_literal:
CD66c + AT2s have similar transcriptomes compared to a previously described AT2 subset found near the respiratory bronchioles (RB, SCGB3A2 + cells at the airway termini) in the human lung

summary:
In Homo sapiens lung, the alveolar epithelial type 2 cell subset near the respiratory bronchioles is marked by SCGB3A2 expression.


claim_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e:claim:2a1a493e35b1677bf176
claim_id: claim:2a1a493e35b1677bf176
paper_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e
span_literal:
We first analysed cortical immune cells, which contain mostly microglia but also lesser fractions of perivascular macrophages ( MRC1 + , which encodes macrophage-specific mannose receptor CD206 34 ) and T cells ( CD247 + , which encodes the T cell receptor CD3ζ protein).

summary:
In Homo sapiens brain cortex, perivascular macrophages are marked by positive expression of MRC1 (encoding mannose receptor CD206), while T cells are marked by positive expression of CD247 (encoding T cell receptor CD3 zeta protein).


claim_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e:claim:666ecbde6a08693c6a92
claim_id: claim:666ecbde6a08693c6a92
paper_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e
span_literal:
We first analysed cortical immune cells, which contain mostly microglia but also lesser fractions of perivascular macrophages ( MRC1 + , which encodes macrophage-specific mannose receptor CD206 34 ) and T cells ( CD247 + , which encodes the T cell receptor CD3ζ protein).

summary:
In Homo sapiens brain cortex, T cells are marked by positive expression of CD247 (encoding T cell receptor CD3 zeta protein).


claim_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e:claim:eb0074579039073e0425
claim_id: claim:eb0074579039073e0425
paper_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e
span_literal: C1QC , CD74 , FTL and FTH1 , and downregulation of the homeostatic markers including P2RY12
summary:
In Homo sapiens, the COVID-19-associated microglia subpopulation is marked by positive expression of C1QC, CD74, FTL, and FTH1, and negative expression of the homeostatic marker P2RY12.


claim_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e:claim:f8cb7da98b620f1f06d3
claim_id: claim:f8cb7da98b620f1f06d3
paper_key: hca:0143_10.1038_s41586-021-03710-0_b55ce5f09e
span_literal:
astrocyte cluster associated with COVID-19 that is marked by established inflammation and astrogliosis genes (such as IFITM3 and GFAP ) and upregulated expression of the secreted neurotoxic factor chitinase 3-like 1 (CHI3L1

summary:
In Homo sapiens, the COVID-19-associated astrocyte cluster is marked by positive expression of interferon-induced transmembrane protein 3 (IFITM3), glial fibrillary acidic protein (GFAP), and chitinase 3-like 1 (CHI3L1).


claim_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6:claim:7f0a7dfa74376c0e382c
claim_id: claim:7f0a7dfa74376c0e382c
paper_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6
span_literal: Tfh cells expressed marker transcripts CD3E , CD4 , CD69 , CXCR5 , PDCD1 , and BCL6
summary:
In Homo sapiens, T follicular helper cells expressed marker transcripts CD3E, CD4, CD69, CXCR5, PDCD1, and BCL6.


claim_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6:claim:ab9b5039cd844ac00dbb
claim_id: claim:ab9b5039cd844ac00dbb
paper_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6
span_literal:
The same cell state also expressed the protein markers CD3, CD4, CD45RO, PD-1, ICOS, CXCR3, CXCR5, B and T lymphocyte attenuator (BTLA) and CD18 with intermediate CD57 expression suggesting a transitional Tfh cell state

summary:
In Homo sapiens, T follicular helper cells expressed the protein markers CD3, CD4, CD45RO, PD-1, ICOS, CXCR3, CXCR5, B and T lymphocyte attenuator (BTLA), and CD18 with intermediate CD57 expression.


claim_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6:claim:4fa52f39d024a28e6bbe
claim_id: claim:4fa52f39d024a28e6bbe
paper_key: hca:0144_10.1016_j.ebiom.2025.106036_833fbd27b6
span_literal:
CD4 + Tfh cells comprised of multiple GEPs including GEPs pCD4T_9 and pCD4T_14 that identified the cell state with genes such as PDCD1 and CXCR5 , as well as shared GEPs pCD4T_2 and pCD4T_3 that mapped to many other CD4 + T cell states and included genes such as IL7R , CD96 , and ribosomal genes.

summary:
In Homo sapiens, CD4-positive T follicular helper cells were identified by gene expression programmes including PDCD1 and CXCR5, while shared programmes included IL7R and CD96.


claim_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf:claim:ea9d809b868f021b7605
claim_id: claim:ea9d809b868f021b7605
paper_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf
span_literal:
We annotated two clusters of human stromal cells as potential fascial fibroblasts (fFBs; fFB1 and fFB2) on the basis of their preferential expression of murine TIFF markers, including PI16, SFRP2 and OGN

summary:
In Homo sapiens, fascial fibroblast 1 and fascial fibroblast 2 in skin preferentially express PI16, SFRP2, and OGN, which are murine T helper 2 cell-interacting fascial fibroblast markers.


claim_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf:claim:c5741a64660a4deb1bbf
claim_id: claim:c5741a64660a4deb1bbf
paper_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf
span_literal:
We annotated two clusters of human stromal cells as potential fascial fibroblasts (fFBs; fFB1 and fFB2) on the basis of their preferential expression of murine TIFF markers, including PI16, SFRP2 and OGN

summary:
In Homo sapiens, fascial fibroblast 2 in skin preferentially express PI16, SFRP2, and OGN, which are murine T helper 2 cell-interacting fascial fibroblast markers.


claim_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf:claim:edd0872597bfe8f39813
claim_id: claim:edd0872597bfe8f39813
paper_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf
span_literal:
TIFF-expressed immunological genes such as IL13RA1, CXCL12 and CXCL14 were enriched in human fFB1 and fFB2 cells, although IL18 and IL33 were not

summary:
In Homo sapiens, fascial fibroblast 1 cells are enriched for IL13RA1, CXCL12, and CXCL14, but not IL18 or IL33.


claim_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf:claim:4c9305031a1f2cfd1719
claim_id: claim:4c9305031a1f2cfd1719
paper_key: hca:0145_10.1038_s41586-021-04044-7_8df46052bf
span_literal:
TIFF-expressed immunological genes such as IL13RA1, CXCL12 and CXCL14 were enriched in human fFB1 and fFB2 cells, although IL18 and IL33 were not

summary:
In Homo sapiens, fascial fibroblast 2 cells are enriched for IL13RA1, CXCL12, and CXCL14, but not IL18 or IL33.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:bd7a584ad8439d717d34
claim_id: claim:bd7a584ad8439d717d34
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
Immunohistochemistry for markers of radial glia (SOX2), intermediate progenitors TBR2 (EOMES), and neurons CTIP2 (BCL11B), SATB2, reveals histological and cellular features of normal neurogenesis in the germinal zones of human and chimpanzee cerebral organoids, but a much more extensive intermediate zone and cortical plate in primary samples.

summary:
In Homo sapiens, SOX2 is a marker of radial glia, TBR2 (EOMES) is a marker of intermediate progenitor cells, and CTIP2 (BCL11B) and SATB2 are markers of neurons in the cerebral cortex.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:174dc2dd14eb34863742
claim_id: claim:174dc2dd14eb34863742
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
modules correlated with radial glia cell identity included networks related to young radial glia (organoid.chimp.ME.lavenderblush3: LIX1 , HMGA2 ), outer subventricular zone radial glia (primary.human.ME.palevioletred: HOPX , SLCO1C1 , MOXD1 , S1PR1 ), and mature radial glia (primary.human.ME.magenta: CLU , ATP1A2 , TNC

summary:
In Homo sapiens, HOPX, SLCO1C1, MOXD1, and S1PR1 are markers of outer subventricular zone radial glia in the cerebral cortex.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:a0e00c7da8289eaf51dc
claim_id: claim:a0e00c7da8289eaf51dc
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
modules correlated with inhibitory neurons included networks related to LGE- and CGE-derived (e.g., primary.human.ME.antiquewhite2: PROX1 , SCGN , CALB2 , SP8 ) and MGE-derived (primary.human.ME.yellow3: MAF, LHX6, SST ) interneuron subtypes, with organoids enriched for LGE-derived interneuron subtypes

summary:
In Homo sapiens, PROX1, SCGN, CALB2, and SP8 are markers of lateral ganglionic eminence- and caudal ganglionic eminence-derived interneurons in the cerebral cortex.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:d0b27ebeb1faeafaea46
claim_id: claim:d0b27ebeb1faeafaea46
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
modules correlated with inhibitory neurons included networks related to LGE- and CGE-derived (e.g., primary.human.ME.antiquewhite2: PROX1 , SCGN , CALB2 , SP8 ) and MGE-derived (primary.human.ME.yellow3: MAF, LHX6, SST ) interneuron subtypes, with organoids enriched for LGE-derived interneuron subtypes

summary:
In Homo sapiens, MAF, LHX6, and SST are markers of medial ganglionic eminence-derived interneurons in the cerebral cortex.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:b1e90374a1b4d3a50b9f
claim_id: claim:b1e90374a1b4d3a50b9f
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
summary: In Homo sapiens, FOXG1 is a marker gene for telencephalon regional identity.
span_literal:
The next six rows color cells according to the expression of marker genes for telencephalon regional identity ( FOXG1 ), radial glia ( GLI3 ), cortical excitatory neurons ( NEUROD6 ), inhibitory neurons ( DLX1 ), ventral telencephalon, choroid plexus, and diencephalon ( OTX2 ), and mesenchyme ( DCN ).


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:61d58af158e78cbd0ed3
claim_id: claim:61d58af158e78cbd0ed3
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
We observed increased activation of this pathway in human radial glia, dependent on two receptors up-regulated specifically in human, INSR and ITGB8.

summary:
In Homo sapiens, INSR and ITGB8 are positively expressed in radial glia and are up-regulated specifically in human.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:d50e75927a3c33b13dda
claim_id: claim:d50e75927a3c33b13dda
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
summary: In Homo sapiens, DCC, CNTN2, and NHLH2 are marker genes related to Cajal-Retzius cell identity.
span_literal:
organoid.human.ME.cyan4 contains genes that are related to Cajal-Retzius identity, including DCC, CNTN2, and NHLH2.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:a2f869868e999a4985a8
claim_id: claim:a2f869868e999a4985a8
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
However, the MGE specific module primary.human.ME.yellow3 which contains MGE specific genes MAF, LHX6, and SST is more highly correlated to primary MGE-derived interneurons on the X-axis.

summary:
In Homo sapiens, MAF, LHX6, and SST are specific marker genes for medial ganglionic eminence-derived interneurons.


claim_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000:claim:3e6663e1d62f7a9c0afd
claim_id: claim:3e6663e1d62f7a9c0afd
paper_key: hca:0146_10.1016_j.cell.2019.01.017_63c175b000
span_literal:
In contrast, the module primary.human.ME.antiquewhite2 which contains CGE/LGE genes PROX1, CALB2, and SCGN is more highly correlated with organoid interneurons (Y-axis), as well as with CGE-derived primary interneurons

summary:
In Homo sapiens, PROX1, CALB2, and SCGN are marker genes for caudal ganglionic eminence/lateral ganglionic eminence-derived interneurons.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:6d7d6e12f8923ba89456
claim_id: claim:6d7d6e12f8923ba89456
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
span_literal:
Sections from retinas of eight species immunostained for RBPMS (a pan-RGC marker), CHX10 (also known as VSX2) (a pan-bipolar cell marker) and AP2A (also known as TFAP2A) (a pan-amacrine cell marker) and stained with the nuclear stain DAPI.

summary:
In Homo sapiens retina, RBPMS is a pan-retinal ganglion cell marker, VSX2 (also known as CHX10) is a pan-bipolar cell marker, and TFAP2A (also known as AP2A) is a pan-amacrine cell marker.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:11965fed60fa486b77e0
claim_id: claim:11965fed60fa486b77e0
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
summary: In Homo sapiens retina, POU4F1 is a conserved marker of retinal ganglion cells.
span_literal:
We found that conserved genes within a cell class included many genes encoding known lineage-determining transcription factors, such as POU4F1 (RGCs), VSX2 (bipolar cells and Müller glia), OTX2 (photoreceptors and bipolar cells), TFAP2A–C (amacrine cells), ONECUT1/2 (horizontal cells) and CRX (photoreceptors)


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:396fb6ce385dc910629c
claim_id: claim:396fb6ce385dc910629c
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
span_literal:
We found that conserved genes within a cell class included many genes encoding known lineage-determining transcription factors, such as POU4F1 (RGCs), VSX2 (bipolar cells and Müller glia), OTX2 (photoreceptors and bipolar cells), TFAP2A–C (amacrine cells), ONECUT1/2 (horizontal cells) and CRX (photoreceptors)

summary:
In Homo sapiens retina, VSX2 is a conserved marker of bipolar cells. In Homo sapiens retina, OTX2 is a conserved marker of bipolar cells.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:bf11fbc13c5bf71f0bbc
claim_id: claim:bf11fbc13c5bf71f0bbc
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
summary:
In Homo sapiens retina, OTX2 is a conserved marker of photoreceptors. In Homo sapiens retina, CRX is a conserved marker of photoreceptors.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:7bf1441a30c031ce5356
claim_id: claim:7bf1441a30c031ce5356
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
summary: In Homo sapiens retina, GAD1 is a marker for GABAergic amacrine cells.
span_literal:
GAD1 , a marker for GABAergic amacrine cells, is also expressed by some horizontal cells, and ISL1 , a marker for ON bipolar cells, is also expressed by some RGCs, horizontal cells, and amacrine cells.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:66c1bbb969c9e714a3fa
claim_id: claim:66c1bbb969c9e714a3fa
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
span_literal:
Feature plots showing expression within the integrated space of the rod bipolar cell marker PRKCA , the ON bipolar cell marker ISL1 , and the OFF bipolar cell marker GRIK1 .

summary:
In Homo sapiens retina, PRKCA is a marker of rod bipolar cells, ISL1 is a marker of ON bipolar cells, and GRIK1 is a marker of OFF bipolar cells.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:587dbfbf2566d1053c8f
claim_id: claim:587dbfbf2566d1053c8f
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
span_literal: Mammalian RBCs were distinguished by the high expression of PRKCA and LRRTM4
summary:
In Homo sapiens retina, mammalian rod bipolar cells were distinguished by the high expression of PRKCA and LRRTM4.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:cf1e3354fed9c4080c40
claim_id: claim:cf1e3354fed9c4080c40
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
span_literal:
ipRGCs contain the photopigment melanopsin (encoded by OPN4 ), which enables them to generate visually evoked signals without input from photoreceptors

summary:
In Homo sapiens retina, intrinsically photosensitive retinal ganglion cells express OPN4, which encodes the photopigment melanopsin.


claim_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab:claim:16143645beae437aa8ec
claim_id: claim:16143645beae437aa8ec
paper_key: hca:0147_10.1038_s41586-023-06638-9_84d87d2eab
span_literal:
ipRGCs also express the transcription factor-encoding gene EOMES (also known as TBR2 ), although some EOMES -expressing RGCs have not been functionally validated as ipRGCs.

summary:
In Homo sapiens retina, intrinsically photosensitive retinal ganglion cells express the transcription factor-encoding gene EOMES (also known as TBR2).


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:4576781dd22795c95698
claim_id: claim:4576781dd22795c95698
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary: In Homo sapiens quadriceps tendon, fibroblasts are marked by COL1A2, COL3A1, and DCN.
span_literal:
These included fibroblasts ( COL1A2 , COL3A1 , DCN ), macrophages ( CD163 , MRC1 , MSR1 ), vascular endothelial cells (VECs) ( PECAM1 , PTPRB , VWF ), mural cells ( NOTCH3 , PDGFRB , MYO1B ), adipocytes ( PLIN1 , PLIN4 , ADIPOQ ), T cells ( CD247 , SKAP1 , THEMIS ), nervous system cells ( NRXN1 , CADM2 , IL1RAPL2 ), lymphatic endothelial cells ( MMRN1 , PROX1 , PKHD1L1 ), dividing fibroblasts/mural cells and dividing macrophages ( ASPM , DIAPH3 , TOP2A ; more in Supporting information, Supplementary Fig. S4 ), dendritic cells (DCs) ( CLEC4C , CUX2 , BCL11A ), osteoblasts ( IBSP , SP7 , RUNX2 ), granulocytes ( KIT , CPA3 , IL18R1 ) and osteoclasts ( MMP9 , ACP5 , SIGLEC15 ).


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:b6feadb692bfb88708ce
claim_id: claim:b6feadb692bfb88708ce
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary:
In Homo sapiens quadriceps tendon, lymphatic endothelial cells are marked by MMRN1, PROX1, and PKHD1L1.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:ed87af548f8af3eed44c
claim_id: claim:ed87af548f8af3eed44c
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary:
In Homo sapiens quadriceps tendon, dividing fibroblasts/mural cells and dividing macrophages are marked by ASPM, DIAPH3, and TOP2A.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:e51da45514661a52d205
claim_id: claim:e51da45514661a52d205
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Three different fibroblasts subsets were found in healthy quadriceps tendons: FBLN1 hi fibroblasts ( FBLN1 , NOX4 , CILP , COMP ), ABCA10 hi fibroblasts ( ABCA10 , CNTN4 , C6 , ABCA8 ), and NR4A1 hi fibroblasts ( NR4A1 , NR4A3 , NAMPT , SEMA4A ).

summary:
In Homo sapiens healthy quadriceps tendon, FBLN1 hi fibroblasts are marked by FBLN1, NOX4, CILP, and COMP.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:354f92fb3961242429bb
claim_id: claim:354f92fb3961242429bb
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Three different fibroblasts subsets were found in healthy quadriceps tendons: FBLN1 hi fibroblasts ( FBLN1 , NOX4 , CILP , COMP ), ABCA10 hi fibroblasts ( ABCA10 , CNTN4 , C6 , ABCA8 ), and NR4A1 hi fibroblasts ( NR4A1 , NR4A3 , NAMPT , SEMA4A ).

summary:
In Homo sapiens healthy quadriceps tendon, ABCA10 hi fibroblasts are marked by ABCA10, CNTN4, C6, and ABCA8.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:6554fc485a4c6c8a4b71
claim_id: claim:6554fc485a4c6c8a4b71
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Three different fibroblasts subsets were found in healthy quadriceps tendons: FBLN1 hi fibroblasts ( FBLN1 , NOX4 , CILP , COMP ), ABCA10 hi fibroblasts ( ABCA10 , CNTN4 , C6 , ABCA8 ), and NR4A1 hi fibroblasts ( NR4A1 , NR4A3 , NAMPT , SEMA4A ).

summary:
In Homo sapiens healthy quadriceps tendon, NR4A1 hi fibroblasts are marked by NR4A1, NR4A3, NAMPT, and SEMA4A.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:552c962a5df87c928998
claim_id: claim:552c962a5df87c928998
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Ruptured quadriceps tendon fibroblasts were predominantly ADAM12 hi fibroblasts ( ADAM12 , COL3A1 , TNC , POSTN ), as well as dividing cells ( DIAPH3 , TOP2A , CENPE , ASPM ), which included both dividing fibroblasts and mural cells as defined in Fig. 1 .

summary:
In Homo sapiens ruptured quadriceps tendon, ADAM12 hi fibroblasts are marked by ADAM12, COL3A1, TNC, and POSTN.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:f38cf265340688d642f7
claim_id: claim:f38cf265340688d642f7
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Ruptured quadriceps tendon fibroblasts were predominantly ADAM12 hi fibroblasts ( ADAM12 , COL3A1 , TNC , POSTN ), as well as dividing cells ( DIAPH3 , TOP2A , CENPE , ASPM ), which included both dividing fibroblasts and mural cells as defined in Fig. 1 .

summary:
In Homo sapiens ruptured quadriceps tendon, dividing cells are marked by DIAPH3, TOP2A, CENPE, and ASPM.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:47fb40eb94a84a15b036
claim_id: claim:47fb40eb94a84a15b036
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary: In Homo sapiens quadriceps tendon, vascular endothelial cells are marked by PECAM1, VWF, and FLT1.
span_literal:
VECs ( PECAM1 , VWF , FLT1 ) could be separated into venular ( ACKR1 , LIFR , ICAM ), arteriolar ( NEBL , CXCL12, PDXL ), capillary ( COL4A1 , COL4A2 , DYSF ) and dividing VECs.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:5fc546f4eff450aa1dc5
claim_id: claim:5fc546f4eff450aa1dc5
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
VECs ( PECAM1 , VWF , FLT1 ) could be separated into venular ( ACKR1 , LIFR , ICAM ), arteriolar ( NEBL , CXCL12, PDXL ), capillary ( COL4A1 , COL4A2 , DYSF ) and dividing VECs.

summary:
In Homo sapiens quadriceps tendon, venular vascular endothelial cells are marked by ACKR1, LIFR, and ICAM.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:e1d58e7382ac97635cd6
claim_id: claim:e1d58e7382ac97635cd6
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
VECs ( PECAM1 , VWF , FLT1 ) could be separated into venular ( ACKR1 , LIFR , ICAM ), arteriolar ( NEBL , CXCL12, PDXL ), capillary ( COL4A1 , COL4A2 , DYSF ) and dividing VECs.

summary:
In Homo sapiens quadriceps tendon, arteriolar vascular endothelial cells are marked by NEBL, CXCL12, and PDXL.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:86983c91768afca7f77f
claim_id: claim:86983c91768afca7f77f
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary:
In Homo sapiens quadriceps tendon, capillary vascular endothelial cells are marked by COL4A1, COL4A2, and DYSF.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:339fed26c7556995aa0a
claim_id: claim:339fed26c7556995aa0a
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary: In Homo sapiens quadriceps tendon, mural cells are marked by NOTCH3 and PTPRB.
span_literal:
Mural cells ( NOTCH3 , PTPRB ) separated into pericytes ( ABCC9 , EGFLAM , STEAP4 ) and vascular smooth muscle cells (vSMCs) ( MYH11 , ITGA8 , NTRK3 ).


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:2e6d7ded0403be2b6c6a
claim_id: claim:2e6d7ded0403be2b6c6a
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Mural cells ( NOTCH3 , PTPRB ) separated into pericytes ( ABCC9 , EGFLAM , STEAP4 ) and vascular smooth muscle cells (vSMCs) ( MYH11 , ITGA8 , NTRK3 ).

summary:
In Homo sapiens quadriceps tendon, vascular smooth muscle cells are marked by MYH11, ITGA8, and NTRK3.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:ea6f156677d417289467
claim_id: claim:ea6f156677d417289467
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
these MERTK hi LYVE1 lo macrophages expressed high levels of CSTB , TPTRG1 , HMOX1 , and chemokines including CXCL2 , CXCL3 and CXCL8 .

summary:
In Homo sapiens quadriceps tendon, MERTK hi LYVE1 lo macrophages express high levels of CSTB, TPTRG1, HMOX1, CXCL2, CXCL3, and CXCL8.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:995237f6dfa27bf7d36f
claim_id: claim:995237f6dfa27bf7d36f
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
DCs could be separated into CLEC10A hi DCs ( CLEC10A , CD1C , IL1R2 ), CLEC9A hi DCs ( CLEC9A , IDO1 , CLNK ), plasmacytoid DCs (pDCs) ( CLEC4C , IRF8 , PLAC8 ) and VCAN hi DCs/monocytes ( VCAN , FCN , LYZ ).

summary:
In Homo sapiens quadriceps tendon, CLEC10A hi dendritic cells are marked by CLEC10A, CD1C, and IL1R2.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:f627c2ffd5a72a068614
claim_id: claim:f627c2ffd5a72a068614
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
DCs could be separated into CLEC10A hi DCs ( CLEC10A , CD1C , IL1R2 ), CLEC9A hi DCs ( CLEC9A , IDO1 , CLNK ), plasmacytoid DCs (pDCs) ( CLEC4C , IRF8 , PLAC8 ) and VCAN hi DCs/monocytes ( VCAN , FCN , LYZ ).

summary:
In Homo sapiens quadriceps tendon, plasmacytoid dendritic cells are marked by CLEC4C, IRF8, and PLAC8.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:faa3619a14119b2399cb
claim_id: claim:faa3619a14119b2399cb
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary:
In Homo sapiens quadriceps tendon, VCAN hi dendritic cells/monocytes are marked by VCAN, FCN, and LYZ.


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:a71b6428304eee39d12b
claim_id: claim:a71b6428304eee39d12b
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
summary: In Homo sapiens quadriceps tendon, T cells are marked by IL7R, THEMIS, and ANK3.
span_literal:
Lymphocyte subsets included T cells ( IL7R , THEMIS , ANK3 ), natural killer (NK) cells ( NCAM1 , GNLY , KLRD1 ) and B cells ( MS4A1 , BLK , IGHM ).


claim_key: hca:0148_10.1113_jp287812_fd3137bc12:claim:c3d3910ccad25cf3e663
claim_id: claim:c3d3910ccad25cf3e663
paper_key: hca:0148_10.1113_jp287812_fd3137bc12
span_literal:
Two fibroblast subsets were predominantly found in ruptured quadriceps tendons: dividing fibroblasts and ADAM12 hi fibroblasts – which had high expression of genes, including ADAM12 , POSTN , COL1A1 , COL1A2 , COL3A1 and FAP .

summary:
In Homo sapiens ruptured quadriceps tendon, ADAM12 hi fibroblasts have high expression of ADAM12, POSTN, COL1A1, COL1A2, COL3A1, and FAP.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:4e123671b01f58a284aa
claim_id: claim:4e123671b01f58a284aa
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Approximately 35% of analysed cells (7 836 cells) clustered within stromal cell cluster composed of fibroblast (4673 cells) and mesenchymal stem cell (MSC, 3163 cells) subclusters identified by Collagen type I ( COL1A1), Midkine (MDK) and RUNX Family Transcription Factor 2 (RUNX2) expression

summary:
In Homo sapiens dental pulp, fibroblasts are identified by Collagen type I (COL1A1), Midkine (MDK), and RUNX Family Transcription Factor 2 (RUNX2) expression.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:894a312783bf4a684a1f
claim_id: claim:894a312783bf4a684a1f
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal: and Frizzled Related Protein ( FRZB) expression (Fig. 1g ), respectively.
summary:
In Homo sapiens dental pulp, mesenchymal stem cells are identified by Frizzled Related Protein (FRZB) expression.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:9c6d0b7b3308cc00c309
claim_id: claim:9c6d0b7b3308cc00c309
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Furthermore, Myosin Heavy Chain 11 (MYH11) and α-smooth muscle actin ( ACTA2) expression marked a distinct cell populations within MSC subcluster that were clearly distinguishable from the one marked by THY1 expression

summary:
In Homo sapiens dental pulp, a distinct cell population within the mesenchymal stem cell subcluster is marked by Myosin Heavy Chain 11 (MYH11) and alpha-smooth muscle actin (ACTA2) expression, distinguishable from the population marked by THY1.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:df6469e0a37385085c71
claim_id: claim:df6469e0a37385085c71
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
summary: In Homo sapiens dental pulp, the immune cell cluster is identified by PTPRC (CD45) expression.
span_literal:
Nearly 30% of total cells (5777 cells) constituted immune cell cluster identified by PTPRC (CD45) expression.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:bc9addfe61fd65419109
claim_id: claim:bc9addfe61fd65419109
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Further cell clusters included endothelial cells (4126 cells, or ~21%) identified by Platelet And Endothelial Cell Adhesion Molecule 1 (PECAM-1), CD34 and Endoglin (ENG) expression

summary:
In Homo sapiens dental pulp, endothelial cells are identified by Platelet And Endothelial Cell Adhesion Molecule 1 (PECAM-1), CD34, and Endoglin (ENG) expression.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:9390d009656a81f8fc9d
claim_id: claim:9390d009656a81f8fc9d
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Interestingly, key marker genes for T-lymphocytes, namely Granzyme A (GZMA), CD247 and CD3D (Fig. 3a ), which were expressed in the subcluster 1, were also found in the subcluster 2.

summary:
In Homo sapiens dental pulp, T-lymphocytes are marked by Granzyme A (GZMA), CD247, and CD3D expression.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:4e0503f435d0c334daa2
claim_id: claim:4e0503f435d0c334daa2
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Cluster 3 was marked by the exclusive expression of CD163 , Colony Stimulating Factor 1 Receptor (CSF1R) and CD14 (Fig. 3a ), which identify monocyte cell lineage.

summary:
In Homo sapiens dental pulp, the monocyte cell lineage is identified by the exclusive expression of CD163, Colony Stimulating Factor 1 Receptor (CSF1R), and CD14.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:fa15e59be2b44bcd671f
claim_id: claim:fa15e59be2b44bcd671f
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Subcluster 4 was marked by exclusive expression of IGHG1, IGHG3 and IGHG4 , which marks memory and naïve B-cells which were detected in insignificant numbers in the healthy pulp data set

summary:
In Homo sapiens dental pulp, memory and naïve B-cells are marked by exclusive expression of IGHG1, IGHG3, and IGHG4.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:316ecc0d2c7e7cd69d38
claim_id: claim:316ecc0d2c7e7cd69d38
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Co-localisation of CD83, HLA-DRA and IRF8 (Supplementary Fig. 2 ) with CD19, CD22 and Membrane Spanning 4-Domains A1 (MS4A1) (Fig. 3a ) in the subcluster 5 indicates that this cluster is composed mainly of B-lymphocytes.

summary:
In Homo sapiens dental pulp, B-lymphocytes are marked by co-expression of CD83, HLA-DRA, Interferon Regulatory Factor 8 (IRF8), CD19, CD22, and Membrane Spanning 4-Domains A1 (MS4A1).


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:f2541d0f4b3da6a427c6
claim_id: claim:f2541d0f4b3da6a427c6
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Approximately 22% of fibroblasts from carious pulps expressed another known marker of myofibroblasts, Collagen Triple Helix Repeat Containing 1 (CTHRC1) that identifies myofibroblasts in the fibrotic lungs and heart.

summary:
In Homo sapiens, Collagen Triple Helix Repeat Containing 1 (CTHRC1) is a known marker of myofibroblasts.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:ee9ce98bdc1ad083fdab
claim_id: claim:ee9ce98bdc1ad083fdab
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Recent transcriptomics analyses of the fibrotic skin proposed Secreted Frizzled Related Protein (SFRP) 2 and 4 as a new myofibroblast markers.

summary:
In Homo sapiens, Secreted Frizzled Related Protein 2 (SFRP2) and Secreted Frizzled Related Protein 4 (SFRP4) have been proposed as new myofibroblast markers.


claim_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab:claim:aed935d511fbe3be24f9
claim_id: claim:aed935d511fbe3be24f9
paper_key: hca:0149_10.1038_s41368-023-00238-z_c77e60a0ab
span_literal:
Interestingly, the fraction of cells expressing Integrin Binding Sialoprotein (IBSP) , a marker of osteoblast/odontoblast differentiation, 26 in the fibroblast cluster of carious pulps was ~5.4%.

summary:
In Homo sapiens, Integrin Binding Sialoprotein (IBSP) is a marker of osteoblast/odontoblast differentiation.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:b1b40f9ee2dec36e302b
claim_id: claim:b1b40f9ee2dec36e302b
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
we observed a significant increase of CD4 + CD25 + CD127 − Foxp3 + T reg cells in HNSCC compared with OM tissues

summary:
In Homo sapiens, regulatory T cells in head and neck squamous cell carcinoma are marked by CD4, CD25, negative CD127, and FOXP3.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:860fd383c940b4735f12
claim_id: claim:860fd383c940b4735f12
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal: CD11c + CD141 + cross-presenting type 1 classical dendritic cells (cDC1s)
summary:
In Homo sapiens, type 1 classical dendritic cells are marked by positive expression of CD11c and CD141.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:0073947bb534668f7007
claim_id: claim:0073947bb534668f7007
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal: CD11c + CD1c + CD163 − cDC2s
summary:
In Homo sapiens, type 2 classical dendritic cells are marked by positive CD11c, positive CD1c, and negative CD163.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:3a0112cd0e44e5f97fda
claim_id: claim:3a0112cd0e44e5f97fda
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal: CD11c + CD1c + CD163 + DC3s (previously referred to as inflammatory dendritic cells 24 – 26 )
summary:
In Homo sapiens, DC3 cells (inflammatory dendritic cells) are marked by positive CD11c, positive CD1c, and positive CD163.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:509f26d0dc1297403832
claim_id: claim:509f26d0dc1297403832
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
a population expressing high levels of CCR7 , CCL19 and CSF2RA (encoding the GM-CSF receptor) (Fig. 2c ), resembling mature dendritic cells enriched in immunoregulatory molecules 33 (mregDCs)

summary:
In Homo sapiens, mature dendritic cells enriched in immunoregulatory molecules express high levels of CCR7, CCL19, and CSF2RA (encoding the granulocyte-macrophage colony-stimulating factor receptor).


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:46b2342095ab25c3372e
claim_id: claim:46b2342095ab25c3372e
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
HLA-DR-expressing mast cells mainly in HNSCC tissues, marked by the signature genes CLU (encoding mast cell carboxypeptidase A) and GATA2

summary:
In Homo sapiens, mast cells in head and neck squamous cell carcinoma tissues are marked by HLA-DR expression and the signature genes CLU (encoding mast cell carboxypeptidase A) and GATA2.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:143a8aa6a655b90224f0
claim_id: claim:143a8aa6a655b90224f0
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal: mregDCs were the dominant CCL17- and CCL22-expressing population
summary:
In Homo sapiens, mature dendritic cells enriched in immunoregulatory molecules are the dominant CCL17- and CCL22-expressing population.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:615f05721ed5ab14fe74
claim_id: claim:615f05721ed5ab14fe74
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
FAUST identified a single subcluster of CD8 + T cells, and four CD4 + T reg (CD25 + CD127 − ) phenotypes marked by expression of ICOS with combinations of PD-1, TIM3 and HLA-DR as being enriched in HNSCC

summary:
In Homo sapiens, tumour-enriched regulatory T cell phenotypes in head and neck squamous cell carcinoma are marked by CD25, negative CD127, and expression of ICOS with combinations of PD-1, TIM3, and HLA-DR.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:67cc01aa81f9ac471c7b
claim_id: claim:67cc01aa81f9ac471c7b
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
FAUST identified several tumour-enriched phenotypes of CD14 + cells, cDC2s and cDC3s marked by co-expression of CD40 and PD-L1

summary:
In Homo sapiens, tumour-enriched phenotypes of CD14-positive cells, type 2 classical dendritic cells, and DC3 cells are marked by co-expression of CD40 and PD-L1.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:dbba56997c78e9d9a7ec
claim_id: claim:dbba56997c78e9d9a7ec
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
IL1R1 was expressed specifically by tumour-infiltrating T reg cells, but not by tumour-infiltrating CD4 + T cells or CD8 + T cells

summary:
In Homo sapiens, IL1R1 is expressed specifically by tumour-infiltrating regulatory T cells, but not by CD4-positive T cells, CD8-positive T cells, or peripheral blood T cells.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:f9ab82f6af7f3fa9be2c
claim_id: claim:f9ab82f6af7f3fa9be2c
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
Nearly all IL1R1 + T reg cells co-expressed ICOS and IL-18R1 in conjunction with higher levels of the chemokine receptor CXCR6

summary:
In Homo sapiens, IL1R1-positive regulatory T cells co-express ICOS, IL-18R1, and higher levels of the chemokine receptor CXCR6.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:58f0524974f7a1a653f9
claim_id: claim:58f0524974f7a1a653f9
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
both IL1R1 + and IL1R1 − intratumoural T reg cells expressed FOXP3, but CTLA4 expression was significantly increased only in the IL1R1 + fraction

summary:
In Homo sapiens, both IL1R1-positive and IL1R1-negative intratumoural regulatory T cells express FOXP3, but CTLA4 expression is significantly increased only in the IL1R1-positive regulatory T cell fraction.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:d3fa7f754c96c7db32a9
claim_id: claim:d3fa7f754c96c7db32a9
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
More than 50 transcripts were selectively enriched in the IL1R1 + cluster, including TNFRSF18 (which encodes GITR) and TNFRSF9 (which encodes 4-1BB), which has been suggested as a pan-cancer T reg target 37

summary:
In Homo sapiens, IL1R1-positive regulatory T cells are selectively enriched for TNFRSF18 (which encodes glucocorticoid-induced tumor necrosis factor receptor-related protein) and TNFRSF9 (which encodes 4-1BB).


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:268be7d3aa2947324731
claim_id: claim:268be7d3aa2947324731
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal:
unsupervised clustering revealed three T reg clusters: IL1R1 − , IL1R1 + and an actively proliferating IL1R1 + T reg cluster marked by MKI67 and TOP2A

summary:
In Homo sapiens, an actively proliferating IL1R1-positive regulatory T cell cluster is marked by MKI67 and TOP2A.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:b20bbeb35430d3e4ba37
claim_id: claim:b20bbeb35430d3e4ba37
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal: IL1R1 + ICOS + T reg cells
summary:
In Homo sapiens, nearly all CD45-positive IL1R1-positive ICOS-positive cells are regulatory T cells, indicating that co-expression of IL1R1 and ICOS uniquely identifies this population among haematopoietic cells.


claim_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc:claim:ddae9e28fc31fa814530
claim_id: claim:ddae9e28fc31fa814530
paper_key: hca:0151_10.1038_s41586-022-04718-w_1bf3167cbc
span_literal: among intratumoural T cells, expression of IL1R1 transcript was largely restricted to T reg cells
summary:
In Homo sapiens, among intratumoural T cells, expression of IL1R1 transcript is largely restricted to regulatory T cells.


claim_key: hca:0152_10.15252_embr.201847483_d14f9b2105:claim:c8b149b85f0112531088
claim_id: claim:c8b149b85f0112531088
paper_key: hca:0152_10.15252_embr.201847483_d14f9b2105
span_literal:
A distinct SIX2‐expressing cluster was identified as a nephron progenitor‐like population based on expression of other known markers, including CITED1 , DAPL1 , EYA1 , and SALL1 .

summary:
In Homo sapiens kidney organoids, a nephron progenitor-like population is identified by expression of SIX2, CITED1, DAPL1, EYA1, and SALL1.


claim_key: hca:0152_10.15252_embr.201847483_d14f9b2105:claim:ae1efb0d4e720317ea26
claim_id: claim:ae1efb0d4e720317ea26
paper_key: hca:0152_10.15252_embr.201847483_d14f9b2105
summary: In Homo sapiens kidney organoids, stromal populations express COL1A1, COL3A1, DCN, and CXCL12.
span_literal:
Multiple stromal populations were also identified, which expressed collagens COL1A1 and COL3A1 , as well as kidney stromal markers DCN and CXCL12 .


claim_key: hca:0152_10.15252_embr.201847483_d14f9b2105:claim:ba900bf97ce0eeb8ae1a
claim_id: claim:ba900bf97ce0eeb8ae1a
paper_key: hca:0152_10.15252_embr.201847483_d14f9b2105
summary: In Homo sapiens kidney organoids, proximal tubule cells are marked by EPCAM and LTL positivity.
span_literal:
Immunofluorescence of SIX2 EGFP/EGFP organoid demonstrating expression and correct localization of nephron segment‐specific markers for proximal tubules (EPCAM + /LTL + ; blue/green), distal tubules (EPCAM + ; green), collecting duct (EPCAM + /GATA3 + ; green/red), and glomeruli (NPHS1 + ; gray).


claim_key: hca:0152_10.15252_embr.201847483_d14f9b2105:claim:1f461eb7e06d60d64a49
claim_id: claim:1f461eb7e06d60d64a49
paper_key: hca:0152_10.15252_embr.201847483_d14f9b2105
summary: In Homo sapiens fetal kidney, nephron progenitor cells co-express SIX2, MEIS1, and FOXD1.
span_literal:
recent single‐cell RNAseq analysis of human fetal kidney has revealed substantial overlap between these two progenitor populations, with co‐expression of SIX2 , MEIS1 , and FOXD1 detected within human nephron progenitors


claim_key: hca:0152_10.15252_embr.201847483_d14f9b2105:claim:ec03223245558408e364
claim_id: claim:ec03223245558408e364
paper_key: hca:0152_10.15252_embr.201847483_d14f9b2105
summary: In Homo sapiens kidney organoids, renal stromal cells are marked by MEIS1 positivity.
span_literal:
Immunostaining of SIX2 Cre/Cre :GAPDH dual kidney organoids shows localization of mCherry cells within proximal (LTL + /EPCAM + ), distal (LTL − /EPCAM + ), and glomerular (NPHS1 + ) nephron segments and within renal stroma (MEIS1 + ) but not within the CD31 + vasculature.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:cfc2c14589760eee1561
claim_id: claim:cfc2c14589760eee1561
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
summary: In Homo sapiens, Deleted in azoospermia like (DAZL) is a marker of human primordial germ cells.
span_literal:
we performed RNA fluorescence in situ hybridization (FISH) for XACT on prenatal ovaries together with immunostaining for the germ cell-specific protein Deleted in azoospermia like (DAZL), which marks hPGCs


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:e26a574e6547ef6af266
claim_id: claim:e26a574e6547ef6af266
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
These findings uncover XACT as hPGC-marker, describe XCD associated with XIST -expression in hPGCs, and suggest that XCD evolved in humans to regulate X-linked genes in pre-implantation embryos and PGCs.

summary:
In Homo sapiens, XACT is a marker of human primordial germ cells, and XIST is expressed in human primordial germ cells.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:af6bbad6559284dc511e
claim_id: claim:af6bbad6559284dc511e
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
Clusters 0–5 represent hPGCs expressing the transcription factors NANOG and OCT4 , together with the hPGC markers NANOS3, PRDM1 and SOX17

summary:
In Homo sapiens, human primordial germ cells express the markers NANOG, OCT4, NANOS3, PRDM1, and SOX17.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:935d917d2625a21e8b4a
claim_id: claim:935d917d2625a21e8b4a
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
Starting in cluster 6, we observed downregulation of naïve-like pluripotency genes and upregulation of the meiotic licensing gene STRA8 42 and of genes encoding RNA binding proteins such as DAZL and DDX4 ( VASA ) (clusters 6–7).

summary:
In Homo sapiens, meiotic germ cells upregulate STRA8, DAZL, and DDX4 (VASA) upon differentiation from human primordial germ cells.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:153d4d3dea6f59eae43f
claim_id: claim:153d4d3dea6f59eae43f
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
This was followed by expression of the meiotic prophase I genes SPO11 and SYCP1 in clusters 8–9, and ultimately, in cluster 10, up-regulation of primordial oocyte (PO) genes including the Zona Pellucida Protein 3 ( ZP3 ) 43

summary:
In Homo sapiens, meiotic germ cells express SPO11 and SYCP1, and primordial oocytes upregulate Zona Pellucida Protein 3 (ZP3).


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:d756f105c0062b01e6e6
claim_id: claim:d756f105c0062b01e6e6
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
Collectively, these data uncover the lncRNA XACT as a new marker of male and female hPGCs in vivo and in vitro.

summary:
In Homo sapiens, the long non-coding RNA XACT is a marker of human primordial germ cells in vivo and in vitro.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:41c4dd6943faed839e93
claim_id: claim:41c4dd6943faed839e93
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
summary: In Homo sapiens, XACT is described as a unique marker of human primordial germ cells.
span_literal:
From this analysis, we describe XACT as a unique marker of hPGCs, and speculate that it could be used to trace hPGCs from the time of lineage specification by RNA FISH.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:cf706db591a58f3cdc95
claim_id: claim:cf706db591a58f3cdc95
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
We observed XACT transcripts in nearly all female hPGCs (DAZL-positive cells) at weeks 7–8 post-fertilization (pf), whereas somatic cells (DAZL-negative) lacked XACT expression

summary:
In Homo sapiens, XACT is expressed in human primordial germ cells but not in somatic cells, and DAZL marks human primordial germ cells.


claim_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b:claim:49f68921afae923d012e
claim_id: claim:49f68921afae923d012e
paper_key: hca:0153_10.1038_s41556-020-00607-4_a7b29ac44b
span_literal:
Germ cell clusters were identified by expression of germ cell-specific markers such NANOS3 , DAZL , DDX4 , SYCP1 .

summary:
In Homo sapiens, germ cells are identified by expression of germ cell-specific markers NANOS3, DAZL, DDX4, and SYCP1.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:d0ca2522f5c1610ca717
claim_id: claim:d0ca2522f5c1610ca717
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
For example, G6PC2 , ADCYAP1 and HADH in β-cells all have been demonstrated to be involved in maintaining glycemia 32 – 34 .

summary:
In Homo sapiens, G6PC2, ADCYAP1, and HADH are identity markers of pancreatic beta cells involved in maintaining glycemia.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:cad9b200bcf4df5f3a22
claim_id: claim:cad9b200bcf4df5f3a22
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Amongst the top regulated transcription factors, key identity regulators PDX1 , NKX6-1 and MAFA are highly regulated, while ENTPD3 is one of the top regulated cell surface markers 32 .

summary:
In Homo sapiens, PDX1, NKX6-1, MAFA, and ENTPD3 are top regulated identity markers of pancreatic beta cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:f063eb1f22820c8b98c6
claim_id: claim:f063eb1f22820c8b98c6
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal: In α-cells, TTR 35 and SLC7A2 36 are amongst the top regulated genes.
summary:
In Homo sapiens, TTR and SLC7A2 are among the top regulated identity genes of pancreatic alpha cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:a0b6414d7e06cd2172ed
claim_id: claim:a0b6414d7e06cd2172ed
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
IRX2 33 is recognized as the most strongly regulated transcription factor, while TM4SF4 18 and FAP 37 are the most highly regulated cell surface markers (Fig. 1C , Fig. S3A ).

summary:
In Homo sapiens, IRX2 is the most strongly regulated transcription factor and TM4SF4 and FAP are the most highly regulated cell surface markers of pancreatic alpha cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:6078f516641e6e2b5b48
claim_id: claim:6078f516641e6e2b5b48
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
For γ-cells, these included the transcription factors ETV1 38 PAX6 39 and ARX 40 , where HHEX 41 , ETV1 38 and ISL1 42 were found in δ-cells.

summary:
In Homo sapiens, the transcription factors ETV1, PAX6, and ARX are identity markers of pancreatic gamma cells, while HHEX, ETV1, and ISL1 are identity markers of pancreatic delta cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:368a137a1982a260d932
claim_id: claim:368a137a1982a260d932
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
summary: In Homo sapiens, FXYD2 and TM4SF4 are top identity markers of pancreatic gamma cells.
span_literal:
Other interesting top markers for γ-cells included FXYD2 43 and TM4SF4 18 , and for δ-cells CD9 44 , LEPR 45 and FFAR4 46 (Fig. 1C , Fig. S3A ).


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:4edd4953cd738678e658
claim_id: claim:4edd4953cd738678e658
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
We thus confirmed that IAPP and GSN have higher expression in β- than α-cells, while TTR , GLS , SPINT2 and SERPINA1 were more highly expressed in α- than β-cells (Fig. S4A–C ).

summary:
In Homo sapiens, IAPP and GSN have higher expression in pancreatic beta cells than in pancreatic alpha cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:d52574a04afda8dd4919
claim_id: claim:d52574a04afda8dd4919
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
We thus confirmed that IAPP and GSN have higher expression in β- than α-cells, while TTR , GLS , SPINT2 and SERPINA1 were more highly expressed in α- than β-cells (Fig. S4A–C ).

summary:
In Homo sapiens, TTR, GLS, SPINT2, and SERPINA1 are more highly expressed in pancreatic alpha cells than in pancreatic beta cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:9c8ea7f5d5a5b2c3ab73
claim_id: claim:9c8ea7f5d5a5b2c3ab73
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
We found TTR , GPX3 , SLC7A2 and FAP in α-cells, which were also in the above top 10 α-cell identity gene list, besides well-known transcription factors like IRX2 and MAFB (Figs. 1C , 2D , Supplementary data 1 and 5 ).

summary:
In Homo sapiens, TTR, GPX3, SLC7A2, FAP, IRX2, and MAFB are identity markers of pancreatic alpha cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:e42e0a33a3c44ed93cd8
claim_id: claim:e42e0a33a3c44ed93cd8
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Regarding β-cells, we found top markers like ADCYAP1 and HADH , besides well-known transcription factors like PDX1 , MAFA and NKX6-1 (Figs. 1B–C , 2D , Supplementary data 2 and 5 ).

summary:
In Homo sapiens, ADCYAP1, HADH, PDX1, MAFA, and NKX6-1 are identity markers of pancreatic beta cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:19c8e12ed1878d752afb
claim_id: claim:19c8e12ed1878d752afb
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
summary: In Homo sapiens, STMN2, SERTM1, PAX6, and ETV1 are identity markers of pancreatic gamma cells.
span_literal:
In γ-cells, top markers like STMN2 and SERTM1 were retrieved, just like previously validated transcription factors like PAX6 and ETV1 , while δ-cells expressed top markers like RGS2 , SLC38A1 and SEC11C , together with transcription factor HHEX (Figs. 1C , 2D , Supplementary data 3 , 4 and 5 ).


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:f79dd121e47ba118bac8
claim_id: claim:f79dd121e47ba118bac8
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Previously described ε-cell-specific genes, like SPINK1 , APOH, ASCL1 and FRZB 49 , were expressed in our dataset as well.

summary:
In Homo sapiens, SPINK1, APOH, ASCL1, and FRZB are specific identity genes of pancreatic epsilon cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:bf6943b3cf2a5ca7c225
claim_id: claim:bf6943b3cf2a5ca7c225
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
summary: In Homo sapiens, F10 and ETV1 are strongly expressed in pancreatic epsilon cells.
span_literal:
Interestingly, we also found α- and γ-cell-related markers, such as F10 and ETV1 , to be strongly expressed in ε-cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:15eeb6f6706417c1b987
claim_id: claim:15eeb6f6706417c1b987
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Particularly, the expression of ARX , a well-established key regulator of α-cell identity 50 , 51 , was found to be more highly expressed in both γ- and ε-cells, and we detected it on the protein level in γ-cells as well (Fig. 2D ; Fig. S4D ; Supplementary data 5 ).

summary:
In Homo sapiens, ARX, a well-established key regulator of pancreatic alpha cell identity, is more highly expressed in both pancreatic gamma cells and pancreatic epsilon cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:797136174cda0c9e30e0
claim_id: claim:797136174cda0c9e30e0
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Particularly, the expression of ARX , a well-established key regulator of α-cell identity 50 , 51 , was found to be more highly expressed in both γ- and ε-cells, and we detected it on the protein level in γ-cells as well (Fig. 2D ; Fig. S4D ; Supplementary data 5 ).

summary:
In Homo sapiens, ARX, a well-established key regulator of pancreatic alpha cell identity, is more highly expressed in pancreatic epsilon cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:675876855ed13568154b
claim_id: claim:675876855ed13568154b
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal: three genes were consistently found in all of the 21 β-cell analyses: INS , IAPP and G6PC2 .
summary:
In Homo sapiens, INS, IAPP, and G6PC2 are the most consistently found identity genes of pancreatic beta cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:20c3816070a32ae9b09a
claim_id: claim:20c3816070a32ae9b09a
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Equally interesting, we were able to define cell surface markers that were specifically regulated between α- and β-cells, like serine peptidase inhibitor SERPINA1 in α-cells and serine peptidase PRSS23 in β-cells.

summary:
In Homo sapiens, SERPINA1 is a cell surface marker specifically regulated in pancreatic alpha cells compared to pancreatic beta cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:8a4075f93697381ac06a
claim_id: claim:8a4075f93697381ac06a
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
Equally interesting, we were able to define cell surface markers that were specifically regulated between α- and β-cells, like serine peptidase inhibitor SERPINA1 in α-cells and serine peptidase PRSS23 in β-cells.

summary:
In Homo sapiens, PRSS23 is a cell surface marker specifically regulated in pancreatic beta cells compared to pancreatic alpha cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:b4f6a24b195a47405ddb
claim_id: claim:b4f6a24b195a47405ddb
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
summary: In Homo sapiens, INS, IAPP, DLK1, and RBP4 are key genes related to pancreatic beta cell identity.
span_literal:
Bi-hormonal cells in the α-cluster upregulated key genes related to β-cell identities, like INS, IAPP, DLK1 and RBP4 .


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:7bd0fa26312d0691b6ac
claim_id: claim:7bd0fa26312d0691b6ac
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
summary: In Homo sapiens, GCG, ARX, FEV, and TM4SF4 are genes related to pancreatic alpha cell identity.
span_literal:
Inversely, bi-hormonal cells in the β-cell cluster upregulate α-cell-related genes like GCG, ARX, FEV and TM4SF4 (Fig. S2A ).


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:c9a8fc731ab202c0aba9
claim_id: claim:c9a8fc731ab202c0aba9
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
summary: In Homo sapiens, GCG, TTR, ARX, IRX2, and PCSK2 are key markers of pancreatic alpha cells.
span_literal:
For each cluster, we tried to assign one of the islet cell types based on the expression of key markers, like GCG , TTR , ARX , IRX2 or PCSK2 in α-cells, INS , IAPP , PDX1 , MAFA , NKX6-1 , ABCC8 or PCSK1 in β-cells, PPY , STMN2 , ETV1 or SLC6A4 in γ-cells and SST , LEPR , BCHE , HHEX and RGS2 in δ-cells.


claim_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22:claim:7a86394dd7e85242cc1b
claim_id: claim:7a86394dd7e85242cc1b
paper_key: hca:0155_10.1038_s41467-022-29588-8_ec4c5a4a22
span_literal:
For each cluster, we tried to assign one of the islet cell types based on the expression of key markers, like GCG , TTR , ARX , IRX2 or PCSK2 in α-cells, INS , IAPP , PDX1 , MAFA , NKX6-1 , ABCC8 or PCSK1 in β-cells, PPY , STMN2 , ETV1 or SLC6A4 in γ-cells and SST , LEPR , BCHE , HHEX and RGS2 in δ-cells.

summary:
In Homo sapiens, INS, IAPP, PDX1, MAFA, NKX6-1, ABCC8, and PCSK1 are key markers of pancreatic beta cells.


claim_key: hca:0156_10.1101_2020.12.21.423830_b1006f56a0:claim:f8749137afe3ccf9eef2
claim_id: claim:f8749137afe3ccf9eef2
paper_key: hca:0156_10.1101_2020.12.21.423830_b1006f56a0
span_literal:
One notable exception to this observation is the gene IFNG, which encodes the type II IFN cytokine IFN-γ. IFN-γ is a crucial mediator of antiviral immunity (Kang et al., 2018), but shows an expression pattern that is almost exclusive to NKT cells in the IAV-infected condition

summary:
In Homo sapiens, IFNG shows an expression pattern that is almost exclusive to natural killer T cells in the influenza A virus-infected condition in peripheral blood mononuclear cells.


claim_key: hca:0157_10.1126_science.abg0928_3795ca9b86:claim:223c11c2ff38c2921955
claim_id: claim:223c11c2ff38c2921955
paper_key: hca:0157_10.1126_science.abg0928_3795ca9b86
span_literal:
A small set of 29 eGenes were also only detectable following infection, including the key IFN-inducible genes OAS1 ( Fig. 3B ), IFI44L , IFIT1 , IRF1 , and ISG15 ( Fig. S4C ).

summary:
In Homo sapiens, OAS1, IFI44L, IFIT1, IRF1, and ISG15 are key interferon-inducible genes whose expression quantitative trait loci are only detectable following influenza A virus infection in peripheral blood mononuclear cells.


claim_key: hca:0157_10.1126_science.abg0928_3795ca9b86:claim:dc8c251f17d698e63247
claim_id: claim:dc8c251f17d698e63247
paper_key: hca:0157_10.1126_science.abg0928_3795ca9b86
span_literal:
S100A8 / A9 are systemically upregulated in immune cells, particularly monocytes, in severe, late-stage COVID-19 patients ( 23 ).

summary:
In Homo sapiens, S100A8 and S100A9 are upregulated in monocytes in severe, late-stage COVID-19 patients.


claim_key: hca:0157_10.1126_science.abg0928_3795ca9b86:claim:3fabf8fa2c2d822766e5
claim_id: claim:3fabf8fa2c2d822766e5
paper_key: hca:0157_10.1126_science.abg0928_3795ca9b86
span_literal:
S100A4/A6 / A8 expression has been associated with patient improvement when upregulated early in the course of COVID-19 infection ( 21 ), and S100A8 / A9 are systemically upregulated in immune cells, particularly monocytes, in severe, late-stage COVID-19 patients ( 23 ).

summary:
In Homo sapiens, S100A4, S100A6, and S100A8 expression in immune cells is associated with patient improvement when upregulated early in the course of COVID-19 infection.


claim_key: hca:0157_10.1126_science.abg0928_3795ca9b86:claim:c28e89d74b7f3155dc61
claim_id: claim:c28e89d74b7f3155dc61
paper_key: hca:0157_10.1126_science.abg0928_3795ca9b86
span_literal:
In our data, S100A4 , S100A6 , and S100A8 are all significantly more highly expressed with greater European ancestry early after IAV infection ( Fig. 4E , Table S5 ), consistent with a potential contribution of genetic ancestry to observed differences in COVID-19 susceptibility between African Americans and European Americans.

summary:
In Homo sapiens, S100A4, S100A6, and S100A8 are more highly expressed in monocytes from individuals with greater European ancestry early after influenza A virus infection.


claim_key: hca:0158_10.2337_db21-0830_d021248f76:claim:4be22a0b332a66f3a282
claim_id: claim:4be22a0b332a66f3a282
paper_key: hca:0158_10.2337_db21-0830_d021248f76
summary: In Homo sapiens skin, endothelial cells are marked by CDH5, VWF, and PECAM1.
span_literal:
These include CDH5 , VWF , and PECAM1 for endothelial cells; CD3D , CD2 , and PTPRC for T cells; APOE , CXCL12 , and APOD for fibro 1; COL1A1 , COL2A2 , and MMP2 for fibro 2; TAGLN , ACTA2 , and TPM2 for smooth muscle cells (SMCs); NKG7 , GNLY , and CCL4 for natural killer (NK) cells; KRT14, KRT1, and KRT10 for kera A; LYZ , CXCL8 , and IL1B for myeloid cells; TPSAB1 , TPSB2 , and CPA3 for mast cells; LYVE1 , CCL21 , and TFF3 for lymphatic endothelial cells (LECs); KRT19 , KRT7 , and AQP5 for kera B; and DCT , TYRP1 , and MLANA for melanocytes ( Fig. 1 C and D ).


claim_key: hca:0158_10.2337_db21-0830_d021248f76:claim:52e774b265e64f740224
claim_id: claim:52e774b265e64f740224
paper_key: hca:0158_10.2337_db21-0830_d021248f76
span_literal:
Cluster 4 (SMCs) included established characteristics of pericytes, as evident by the high expression of published markers ( 44 , 45 ), such as SMA ( ACTA2 ), DES , NG2 , and RGS5 ( Supplementary Fig. 1 E ).

summary:
In Homo sapiens skin, pericytes show high expression of smooth muscle actin (ACTA2), DES, NG2, and RGS5.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:729c4baf3f0e1565b885
claim_id: claim:729c4baf3f0e1565b885
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal:
Among the keratinocyte-specific genes, Kera1 showed high abundance (more than log 2 folds) of KRT1 , KRT5 , KRT14 , KRT10 , KRT16 , and KRT6A , representing the stratified epithelium ( 30 ).

summary:
In Homo sapiens, keratinocyte subpopulation Kera1 is marked by high abundance of KRT1, KRT5, KRT14, KRT10, KRT16, and KRT6A, representing the stratified epithelium.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:1e75e2fb267e37cde39b
claim_id: claim:1e75e2fb267e37cde39b
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal:
In contrast, Kera2 was characterized by high abundance of KRT7 , KRT8 , KRT18 , and KRT19 , which are known to be characteristic markers of nonstratified (simple) epithelium ( 30 ).

summary:
In Homo sapiens, keratinocyte subpopulation Kera2 is characterized by high abundance of KRT7, KRT8, KRT18, and KRT19, which are markers of nonstratified simple epithelium.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:b5ac29223e36a41c8515
claim_id: claim:b5ac29223e36a41c8515
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal:
Kera2 was identified to highly express transcription regulators Elongin-B, Prohibitin, and Cited4 (top 3 candidates), all known for their role in EMT ( 31 – 34 ) ( Figure 3C ).

summary:
In Homo sapiens, keratinocyte subpopulation Kera2 highly expresses the transcription regulators Elongin-B, Prohibitin, and CITED4, all known for their role in epithelial-mesenchymal transition.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:9a06edaff6f499626164
claim_id: claim:9a06edaff6f499626164
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal:
Furthermore, Kera2 showed high abundance of distinct metabolic enzymes, such as GAPDH , cytochrome c oxidase subunit isoform ( COX7A1 ), and aldo-keto reductase 1C1 ( AKR1C1 ) ( 35 – 37 ) ( Figure 3D ).

summary:
In Homo sapiens, keratinocyte subpopulation Kera2 shows high abundance of GAPDH, cytochrome c oxidase subunit isoform COX7A1, and aldo-keto reductase 1C1 AKR1C1.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:6e748ec61800e0f332bf
claim_id: claim:6e748ec61800e0f332bf
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal: Kera1 was marked as KRT14 + KRT1 + , while Kera2 was marked as KRT19 + KRT7 + ( Figure 3G ).
summary:
In Homo sapiens, keratinocyte subpopulation Kera1 is marked by KRT14 and KRT1, while keratinocyte subpopulation Kera2 is marked by KRT19 and KRT7.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:95b5f0d6799af61c3e40
claim_id: claim:95b5f0d6799af61c3e40
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal:
Specifically, 2 distinct keratinocyte clusters were identified as Kera1 ( KRT14 + KRT1 + ) and Kera2 ( KRT19 + KRT7 + ).

summary:
In Homo sapiens, two distinct keratinocyte clusters were identified: keratinocyte subpopulation Kera1 marked by KRT14 and KRT1, and keratinocyte subpopulation Kera2 marked by KRT19 and KRT7.


claim_key: hca:0159_10.1172_jci157279_71a5ff671c:claim:261e09fe86bad3ab0976
claim_id: claim:261e09fe86bad3ab0976
paper_key: hca:0159_10.1172_jci157279_71a5ff671c
span_literal:
Additionally, enriched in KRT8 and KRT18 , evident in fetal mesenchymal cells ( 30 ), Kera2 is rich in genes relevant to cell plasticity.

summary:
In Homo sapiens, keratinocyte subpopulation Kera2 is enriched in KRT8 and KRT18, genes relevant to cell plasticity.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:62d05c7b6118ba6665ac
claim_id: claim:62d05c7b6118ba6665ac
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
summary: In Homo sapiens, DDX4 is a positive marker of germ cells.
span_literal:
Browser snapshots of DDX4 (germ cell marker), FGFR3 (hSSC marker), KIT and SYCP3 (differentiating spermatogonia marker), GATA4 (Sertoli cell marker), and LHCGR (Leydig cell marker).


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:5ca837401e9c028ebefe
claim_id: claim:5ca837401e9c028ebefe
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
the germ cell marker ( DDX4 ) was expressed in both SSEA4 + and c-KIT + cells, the self-renewal marker ( FGFR3 ) was upregulated in SSEA4 + hSSCs, differentiating markers ( KIT and SYCP3 ) were upregulated in c-KIT + spermatogonia, and known markers of Sertoli cells ( GATA4 ) and Leydig cells ( LHCGR ) were extremely low or absent

summary:
In Homo sapiens, DDX4 is a positive germ cell marker expressed in both SSEA4+ human spermatogonial stem cells and c-KIT+ spermatogonia.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:6566fc2b38f2331b5a71
claim_id: claim:6566fc2b38f2331b5a71
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
the germ cell marker ( DDX4 ) was expressed in both SSEA4 + and c-KIT + cells, the self-renewal marker ( FGFR3 ) was upregulated in SSEA4 + hSSCs, differentiating markers ( KIT and SYCP3 ) were upregulated in c-KIT + spermatogonia, and known markers of Sertoli cells ( GATA4 ) and Leydig cells ( LHCGR ) were extremely low or absent

summary:
In Homo sapiens, FGFR3 is a positive self-renewal marker upregulated in SSEA4+ human spermatogonial stem cells.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:9ac7046f6633104d7eb0
claim_id: claim:9ac7046f6633104d7eb0
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
the germ cell marker ( DDX4 ) was expressed in both SSEA4 + and c-KIT + cells, the self-renewal marker ( FGFR3 ) was upregulated in SSEA4 + hSSCs, differentiating markers ( KIT and SYCP3 ) were upregulated in c-KIT + spermatogonia, and known markers of Sertoli cells ( GATA4 ) and Leydig cells ( LHCGR ) were extremely low or absent

summary:
In Homo sapiens, KIT and SYCP3 are positive differentiating markers upregulated in c-KIT+ spermatogonia.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:1581c3e09f9259c4957c
claim_id: claim:1581c3e09f9259c4957c
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
the expression of core pluripotency genes ( OCT4 , NANOG , SOX2 ) was found to be low or undetectable in hSSCs and spermatogonia, although other pluripotency-related factors were expressed

summary:
In Homo sapiens, the expression of core pluripotency genes OCT4, NANOG, and SOX2 was found to be low or undetectable in human spermatogonial stem cells.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:7435210b4cd19cc11d8e
claim_id: claim:7435210b4cd19cc11d8e
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
the expression of core pluripotency genes ( OCT4 , NANOG , SOX2 ) was found to be low or undetectable in hSSCs and spermatogonia, although other pluripotency-related factors were expressed

summary:
In Homo sapiens, the expression of core pluripotency genes OCT4, NANOG, and SOX2 was found to be low or undetectable in spermatogonia.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:ee2eae01e1824c39b2d3
claim_id: claim:ee2eae01e1824c39b2d3
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
we found DMRT1 , a key differentiation factor known to antagonize pluripotency in the mouse, expressed at markedly higher levels in hSSCs/spermatogonia than ESCs

summary:
In Homo sapiens, DMRT1 is expressed at markedly higher levels in human spermatogonial stem cells/spermatogonia than in embryonic stem cells.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:dcaaacb56cef81c95c51
claim_id: claim:dcaaacb56cef81c95c51
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
Here, we chose GFRA1 , BCL6 , FGFR3 , ID4 , SALL4 , and ETV5 as hSSC markers, and KIT , SOHLH2 , SYCE3 , SSX3 , SYCP3 , and NR6A1 as spermatogonia markers, based on work in the mouse and results from our bulk datasets.

summary:
In Homo sapiens, GFRA1, BCL6, FGFR3, ID4, SALL4, and ETV5 are positive markers of human spermatogonial stem cells.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:a9f45bef27d7116d671f
claim_id: claim:a9f45bef27d7116d671f
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
SSEA4-enriched genes included the prominent SSC markers in mice (e.g., ID4 , FGFR3 , SALL4 , ETV5 ), as well as many new candidate hSSC markers, including TCF7 , PIWIL2 , BMPR1A/B , L1TD1 , and TXNIP .

summary:
In Homo sapiens, ID4, FGFR3, SALL4, ETV5, TCF7, PIWIL2, BMPR1A/B, L1TD1, and TXNIP are positive markers of human spermatogonial stem cells.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:3f90ab0f8ce85ad4b018
claim_id: claim:3f90ab0f8ce85ad4b018
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal: NANOG and POU5F1/OCT4
summary:
In Homo sapiens, NANOG and POU5F1/OCT4 are transcriptionally silent and epigenetically repressed in human spermatogonial stem cells.


claim_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8:claim:78144c66edb6962d9c9d
claim_id: claim:78144c66edb6962d9c9d
paper_key: hca:0160_10.1016_j.stem.2017.09.003_8fb14888a8
span_literal:
Notably, although SOX2 is transcriptionally silent, its promoter has open chromatin and is DNA hypomethylated, consistent with its bivalent status in the mouse

summary:
In Homo sapiens, SOX2 is transcriptionally silent in human spermatogonial stem cells, although its promoter has open chromatin and is DNA hypomethylated.


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:a97e0f502764d1fef691
claim_id: claim:a97e0f502764d1fef691
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
summary: In Homo sapiens kidney allograft biopsies, T cells are defined by expression of CD3E.
span_literal:
Cell types were defined by expression of typical markers including CD3E for T cells, MS4A1 (CD20) for B cells, SDC1 (CD138) for plasma cells, and TPSAB1 (tryptase) for mast cells ( Figure 4B ).


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:eba2e04196137397f0e5
claim_id: claim:eba2e04196137397f0e5
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
summary:
In Homo sapiens kidney allograft biopsies, mast cells are defined by expression of TPSAB1 (tryptase).


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:8bc1e6d6c449936662a6
claim_id: claim:8bc1e6d6c449936662a6
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal: Subcluster 2 was an activated T cell cluster expressing GZMB , PRF1 , and GNLY .
summary:
In Homo sapiens kidney allograft biopsies, activated T cell subcluster 2 expresses GZMB, PRF1, and GNLY.


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:7cc1fadbcdf553b839be
claim_id: claim:7cc1fadbcdf553b839be
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal:
Recipient macrophages differentially express CD16( FCGR3A ) and CD68 , whereas donor macrophages differentially express CD14 ( Figure 3F ).

summary:
In Homo sapiens kidney allograft biopsies, recipient-origin macrophages differentially express FCGR3A (CD16) and CD68 compared with donor-origin macrophages.


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:6b127eb997231f633547
claim_id: claim:6b127eb997231f633547
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal:
Recipient macrophages differentially express CD16( FCGR3A ) and CD68 , whereas donor macrophages differentially express CD14 ( Figure 3F ).

summary:
In Homo sapiens kidney allograft biopsies, donor-origin macrophages differentially express CD14 compared with recipient-origin macrophages.


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:19772e277323ffa5ab1d
claim_id: claim:19772e277323ffa5ab1d
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal:
Many of the top genes defining recipient T cells and rejecting T cells encode for cytotoxic genes such as natural killer cell granule protein 7 ( NKG7 ), granulysin ( GNLY ), granzyme B ( GZMB ), and perforin ( PRF1 ) ( Figure 5B ).

summary:
In Homo sapiens kidney allograft biopsies, recipient-origin T cells are defined by expression of natural killer cell granule protein 7 (NKG7), granulysin (GNLY), granzyme B (GZMB), and perforin (PRF1).


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:6b48c75ae087a72a26f5
claim_id: claim:6b48c75ae087a72a26f5
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal:
Genes differentially expressed in donor-origin T cells and nonrejecting T cells included IL32 , CD52 , MIF , S100A6 , S100A11 , and LTB .

summary:
In Homo sapiens kidney allograft biopsies, donor-origin T cells differentially express IL32, CD52, MIF, S100A6, S100A11, and LTB.


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:88d3e5915d6db7b4985a
claim_id: claim:88d3e5915d6db7b4985a
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal: FEM1C and TERF2IP , are differentially expressed in recipient macrophages
summary:
In Homo sapiens kidney allograft biopsies, recipient-origin macrophages differentially express FEM1C and TERF2IP, top genes of interferon gamma- and tumor necrosis factor-stimulated macrophages.


claim_key: hca:0161_10.1681_asn.2020030326_bf5d42b566:claim:0389f9394ee3bb341f52
claim_id: claim:0389f9394ee3bb341f52
paper_key: hca:0161_10.1681_asn.2020030326_bf5d42b566
span_literal:
The top gene expressed by IL-4–stimulated macrophages, KIAA1671 , was differentially expressed by donor macrophages.

summary:
In Homo sapiens kidney allograft biopsies, donor-origin macrophages differentially express KIAA1671, the top gene of interleukin-4-stimulated macrophages.


claim_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c:claim:aaba9c9ee6717d720ab0
claim_id: claim:aaba9c9ee6717d720ab0
paper_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c
span_literal:
EH Domain-Containing 3 (EHD3) expression was used to confirm the identity of GECs and distinguish them from peritubular capillary endothelial cells and arteriolar endothelial cells as previously reported ( Figure 3a ).

summary:
In Homo sapiens, EH domain-containing 3 (EHD3) expression was used to confirm the identity of glomerular endothelial cells and distinguish them from peritubular capillary endothelial cells and arteriolar endothelial cells.


claim_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c:claim:474ae31eff357b067915
claim_id: claim:474ae31eff357b067915
paper_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c
summary: In Homo sapiens, podocytes were identified by WT1, NPHS1, and NPHS2 gene expression.
span_literal:
A total number of 179 podocytes were identified by WT1 , NPHS1 , and NPHS2 gene expression ( Figure 3b ).


claim_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c:claim:e7875f02fb0b5082f7fb
claim_id: claim:e7875f02fb0b5082f7fb
paper_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c
span_literal: Dot plot showing the podocyte-specific expression of NPHS1, NPHS2, and SYNPO.
summary:
In Homo sapiens, podocytes show podocyte-specific expression of NPHS1, NPHS2, and SYNPO (synaptopodin).


claim_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c:claim:11301188bf5a91f015bc
claim_id: claim:11301188bf5a91f015bc
paper_key: hca:0162_10.1016_j.kint.2021.11.031_93f85a569c
span_literal:
The dot plot indicates EC2 with a large number of cells expressing EHD3. Prior reports document the glomerular endothelial cell–specific expression of EHD3.

summary:
In Homo sapiens, glomerular endothelial cells show cell-specific expression of EH domain-containing 3 (EHD3).


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:8b1251530c241d9ab184
claim_id: claim:8b1251530c241d9ab184
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
naïve and memory cells expressed high levels of genes such as CD19 and could be further annotated as naïve (clusters B3, B8, and B9) or memory (clusters B2, B4, and B5) on the basis of high or low expression of IGHD , respectively.

summary:
In Homo sapiens, naïve B cells express high levels of CD19 and IGHD, while memory B cells express high levels of CD19 and low levels of IGHD.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:0bee8a1d1ef4c882e476
claim_id: claim:0bee8a1d1ef4c882e476
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
Eleven plasma cell clusters were identified on the basis of high expression of PRDM1 and XBP1 , and low expression of CD19 .

summary:
In Homo sapiens, plasma cells are identified by high expression of PRDM1 and XBP1 and low expression of CD19.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:668ebcdd91e8f7673df7
claim_id: claim:668ebcdd91e8f7673df7
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
Seven clusters (T3, T4, T6, T9, T11, T12, and T17) with high expression of SELL (CD62L), CCR7, LEF1 , and TCF7 expression were annotated as naïve/memory.

summary:
In Homo sapiens, naïve/memory T cells are characterized by high expression of SELL, CCR7, LEF1, and TCF7.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:799ae70231d478f24c06
claim_id: claim:799ae70231d478f24c06
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
Four CD8 + T cell clusters (T1, T2, T10, and T14) expressed transcripts suggestive of a resident memory T (T RM ) cell phenotype ( 23 ) , with high expression of CD69, ITGAE (CD103), CD101 , CCR6 , and ITGA1 (CD49a) along with low expression of KLF2 and S1PR1 .

summary:
In Homo sapiens, CD8-positive tissue-resident memory T cells express high levels of CD69, ITGAE, CD101, CCR6, and ITGA1, along with low expression of KLF2 and S1PR1.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:2ac4997e9509bd98db07
claim_id: claim:2ac4997e9509bd98db07
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
Cells from the T7 cluster expressed transcripts indicative of regulatory T (T reg ) cells ( 26 ), including high FOXP3 and ILR2RA (CD25) expression along with low IL7R expression.

summary:
In Homo sapiens, regulatory T cells are characterized by high FOXP3 and IL2RA expression along with low IL7R expression.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:ca5694c39b717296cc84
claim_id: claim:ca5694c39b717296cc84
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
Cells from the T5 cluster expressed transcripts suggestive of T follicular helper (T FH ) cells ( 27 ), including high CXCR5 , PDCD1 (PD1), ICOS , and BCL6 expression.

summary:
In Homo sapiens, T follicular helper cells are characterized by high expression of CXCR5, PDCD1, ICOS, and BCL6.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:c9ee8dd1e9e33894a632
claim_id: claim:c9ee8dd1e9e33894a632
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
span_literal:
Cells from the T15 cluster expressed transcripts indicative of mucosal-associated invariant T (MAIT) cells ( 28 ), including ZBTB16 and TRAV1–2 .

summary:
In Homo sapiens, mucosal-associated invariant T cells are characterized by expression of ZBTB16 and TRAV1-2.


claim_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647:claim:9217332887f0e1c5d43b
claim_id: claim:9217332887f0e1c5d43b
paper_key: hca:0163_10.1126_sciimmunol.abb4432_91494cf647
summary: In Homo sapiens, gamma delta T cell cluster T8 expresses high levels of CCR7.
span_literal:
For example, T8 cluster cells expressed high levels of CCR7 ; T13 cells expressed high levels of KLRB1 (CD161) and S100B; and T16 cells expressed high levels of KLRC1 (NKG2A), GNLY , and XCL1 .


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:c59d6cc3a48c74916bb5
claim_id: claim:c59d6cc3a48c74916bb5
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal: Basal and myoepithelial cells were defined by the expression of TP63 , KRT5/14 , CNN1 , and ACTA2
summary:
In Homo sapiens submandibular gland, basal cells are defined by the expression of TP63, KRT5, and KRT14.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:d28c258f7dfe1a68bbc0
claim_id: claim:d28c258f7dfe1a68bbc0
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal: Basal and myoepithelial cells were defined by the expression of TP63 , KRT5/14 , CNN1 , and ACTA2
summary:
In Homo sapiens submandibular gland, myoepithelial cells are defined by the expression of TP63, KRT5, KRT14, CNN1, and ACTA2.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:0f44980a496922630547
claim_id: claim:0f44980a496922630547
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
While ductal cells expressed markers including KRT7/19 , SLC5A5 , and MUCL1 , acinar cells were enriched for expression of PIP , LPO , STATH , MUC5B , and TFF3

summary:
In Homo sapiens submandibular gland, ductal cells express markers including KRT7, KRT19, SLC5A5, and MUCL1.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:64b1b30f1ff92403452d
claim_id: claim:64b1b30f1ff92403452d
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
While ductal cells expressed markers including KRT7/19 , SLC5A5 , and MUCL1 , acinar cells were enriched for expression of PIP , LPO , STATH , MUC5B , and TFF3

summary:
In Homo sapiens submandibular gland, acinar cells are enriched for expression of PIP, LPO, STATH, MUC5B, and TFF3.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:7e5f341531a9dff23623
claim_id: claim:7e5f341531a9dff23623
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
summary: In Homo sapiens submandibular gland, B cells express CD79A, CD19, IGHM, and MZB1.
span_literal:
Additionally, we identified a number of immune cell types, including CD79A , CD19 , IGHM , and MZB1 expressing B cells; T cells enriched for expression of CD3G , CD3D , and CD3E; and monocytes marked by the expression of AIF1 , CD68 , and ITGAX


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:493ad5b6807262f9e49d
claim_id: claim:493ad5b6807262f9e49d
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
Additionally, we identified a number of immune cell types, including CD79A , CD19 , IGHM , and MZB1 expressing B cells; T cells enriched for expression of CD3G , CD3D , and CD3E; and monocytes marked by the expression of AIF1 , CD68 , and ITGAX

summary:
In Homo sapiens submandibular gland, monocytes are marked by the expression of AIF1, CD68, and ITGAX.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:e9a972154a7749325bbb
claim_id: claim:e9a972154a7749325bbb
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
Our analysis identified 3 acinar cell clusters consisting of serous acinar cells, which were defined by enriched expression levels of PIP and STATH ; mucous acinar cells with high expression levels of MUC5B and TFF3 ; and seromucous acinar cells that expressed genes common to both mucous and serous acinar cells

summary:
In Homo sapiens submandibular gland, serous acinar cells are defined by enriched expression levels of PIP and STATH.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:4ac60dd266879be1ad07
claim_id: claim:4ac60dd266879be1ad07
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
Our analysis identified 3 acinar cell clusters consisting of serous acinar cells, which were defined by enriched expression levels of PIP and STATH ; mucous acinar cells with high expression levels of MUC5B and TFF3 ; and seromucous acinar cells that expressed genes common to both mucous and serous acinar cells

summary:
In Homo sapiens submandibular gland, mucous acinar cells have high expression levels of MUC5B and TFF3.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:ad42122e437761146006
claim_id: claim:ad42122e437761146006
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
We also identified 3 ductal cell clusters, of which 2 were prominent: striated ducts, defined by enriched expression of MUC1 and SLC5A5 , and intercalated ducts with enriched expression levels of KIT and SOX9

summary:
In Homo sapiens submandibular gland, striated duct cells are defined by enriched expression of MUC1 and SLC5A5.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:76a930d25a39c42ca857
claim_id: claim:76a930d25a39c42ca857
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
We also identified 3 ductal cell clusters, of which 2 were prominent: striated ducts, defined by enriched expression of MUC1 and SLC5A5 , and intercalated ducts with enriched expression levels of KIT and SOX9

summary:
In Homo sapiens submandibular gland, intercalated duct cells have enriched expression levels of KIT and SOX9.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:6149587b1f798f060344
claim_id: claim:6149587b1f798f060344
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
summary: In Homo sapiens submandibular gland, a population of ductal cells is marked by ASCL3.
span_literal:
Interestingly, we also identified a relatively small population of ASCL3 -marked ductal cells, similar to what has been reported in the mouse SMG


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:0fcdd13d264ec50e6df1
claim_id: claim:0fcdd13d264ec50e6df1
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
We therefore interrogated our human scRNA-seq data sets for cell types enriched for expression of ionocyte markers FOXI1 , FOXI2 , CFTR , SLC12A2 , and KCNMA1

summary:
In Homo sapiens, ionocytes are enriched for expression of ionocyte markers FOXI1, FOXI2, CFTR, SLC12A2, and KCNMA1.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:27feb80c70bc3647c934
claim_id: claim:27feb80c70bc3647c934
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
Of particular interest were mucous acinar cells, a cell population marked by NKX3-1 , a transcription factor that so far has not been associated with SMG biology.

summary:
In Homo sapiens submandibular gland, mucous acinar cells are marked by NKX3-1, a transcription factor.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:598f2b21369dd733fb0c
claim_id: claim:598f2b21369dd733fb0c
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
While acinar cells could be broadly separated based on various mucous ( MUC5B , TFF3 ) and serous-specific markers ( PIP and STATH ), distinct seromucous cells were found to be of a hybrid molecular nature expressing markers for both cell types.

summary:
In Homo sapiens submandibular gland, mucous acinar cells are marked by MUC5B and TFF3, while serous acinar cells are marked by PIP and STATH, and seromucous cells express markers for both cell types.


claim_key: hca:0164_10.1177_00220345221147908_13bf485ac8:claim:8189902553bea1e3f293
claim_id: claim:8189902553bea1e3f293
paper_key: hca:0164_10.1177_00220345221147908_13bf485ac8
span_literal:
While acinar cells could be broadly separated based on various mucous ( MUC5B , TFF3 ) and serous-specific markers ( PIP and STATH ), distinct seromucous cells were found to be of a hybrid molecular nature expressing markers for both cell types.

summary:
In Homo sapiens submandibular gland, serous acinar cells are marked by serous-specific markers PIP and STATH.


claim_key: hca:0165_10.1111_cpr.13557_b323e8d65a:claim:4281b1b57fd779c16390
claim_id: claim:4281b1b57fd779c16390
paper_key: hca:0165_10.1111_cpr.13557_b323e8d65a
span_literal:
The expression of typical cardiomyocytes markers such as TNNT1 and ACTN1 , and HCM markers such as NPPA and NPPB validated the cell type and the states

summary:
In Homo sapiens, cardiomyocytes are marked by expression of TNNT1 and ACTN1, while hypertrophic cardiomyopathy cardiomyocytes are marked by NPPA and NPPB.


claim_key: hca:0165_10.1111_cpr.13557_b323e8d65a:claim:9d1b840bfb3428ec039e
claim_id: claim:9d1b840bfb3428ec039e
paper_key: hca:0165_10.1111_cpr.13557_b323e8d65a
span_literal:
The expression of typical cardiomyocytes markers such as TNNT1 and ACTN1 , and HCM markers such as NPPA and NPPB validated the cell type and the states

summary:
In Homo sapiens, hypertrophic cardiomyopathy cardiomyocytes are marked by expression of NPPA and NPPB.


claim_key: hca:0165_10.1111_cpr.13557_b323e8d65a:claim:38a6792ed5520617ed69
claim_id: claim:38a6792ed5520617ed69
paper_key: hca:0165_10.1111_cpr.13557_b323e8d65a
summary: In Homo sapiens, non-cardiomyocyte cells are marked by expression of FABP5, PECAM1, VWF, and ENG.
span_literal:
Differential expression analysis identified a cluster up‐regulating many non‐cardiomyocyte marker genes (including FABP5 , PECAM1 , VWF and ENG ) while having fewer down‐regulated genes


claim_key: hca:0165_10.1111_cpr.13557_b323e8d65a:claim:e4ba831b2f7ca6e6ee64
claim_id: claim:e4ba831b2f7ca6e6ee64
paper_key: hca:0165_10.1111_cpr.13557_b323e8d65a
span_literal: Cluster 2 exhibited the highest levels of canonical HCM markers NPPA and NPPB
summary:
In Homo sapiens, hypertrophic cardiomyopathy cardiomyocyte cluster 2 exhibits the highest levels of canonical hypertrophic cardiomyopathy markers NPPA and NPPB.


claim_key: hca:0165_10.1111_cpr.13557_b323e8d65a:claim:c051ff2b4154ce0de4c9
claim_id: claim:c051ff2b4154ce0de4c9
paper_key: hca:0165_10.1111_cpr.13557_b323e8d65a
span_literal: Cluster 3 showed activation of the growth factor pathway, including the high expression of FGF12 .
summary:
In Homo sapiens, hypertrophic cardiomyopathy cardiomyocyte cluster 3 is characterized by high expression of FGF12.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:9ff5445f65d16ba70d96
claim_id: claim:9ff5445f65d16ba70d96
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
summary: In Homo sapiens, inflammatory monocytes are marked by high expression of IL1B, IL6, and CXCL3.
span_literal:
inflammatory monocytes (*IL1B, IL6* & *CXCL3* high) and cDC3s (monocyte-like dendritic cells) appear to migrate out of the circulation.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:8cdf3cd275663551f178
claim_id: claim:8cdf3cd275663551f178
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
classical MAIT cells and activated MAIT cells with higher expression of cytotoxicity and activation markers such as *PRF1* and *CD27

summary:
In Homo sapiens, activated mucosal-associated invariant T cells are distinguished from classical mucosal-associated invariant T cells by higher expression of PRF1 and CD27.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:64462bd7a566fa64bcdf
claim_id: claim:64462bd7a566fa64bcdf
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
CD4+, CD8+ and regulatory T cell states that highly expressed T cell activation markers such as *CD38*, *CD28*, *CD27* and *ICOS

summary:
In Homo sapiens, activated CD4+ T cells highly express the activation markers CD38, CD28, CD27, and ICOS.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:f39e31addd2f53ef7daf
claim_id: claim:f39e31addd2f53ef7daf
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
CD8+ and regulatory T cell states that highly expressed T cell activation markers such as *CD38*, *CD28*, *CD27* and *ICOS

summary:
In Homo sapiens, activated CD8+ T cells highly express the activation markers CD38, CD28, CD27, and ICOS.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:637f9f3cd0bce6775620
claim_id: claim:637f9f3cd0bce6775620
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
regulatory T cell states that highly expressed T cell activation markers such as *CD38*, *CD28*, *CD27* and *ICOS

summary:
In Homo sapiens, activated regulatory T cells highly express the activation markers CD38, CD28, CD27, and ICOS.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:088503897e19d1ecafb6
claim_id: claim:088503897e19d1ecafb6
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
activated regulatory T cells was highest at day 14 at the site of infection (**Fig. 3c**), where they strongly upregulated expression of the anti-inflammatory cytokine IL-10

summary:
In Homo sapiens, activated regulatory T cells strongly upregulate expression of the anti-inflammatory cytokine IL10.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:e2431cf78ca05c8c4140
claim_id: claim:e2431cf78ca05c8c4140
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
summary: In Homo sapiens, activated CD4+ T cells express high amounts of the cytotoxicity gene PRF1.
span_literal:
Activated CD4+ T cells express high amounts of cytotoxicity genes (e.g. *PRF1*, see **Fig. 3b** and **Extended Data Fig. 3a & 4a)** that are normally expressed in NK and CD8+ T cells.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:b584218cf870e426823e
claim_id: claim:b584218cf870e426823e
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
ITGAE* or CD103, **Extended Data Fig. 3a**) which appeared in the nasopharynx during sustained infections and which were annotated as “infiltrating memory T cells

summary:
In Homo sapiens, infiltrating memory T cells lack expression of tissue-residency markers such as ITGAE (CD103).


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:aa2ac4142c8847d2dc48
claim_id: claim:aa2ac4142c8847d2dc48
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
summary: In Homo sapiens, acute-phase response positive ciliated cells show high expression of SAA1.
span_literal:
we detect a relatively abundant subset of ciliated cells with high expression of acute-phase response (APR) genes such as SAA1.


claim_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe:claim:33ce51364431cc6ccaac
claim_id: claim:33ce51364431cc6ccaac
paper_key: hca:0166_10.1101_2023.04.13.23288227_0c5bc13bbe
span_literal:
ciliated cells exhibited a unique response to high viral amounts, upregulating AP1 and NFKB signaling, and multiple genes with known anti-inflammatory functions such as ERG111, NFKBIA12, GDF1513, HES114, PER115, TNFAIP316, and NR4A1

summary:
In Homo sapiens, hyper-infected ciliated cells upregulate anti-inflammatory genes including EGR1, NFKBIA, GDF15, HES1, PER1, TNFAIP3, and NR4A1.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:47423b55c1fdab2bf367
claim_id: claim:47423b55c1fdab2bf367
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
summary: In Homo sapiens fetal neocortex, endothelial cells are marked by PECAM1 expression.
span_literal:
We identified a single cell expressing PECAM1 and many other endothelial markers and five interneurons derived from the ventral telencephalon (marked by GAD1 , DLX1/2/5/6 , and ERBB4 ; Fig. S1 C ), and we excluded these cells from further analyses.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:674886a117a62621e801
claim_id: claim:674886a117a62621e801
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
We identified a single cell expressing PECAM1 and many other endothelial markers and five interneurons derived from the ventral telencephalon (marked by GAD1 , DLX1/2/5/6 , and ERBB4 ; Fig. S1 C ), and we excluded these cells from further analyses.

summary:
In Homo sapiens fetal neocortex, interneurons derived from the ventral telencephalon are marked by GAD1, DLX1, DLX2, DLX5, DLX6, and ERBB4.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:a0370ffb679d31b64532
claim_id: claim:a0370ffb679d31b64532
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
AP1 and AP2) had a high correlation with bulk VZ, expressed genes involved in forebrain development (group A) and cell adhesion (group E), and were marked by coexpression of RG markers PAX6, GLI3, SOX2, HES1, and VIM and the AP marker PROM1

summary:
In Homo sapiens fetal neocortex, apical progenitors are marked by coexpression of radial glia markers PAX6, GLI3, SOX2, HES1, and VIM and the apical progenitor marker PROM1.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:332d55b9202939771b98
claim_id: claim:332d55b9202939771b98
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
AP1 cells (16 cells) expressed cell-cycle genes (group F) enriched during S/G2/M phase progression (e.g., MKI67 ), whereas AP2 cells (24 cells) did not.

summary:
In Homo sapiens fetal neocortex, apical progenitor 1 cells express cell-cycle genes such as MKI67, whereas apical progenitor 2 cells do not.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:f12ae4e4fc77f86bfc73
claim_id: claim:f12ae4e4fc77f86bfc73
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
BP1, 11 cells) that had maximum correlations with bulk iSVZ and expressed RG markers PAX6 , GLI3 , and ASPM as well as early BP markers INSM1 , EOMES , and HES6 but lacked expression of VIM and SOX2

summary:
In Homo sapiens fetal neocortex, basal progenitor 1 cells express PAX6, GLI3, ASPM, INSM1, EOMES, and HES6 but lack expression of VIM and SOX2.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:2aec5cb19eedcb92a0cd
claim_id: claim:2aec5cb19eedcb92a0cd
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
In addition, these BP1 cells expressed a core of proneural genes, including NEUROD4 , as well as many of the same S/G2/M cell-cycle regulators expressed in AP1 cells in the VZ (groups A, F, and G).

summary:
In Homo sapiens fetal neocortex, basal progenitor 1 cells express proneural genes including NEUROD4.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:a00dc4d3ef7e01efe2d4
claim_id: claim:a00dc4d3ef7e01efe2d4
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
Furthermore, we identified a cluster (BP2, 10 cells) containing cells with highest correlation with bulk iSVZ and oSVZ and that was defined by coexpression of EOMES and early neuronal genes including NEUROD6 (group B) but did not express ASPM and other S/G2/M cell-cycle regulators.

summary:
In Homo sapiens fetal neocortex, basal progenitor 2 cells are defined by coexpression of EOMES and NEUROD6 but do not express ASPM.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:0b70319ba7c971355b3c
claim_id: claim:0b70319ba7c971355b3c
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
Each of these clusters expressed a large group of neuronal genes (group B, including MYT1L, BCL11B, and TBR1 ) enriched for GO (gene ontology) terms involved in neuronal differentiation.

summary:
In Homo sapiens fetal neocortex, neuron clusters express neuronal genes including MYT1L, BCL11B, and TBR1.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:eace3cc5717489d54398
claim_id: claim:eace3cc5717489d54398
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal: NPCs and Ns, FOXG1, NFIA, and NFIB
summary:
In Homo sapiens, neural progenitor cells and neurons from dorsal forebrain-like regions of cerebral organoids express FOXG1, NFIA, and NFIB, while neurons additionally express NEUROD6.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:b1c2f602ae11602100eb
claim_id: claim:b1c2f602ae11602100eb
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
cluster c4 is neurons from organoid dorsal forebrain-like regions (cerebral cortex) based on enriched expression of genes expressed in nearly all fetal cerebral cortex NPCs or neurons (i.e., NPCs and Ns, FOXG1, NFIA, and NFIB; Ns, NEUROD6

summary:
In Homo sapiens, neurons from dorsal forebrain-like regions of cerebral organoids express FOXG1, NFIA, NFIB, and NEUROD6.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:f015b95ce47c2780a734
claim_id: claim:f015b95ce47c2780a734
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
Instead, many NPCs in c5 and c6 express OTX2 and are likely a mixture of ventral telencephalic or hippocampal NPCs and NPCs from immature dorsal telencephalic regions.

summary:
In Homo sapiens cerebral organoids, neural progenitor cells in clusters c5 and c6 express OTX2 and are likely ventral telencephalic or hippocampal neural progenitor cells.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:ca61f37ce26a9f4a9c63
claim_id: claim:ca61f37ce26a9f4a9c63
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
c8 and c9 contain cycling and noncycling cells that express R-spondin genes and WNT2B and are likely from the hem signaling center in the dorsal/ventral boundary region.

summary:
In Homo sapiens cerebral organoids, cells from the hem signaling center express R-spondin genes and WNT2B.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:87dd358162f3d8ea96e7
claim_id: claim:87dd358162f3d8ea96e7
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
We identified two clusters of cells (c4 and c7) that shared high expression of certain neuronal markers such as MYT1L , DCX , NRXN1 , TBR1 , and MAP2 and were anticorrelated with genes highly expressed in NPCs

summary:
In Homo sapiens cerebral organoids, neuron clusters express neuronal markers MYT1L, DCX, NRXN1, TBR1, and MAP2.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:f3408dd6f75ffb3409ac
claim_id: claim:f3408dd6f75ffb3409ac
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
Cluster c4 cells express FOXG1 , NFIA , NFIB , and NEUROD6 , suggesting that they are neurons in organoid regions resembling the fetal cortex

summary:
In Homo sapiens cerebral organoids, cluster c4 neurons express FOXG1, NFIA, NFIB, and NEUROD6, resembling fetal cortex neurons.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:859c909fffe74eac70e1
claim_id: claim:859c909fffe74eac70e1
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
Cells in cluster c7 instead express LHX9 , EBF1 , ZFHX3 , ZFHX4 , and/or SOX14 , which are highly expressed in other fetal forebrain structures such as the striatum, hippocampus, and thalamus

summary:
In Homo sapiens cerebral organoids, cluster c7 neurons express LHX9, EBF1, ZFHX3, ZFHX4, and/or SOX14, which are markers of other fetal forebrain structures.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:8a1b038cdab7c5c17b95
claim_id: claim:8a1b038cdab7c5c17b95
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
summary: In Homo sapiens cerebral organoids, interneuron-like cells coexpress GAD1, GAD2, SOX14, and ERBB4.
span_literal:
Notably, we found four cells from cluster c7 that coexpress GAD1 , GAD2 , SOX14 , and ERBB4 , suggesting these are interneuron-like cells derived from the ventral forebrain-like regions in the organoid.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:70f1596922d2a15abef3
claim_id: claim:70f1596922d2a15abef3
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
NPC clusters c5 and c6 are composed of cells from the earliest time points (33–37 d) and express NPC markers such as VIM , PAX6 , and NES

summary:
In Homo sapiens cerebral organoids, neural progenitor cell clusters c5 and c6 express neural progenitor cell markers VIM, PAX6, and NES.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:8047b657d385a1b0f496
claim_id: claim:8047b657d385a1b0f496
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal:
In contrast, some NPCs from the later time points (41–65 d, cluster c1 and c2) highly express NPC markers PAX6 , VIM , and NES , as well as genes expressed in nearly all fetal cortex cells such as FOXG1 , NFIA , and NFIB , but do not express OTX2 , suggesting these NPCs derive from cortical regions resembling the fetal cerebral cortex.

summary:
In Homo sapiens cerebral organoids, neural progenitor cells in clusters c1 and c2 express PAX6, VIM, NES, FOXG1, NFIA, and NFIB but do not express OTX2.


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:91cef2360f684e70c306
claim_id: claim:91cef2360f684e70c306
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
summary: In Homo sapiens cerebral organoids, mesenchymal cells express DCN, LUM, COL1A2, and COL5A1.
span_literal:
Further, we identified cycling and noncycling mesenchymal cells (c10 and c11) that express DCN , LUM , COL1A2 , COL5A1 , and many components of the ECM, suggesting these cells form connective tissue within the organoid


claim_key: hca:0167_10.1073_pnas.1520760112_985a5e340f:claim:4bffcb15f69ff1f176e8
claim_id: claim:4bffcb15f69ff1f176e8
paper_key: hca:0167_10.1073_pnas.1520760112_985a5e340f
span_literal: early NPCs also express the pluripotency marker LIN28A
summary:
In Homo sapiens cerebral organoids, early neural progenitor cells express the pluripotency marker LIN28A.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:fd453c16893a75133370
claim_id: claim:fd453c16893a75133370
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
In this analysis, we observed two secretory cell populations, both expressing the canonical marker SCGB1A1 , but with a distinct population expressing high levels of SCGB3A2

summary:
In Homo sapiens, respiratory airway secretory cells express high levels of SCGB3A2, while both secretory cell populations express the canonical marker SCGB1A1.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:dbd7e49238864c29fa9f
claim_id: claim:dbd7e49238864c29fa9f
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
Bi-gene plots showing expression of SCGB1A1 , SCGB3A2 or cells expressing both of these genes, which identifies RAS cells.

summary:
In Homo sapiens, respiratory airway secretory cells are identified by co-expression of SCGB1A1 and SCGB3A2.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:c1049f3fdbc73b490e7e
claim_id: claim:c1049f3fdbc73b490e7e
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal: SCGB3A2 + cells were cuboidal in shape and were interspersed with SFTPC + or LAMP3 + AT2 cells
summary:
In Homo sapiens, respiratory airway secretory cells express SCGB3A2, while alveolar type 2 cells express SFTPC or LAMP3.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:fbc31e559cd664f6ce07
claim_id: claim:fbc31e559cd664f6ce07
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
The gene expression changes along the RAS cell–AT2 cell trajectory highlight several genes that are known to be involved in AT2 cell differentiation and maturation including WIF1 and SFTPC , suggesting that RAS cells may serve as a putative progenitor for the AT2 cell lineage

summary:
In Homo sapiens, the respiratory airway secretory cell to alveolar type 2 cell trajectory involves WIF1 and SFTPC, genes known to be involved in alveolar type 2 cell differentiation and maturation.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:aa11f6e7a837d24c1cf7
claim_id: claim:aa11f6e7a837d24c1cf7
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal: This analysis identified CEACAM6 (CD66c) as a possible marker for RAS cells
summary:
In Homo sapiens, CEACAM6 (CD66c) was identified as a possible marker for respiratory airway secretory cells.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:30d8797159a54d7dee3d
claim_id: claim:30d8797159a54d7dee3d
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
Inhibition of Notch in iRAS cell airway cultures led to reduced expression of cardinal RAS-cell-specific genes, including SCGB3A2 and SCGB1A1

summary:
In Homo sapiens, respiratory airway secretory cells specifically express cardinal genes SCGB3A2 and SCGB1A1, which are reduced upon Notch inhibition.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:c33c16e006e39762be09
claim_id: claim:c33c16e006e39762be09
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
By contrast, inhibiting Notch during the iRAS cell to iAT2 cell transition resulted in enhanced SFTPC , ABCA3 and PBC expression, as assessed by increased mean fluorescent reporter expression and by quantitative PCR (qPCR)

summary:
In Homo sapiens, induced alveolar type 2 cells show enhanced expression of SFTPC, ABCA3, and PBC when Notch is inhibited during differentiation from induced respiratory airway secretory cells.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:0595af7395827259f24a
claim_id: claim:0595af7395827259f24a
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
RAS cells are identified by the co-expression of SCGB1A1 and SCGB3A2 ; an AT2 population that expresses higher levels of SCGB3A2 is noted.

summary:
In Homo sapiens, respiratory airway secretory cells are identified by co-expression of SCGB1A1 and SCGB3A2, and an alveolar type 2 cell population expressing higher levels of SCGB3A2 is noted in chronic obstructive pulmonary disease.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:48c1e16b429acf4beee6
claim_id: claim:48c1e16b429acf4beee6
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
RAS cells are identified by the co-expression of SCGB1A1 and SCGB3A2 ; an AT2 population that expresses higher levels of SCGB3A2 is noted.

summary:
In Homo sapiens, an alveolar type 2 cell population in chronic obstructive pulmonary disease expresses higher levels of SCGB3A2.


claim_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8:claim:781360dc4bb417c7e122
claim_id: claim:781360dc4bb417c7e122
paper_key: hca:0168_10.1038_s41586-022-04552-0_f98a6428c8
span_literal:
Importantly, cytospin analysis showed that <5% of the CEACAM6 + HT2-280 − NGFR − purified cells expressed the AT2 marker SFTPC

summary:
In Homo sapiens, CEACAM6-positive, HT2-280-negative, NGFR-negative purified cells largely lack expression of the alveolar type 2 cell marker SFTPC.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:ebed270fdc29d6bf0297
claim_id: claim:ebed270fdc29d6bf0297
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
First, one population that expresses SFTPB and SCGB3A2 but lacks SCGB1A1 , FOXJ1 , and SFTPC , is specific to TRBs and we termed them TRB-secretory cells (TRB-SCs)

summary:
In Homo sapiens, terminal and respiratory bronchiole secretory cells express SFTPB and SCGB3A2 but lack SCGB1A1, FOXJ1, and SFTPC.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:4875224bde86608ad5f2
claim_id: claim:4875224bde86608ad5f2
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
SFTPB + SCGB3A2 + SCGB1A1 + cells are localized to distal airways proximal to TBs and therefore we refer to these cells as pre-TB secretory cells (pre-TB-SCs)

summary:
In Homo sapiens, pre-terminal bronchiole secretory cells are marked by SFTPB, SCGB3A2, and SCGB1A1 expression.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:835580d8601f5cfecd8c
claim_id: claim:835580d8601f5cfecd8c
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
Expression of PEG10 , MS4A15 , NAPSA and H19 , or lack of SPARCL1 and TMEM45A among others, distinguishes TRB-SCs from pre-TB-SCs

summary:
In Homo sapiens, terminal and respiratory bronchiole secretory cells are distinguished from pre-terminal bronchiole secretory cells by expression of PEG10, MS4A15, NAPSA, and H19, and lack of SPARCL1 and TMEM45A.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:157b40d87616ab14beb8
claim_id: claim:157b40d87616ab14beb8
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
summary: In Homo sapiens, alveolar type-0 cells are marked by the expression of SFTPB, SCGB3A2, and SFTPC.
span_literal:
The third population is marked by the expression of SFTPB , SCGB3A2 , and SFTPC and is associated with alveolar septae contiguous with respiratory bronchioles and rarely in distal alveolar sacs


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:a15920741cef6eb07d8a
claim_id: claim:a15920741cef6eb07d8a
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
This population shares markers characteristic of both alveolar ( SFTPC, AGER ), and airway epithelial cells ( SCGB3A2 and SOX2 )

summary:
In Homo sapiens, alveolar type-0 cells share markers characteristic of both alveolar cells (SFTPC, AGER) and airway epithelial cells (SCGB3A2 and SOX2).


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:f83c74fd09bfc48477ce
claim_id: claim:f83c74fd09bfc48477ce
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
Fourth, we observed a secretoryciliated “hybrid” cell type, characterized by the co-expression of SCGB3A2, SFTPB, and FOXJ1

summary:
In Homo sapiens, the SCGB3A2-ciliated cell is characterized by co-expression of SCGB3A2, SFTPB, and FOXJ1.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:932a7f59267ec33c49e4
claim_id: claim:932a7f59267ec33c49e4
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
A second population has reduced expression of TP63 and increased expression of secretory cell markers, such as LTF , SCGB1A1 and SOX21 , suggesting that it is comprised of differentiating BCs

summary:
In Homo sapiens, differentiating basal cells have reduced expression of TP63 and increased expression of LTF, SCGB1A1, and SOX21.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:04f1b5dc413229e155ab
claim_id: claim:04f1b5dc413229e155ab
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
The remaining two BC populations coexpress SFTPB and TP63 but they show decreasing ( KRT5 , AQP5 , KRT15 and IL33 ) and increasing ( SLC34A2 , BST2 , RNASE1 , NKX2–1 and MUC1 ) expression pattern of various transcripts

summary:
In Homo sapiens, distal basal cell 1 co-expresses SFTPB and TP63 with higher KRT5, AQP5, KRT15, and IL33, while distal basal cell 2 co-expresses SFTPB and TP63 with higher SLC34A2, BST2, RNASE1, NKX2-1, and MUC1.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:ca06ae7e15e0fb73fc0f
claim_id: claim:ca06ae7e15e0fb73fc0f
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
The remaining two BC populations coexpress SFTPB and TP63 but they show decreasing ( KRT5 , AQP5 , KRT15 and IL33 ) and increasing ( SLC34A2 , BST2 , RNASE1 , NKX2–1 and MUC1 ) expression pattern of various transcripts

summary:
In Homo sapiens, distal basal cell 2 co-expresses SFTPB and TP63 with increased SLC34A2, BST2, RNASE1, NKX2-1, and MUC1.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:5475dd0a8aef7ec1e30a
claim_id: claim:5475dd0a8aef7ec1e30a
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
These fibroblasts are significantly enriched for LGR5, F13A1, PDGFRA, WNT5A , RSPO1 , DLL1 , TGFBI and DIO2

summary:
In Homo sapiens, LGR5-positive fibroblasts are significantly enriched for LGR5, F13A1, PDGFRA, WNT5A, RSPO1, DLL1, TGFBI, and DIO2.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:731c937289318eb036ce
claim_id: claim:731c937289318eb036ce
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
summary: In Homo sapiens, alveolar type-0 cells do not express the classical club cell marker SCGB1A1.
span_literal:
Unlike mouse bronchioalveolar stem cells (BASCs), AT0s do not express classical club cell marker, SCGB1A1 but share molecular signatures with TRB-SCs, AT2, and AT1


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:902ca878e6e9fac643a5
claim_id: claim:902ca878e6e9fac643a5
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
Transcripts for MUC5AC, MSLN and MUC13 were enriched in SFTPB − population whereas SFTPB , SFTPA1 , SFTPA2 , SCGB3A2 , RNASE1 and NAPSA were in SFTPB + populations

summary:
In Homo sapiens, the proximal airway (SFTPB-negative) population is enriched for MUC5AC, MSLN, and MUC13, whereas the distal airway (SFTPB-positive) population is enriched for SFTPB, SFTPA1, SFTPA2, SCGB3A2, RNASE1, and NAPSA.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:854c3dddc7dd7f74cefc
claim_id: claim:854c3dddc7dd7f74cefc
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
Transcripts for MUC5AC, MSLN and MUC13 were enriched in SFTPB − population whereas SFTPB , SFTPA1 , SFTPA2 , SCGB3A2 , RNASE1 and NAPSA were in SFTPB + populations

summary:
In Homo sapiens, the distal airway (SFTPB-positive) epithelial population is enriched for SFTPB, SFTPA1, SFTPA2, SCGB3A2, RNASE1, and NAPSA.


claim_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0:claim:cf40ab8f0163e504f4af
claim_id: claim:cf40ab8f0163e504f4af
paper_key: hca:0169_10.1038_s41586-022-04541-3_a47d9e6ca0
span_literal:
Analysis of these cells for transcriptional regulators showed an overlap with those expressed by AT2s ( ZNF385B , TFCP2L1 and ETV1)

summary:
In Homo sapiens, alveolar type-0 cells express the transcriptional regulators ZNF385B, TFCP2L1, and ETV1, overlapping with alveolar type-2 cells.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:7158b86d961cc32d911f
claim_id: claim:7158b86d961cc32d911f
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
summary: In Homo sapiens, KIT is a positive marker of melanocytes within the basal layer of the epidermis.
span_literal:
fluorescence-activated cell sorting (FACS) analysis was used to increase the capture rate of KIT + melanocytes within the basal layer


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:3a3adec95035e4e17fde
claim_id: claim:3a3adec95035e4e17fde
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal: stem cell and progenitor cell function ( TC4F (ref. 21 ) and CXCL14
summary:
In Homo sapiens, TCF4 and CXCL14 are positively associated with melanocyte stem cell and progenitor cell function.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:4cac8e34df60af9eca6e
claim_id: claim:4cac8e34df60af9eca6e
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
Volar melanocytes presented an increased expression of NTRK2 , ID2 and ID3 —genes previously associated with a subset of melanomas and/or silenced in non-volar cutaneous melanocytes

summary:
In Homo sapiens, volar-enriched melanocytes express increased levels of NTRK2, ID2, and ID3 compared to non-volar cutaneous melanocytes.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:a2f36c32160075621dfd
claim_id: claim:a2f36c32160075621dfd
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
bifurcation genes and post-bifurcation genes were involved in melanosome biogenesis and function ( SLC45A2 , TPCN2 , OCA2 , RAB27A , AP3D1 , ADAM10 , TRAPPC6A , SLC24A5 and ATOX1 ) and/or pigment signalling pathways/ultraviolet response ( MC1R , GNAS and DSTYK

summary:
In Homo sapiens, non-volar cutaneous melanocytes upregulate SLC45A2, TPCN2, OCA2, RAB27A, AP3D1, ADAM10, TRAPPC6A, SLC24A5, ATOX1, MC1R, GNAS, and DSTYK compared to volar melanocytes during pigment bifurcation.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:845bdd1886e751989208
claim_id: claim:845bdd1886e751989208
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
Representative pseudocoloured fluorescence microscopy images of NTRK2 , HPGD and the melanocyte marker DCT (outlined in yellow) mRNA staining in adult volar and non-volar epidermis.

summary:
In Homo sapiens, DCT is a marker of melanocytes, NTRK2 is a marker of volar-enriched melanocytes, and HPGD is a marker of non-volar cutaneous melanocytes.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:c71a1d8a74503549e2d6
claim_id: claim:c71a1d8a74503549e2d6
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
Immunofluorescence co - staining of adult volar and non-volar skin cryo-sections with the c-mel marker HPGD (green) and melanocyte marker KIT (magenta).

summary:
In Homo sapiens, HPGD is a marker of non-volar cutaneous-like melanocytes and KIT is a marker of melanocytes.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:4042f529bb6e4ae0646a
claim_id: claim:4042f529bb6e4ae0646a
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
MSC and FET were enriched for known developmental genes ( SOX11, LYPD1 ) and genes involved in extracellular matrix establishment/remodeling ( COL1A2, PXDN

summary:
In Homo sapiens, melanocyte stem cells and fetal melanocytes are enriched for SOX11, LYPD1, COL1A2, and PXDN.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:2eea22670f13f0865af9
claim_id: claim:2eea22670f13f0865af9
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
summary: In Homo sapiens, fetal melanocytes are enriched for SOX11, LYPD1, COL1A2, and PXDN.
span_literal:
FET were enriched for known developmental genes ( SOX11, LYPD1 ) and genes involved in extracellular matrix establishment/remodeling ( COL1A2, PXDN


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:9ea5c6e80aeefe14ec4f
claim_id: claim:9ea5c6e80aeefe14ec4f
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
ADT group expressed genes involved in innate immunity, inflammation and regulating apoptosis/cell stress in other cell types and tissues ( HLAs, APOD, CLU, LGALS3

summary:
In Homo sapiens, adult melanocytes express HLA genes, APOD, CLU, and LGALS3, which are involved in innate immunity, inflammation, and apoptosis regulation.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:1b250fbdaf9881a080c4
claim_id: claim:1b250fbdaf9881a080c4
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
Among the top DEGs was the melanoma-associated antigen PRAME, further supporting its use as a melanoma molecular diagnostic.

summary:
In Homo sapiens, PRAME is a melanoma-specific gene that is highly expressed in melanoma cells but absent from healthy melanocytes.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:0aa0ae9b901f667cf965
claim_id: claim:0aa0ae9b901f667cf965
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
Expression level of the v-mel gene NTRK2 and the c-mel gene HPGD in all volar melanocytes ( n = 1,634 cells) compared to all non-volar cutaneous melanocytes ( n = 5,192 cells).

summary:
In Homo sapiens, NTRK2 is a marker gene of volar-enriched melanocytes and HPGD is a marker gene of non-volar cutaneous-like melanocytes.


claim_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6:claim:8c754b7591e4450acc98
claim_id: claim:8c754b7591e4450acc98
paper_key: hca:0170_10.1038_s41556-021-00740-8_a1434832b6
span_literal:
Expression level of the v-mel gene NTRK2 and the c-mel gene HPGD in all volar melanocytes ( n = 1,634 cells) compared to all non-volar cutaneous melanocytes ( n = 5,192 cells).

summary:
In Homo sapiens, HPGD is a marker gene of non-volar cutaneous-like melanocytes compared to volar-enriched melanocytes.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:db5b4d7978856519be2a
claim_id: claim:db5b4d7978856519be2a
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
summary: In Homo sapiens oral mucosa, endothelial cells are marked by ACKR1, RAMP2, SELE, VWF, and PECAM1.
span_literal:
Identified endothelial (ACKR1, RAMP2, SELE, VWF, PECAM1), fibroblast (LUM, COL3A1, DCN, COL1A1, CFD), immune (CD69, CD52, CXCR4, PTPRC, HCST), and epithelial (KRT14, KRT5, S100A2, CTSA, SPRR1B) marker genes were cell-type specific and consistent with classical, well-established markers for each respective cell population


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:348116d6cf53bfa5f744
claim_id: claim:348116d6cf53bfa5f744
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.SMC and H.LEC clusters expressed genes related to muscle contraction (such as MYL9, ACTA2) and LEC fate commitment (PROX1)

summary:
In Homo sapiens oral mucosa, smooth muscle cells express MYL9 and ACTA2, genes related to muscle contraction.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:3e44c5e6fd29aed03c59
claim_id: claim:3e44c5e6fd29aed03c59
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.SMC and H.LEC clusters expressed genes related to muscle contraction (such as MYL9, ACTA2) and LEC fate commitment (PROX1)

summary:
In Homo sapiens oral mucosa, lymphatic endothelial cells express PROX1, a gene related to lymphatic endothelial cell fate commitment.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:512d2a6c9613aa70e45e
claim_id: claim:512d2a6c9613aa70e45e
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.VEC 1.1 expressed a gene signature consistent with antigen presentation (HLADMA, CD74), while 1.3 and 1.4 appeared to promote immune and inflammatory responses (such as response to LPS and IFN signaling) and expressed genes relevant to neutrophil recruitment and IFN signaling (CSF3, CXCL2, MX1)

summary:
In Homo sapiens oral mucosa, venular endothelial cell 1.1 expresses HLADMA and CD74, consistent with antigen presentation.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:092170ba1997e49b3a87
claim_id: claim:092170ba1997e49b3a87
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.VEC 1.1 expressed a gene signature consistent with antigen presentation (HLADMA, CD74), while 1.3 and 1.4 appeared to promote immune and inflammatory responses (such as response to LPS and IFN signaling) and expressed genes relevant to neutrophil recruitment and IFN signaling (CSF3, CXCL2, MX1)

summary:
In Homo sapiens oral mucosa, venular endothelial cell 1.3 expresses CSF3, CXCL2, and MX1, genes relevant to neutrophil recruitment and interferon signaling.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:1d5e9ae2d4ddd66e2add
claim_id: claim:1d5e9ae2d4ddd66e2add
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.VEC 1.1 expressed a gene signature consistent with antigen presentation (HLADMA, CD74), while 1.3 and 1.4 appeared to promote immune and inflammatory responses (such as response to LPS and IFN signaling) and expressed genes relevant to neutrophil recruitment and IFN signaling (CSF3, CXCL2, MX1)

summary:
In Homo sapiens oral mucosa, venular endothelial cell 1.4 expresses CSF3, CXCL2, and MX1, genes relevant to neutrophil recruitment and interferon signaling.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:d83245c314c1bac3907b
claim_id: claim:d83245c314c1bac3907b
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.VEC 1.2 cells displayed a gene signature consistent with active pathways for endothelium development (such as FLT1)

summary:
In Homo sapiens oral mucosa, venular endothelial cell 1.2 expresses FLT1, consistent with endothelium development.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:37770c7560bd17512a8b
claim_id: claim:37770c7560bd17512a8b
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.Mel was the most distal epithelial cluster by UMAP ( Figure 2C ) and clearly represented melanocytes based on significant expression of pigmentation genes (PMEL, MLANA)

summary:
In Homo sapiens oral mucosa, melanocytes are marked by significant expression of the pigmentation genes PMEL and MLANA.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:f46c25a49efd019e1cf9
claim_id: claim:f46c25a49efd019e1cf9
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.Epi 1.1 cells were further categorized as basal layer/differentiating keratinocytes with expression of KRT5, KRT14 and KRT15, while H.Epi 1.3 expressed genes involved in keratinization and cornification (SPRR3, CRNN, CNFN ) typically encountered in the outmost layers of the epithelium

summary:
In Homo sapiens oral mucosa, basal layer/differentiating keratinocytes (H.Epi 1.1) express KRT5, KRT14, and KRT15.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:57dea835d1e86912d045
claim_id: claim:57dea835d1e86912d045
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
H.Epi 1.1 cells were further categorized as basal layer/differentiating keratinocytes with expression of KRT5, KRT14 and KRT15, while H.Epi 1.3 expressed genes involved in keratinization and cornification (SPRR3, CRNN, CNFN ) typically encountered in the outmost layers of the epithelium

summary:
In Homo sapiens oral mucosa, keratinocyte subtype H.Epi 1.3 expresses SPRR3, CRNN, and CNFN, genes involved in keratinization and cornification.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:352d63949379f803b558
claim_id: claim:352d63949379f803b558
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
In fact, top expressed genes included antimicrobial and inflammatory factors such as IL1B, SLPI, and S100A8/9, and a top pathway was leukocyte chemotaxis, which reflected primarily recruitment of neutrophils as evident by the expression of CXCL1, CXCL6, CXCL8

summary:
In Homo sapiens gingival mucosa, the gingiva-specific epithelial cell subtype H.Epi 1.2 expresses IL1B, SLPI, S100A8, S100A9, CXCL1, CXCL6, and CXCL8, reflecting antimicrobial and inflammatory functions and neutrophil recruitment.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:315148a1f669d465cd85
claim_id: claim:315148a1f669d465cd85
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
Cluster 1.1 displayed active translation and cluster 1.2 displayed a gene signature corresponding to the prototypic functions of the cell type, including collagen synthesis and tissue remodeling (COL1A1, COL1A2, MMP2)

summary:
In Homo sapiens oral mucosa, fibroblast cluster 1.2 expresses COL1A1, COL1A2, and MMP2, corresponding to collagen synthesis and tissue remodeling.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:17603c542fef1cc1a6e7
claim_id: claim:17603c542fef1cc1a6e7
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
span_literal:
Clusters H.Fib 1.3, 1.4, and 1.5 expressed gene signatures consistent with inflammatory responses, such as regulation of leukocyte proliferation (ANXA1, IGFBP2), granulocyte migration (CXCL1, 2, 8) and complement activation (C3, CFD)

summary:
In Homo sapiens oral mucosa, fibroblast clusters H.Fib 1.3, 1.4, and 1.5 express ANXA1, IGFBP2, CXCL1, CXCL2, CXCL8, C3, and CFD, consistent with inflammatory responses including leukocyte proliferation, granulocyte migration, and complement activation.


claim_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b:claim:763bb77fd9f306ba63ce
claim_id: claim:763bb77fd9f306ba63ce
paper_key: hca:0171_10.1016_j.cell.2021.05.013_6d846f218b
summary: In Homo sapiens, neutrophils uniformly express classical markers CXCL8, CXCR2, and FCGR3B.
span_literal:
cells in this cluster uniformly expressed classical neutrophil markers such as CXCL8, CXCR2 and FCGR3B


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:29c01d89af7d739b83f3
claim_id: claim:29c01d89af7d739b83f3
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
The most foveal enriched cone photoreceptor gene was RIMS2 , a regulator of synaptic membrane exocytosis that has been implicated in a congenital cone-rod synaptic disorder ( 18 ).

summary:
In Homo sapiens, RIMS2 is enriched in foveal cone photoreceptor cells compared to parafoveal cone photoreceptor cells.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:0107697fdb2b9e677ddc
claim_id: claim:0107697fdb2b9e677ddc
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
summary: In Homo sapiens, CPLX4, WRB and SLC4A7 are enriched in foveal cone photoreceptor cells.
span_literal:
Such foveal enriched genes include CPLX4 —which regulates synaptic vesicle fusion at the ribbon synapse ( 19 ), WRB —which supports ribbon synapse structure and function ( 20 ) and SLC4A7 —which encodes a sodium bicarbonate transporter that regulates pH for proper sensory transmission ( 21 ).


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:3525b98fcbb28e3be509
claim_id: claim:3525b98fcbb28e3be509
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
In concordance with our previous studies ( 10 ), the carotenoid cleaving enzyme BCO2 was more highly expressed in parafoveal cones.

summary:
In Homo sapiens, BCO2 is enriched in parafoveal cone photoreceptor cells compared to foveal cone photoreceptor cells.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:01c1442269ec421a8e8d
claim_id: claim:01c1442269ec421a8e8d
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
Compared with the parafovea, foveal cones showed increased expression of the transcription factors POUF2A1 , YBX1 and LBH .

summary:
In Homo sapiens, foveal cone photoreceptor cells show increased expression of the transcription factors POU2AF1, YBX1 and LBH compared with parafoveal cone photoreceptor cells.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:fb44e74acd0629d2966d
claim_id: claim:fb44e74acd0629d2966d
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
summary: In Homo sapiens, foveal rod photoreceptor cells are enriched in PNO1 and RBP7.
span_literal:
Foveal rod photoreceptors were enriched in the RNA-binding gene PNO1 , which is required for ribosome assembly ( 27 ) and the retinol binding protein RBP7.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:93b784c0d08841170bf3
claim_id: claim:93b784c0d08841170bf3
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
In contrast, parafoveal rods were enriched for several cilia-localized genes including SCAPER , which has been implicated in Bardet-Biedl syndrome ( 28 ), and AHI1 , which is a mendelian cause and modifier of Joubert syndrome ( 29 ).

summary:
In Homo sapiens, parafoveal rod photoreceptor cells are enriched for SCAPER and AHI1 compared to foveal rod photoreceptor cells.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:e0675a7e6573a10963d3
claim_id: claim:e0675a7e6573a10963d3
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
summary: In Homo sapiens, foveal Müller cells are enriched for DAPL1.
span_literal:
Foveal Müller cells were enriched for DAPL1 , a G-coupled protein receptor that contains a single-nucleotide polymorphism associated with AMD ( 30 ).


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:ea44d42af22e1a4e3c0a
claim_id: claim:ea44d42af22e1a4e3c0a
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
summary: In Homo sapiens, foveal Müller cells are enriched for FAT1 and CYP26A1.
span_literal:
Likewise, foveal Müller cells were enriched for FAT1 , a protocadherin needed for retinal vascular organization ( 31 ) and CYP26A1 , a retinoic acid catabolizing enzyme ( 32 , 33 ).


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:f1dfe5477445ed447754
claim_id: claim:f1dfe5477445ed447754
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
Finally, foveal Müller cells were enriched for FABP5 , which encodes a fatty-acid binding protein that can regulate retinoic acid signaling ( 34 ).

summary:
In Homo sapiens, foveal Müller cells are enriched for FABP5, which encodes fatty acid binding protein 5.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:26fd77e755f33c05d0f5
claim_id: claim:26fd77e755f33c05d0f5
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
We observed that Müller cells strongly and specifically expressed the visual cycle genes RDH10 , RGR , RLBP1 and RBP1.

summary:
In Homo sapiens, Müller cells strongly and specifically express the visual cycle genes RDH10, RGR, RLBP1 and RBP1.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:cf141392152472b8d37e
claim_id: claim:cf141392152472b8d37e
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
RORB demonstrated the highest expression in horizontal cells and Müller cells ( Fig. 7A ), with comparable expression between the fovea and parafovea ( Supplementary Material, Table S2 ).

summary:
In Homo sapiens, RORB demonstrates the highest expression in horizontal cells and Müller cells in the retina.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:e79d6996d6a9e2e097ba
claim_id: claim:e79d6996d6a9e2e097ba
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
KCNAB2 encodes the voltage-gated potassium channel β2 subunit ( 42 ), which demonstrated the highest expression in RGCs and amacrine cells ( Fig. 7G ).

summary:
In Homo sapiens, KCNAB2 demonstrates the highest expression in retinal ganglion cells and amacrine cells.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:d6b1c3db46ca3586f9db
claim_id: claim:d6b1c3db46ca3586f9db
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
Compared with the parafovea, foveal cones showed increased expression of the transcription coactivator POUF2A1, which interacts with OCT1 and OCT2.

summary:
In Homo sapiens, foveal cone photoreceptor cells show increased expression of the transcription coactivator POU2AF1 compared with parafoveal cone photoreceptor cells.


claim_key: hca:0172_10.1093_hmg_ddab140_444d3c140d:claim:9ee30549a34809acfbc3
claim_id: claim:9ee30549a34809acfbc3
paper_key: hca:0172_10.1093_hmg_ddab140_444d3c140d
span_literal:
Foveal cones were also enriched in the limb bud and heart (LBH) transcriptional coactivator, which interacts with OTX2 to regulate photoreceptor differentiation in a zebrafish model ( 50 ).

summary:
In Homo sapiens, foveal cone photoreceptor cells are enriched in the limb bud and heart transcriptional coactivator LBH.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:466e2079a952c0116dbf
claim_id: claim:466e2079a952c0116dbf
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
Adipocytes were easily identified in both hSAT and hVAT by expressing adiponectin ( ADIPOQ ) and additional adipocyte markers AQP7 , LPL and PLIN1 (Fig. 1b,c ).

summary:
In Homo sapiens, adipocytes were identified by expression of adiponectin (ADIPOQ), AQP7, LPL, and PLIN1 in both subcutaneous and visceral adipose tissues.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:b3ed6317e65abdb75f4a
claim_id: claim:b3ed6317e65abdb75f4a
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
In hSAT, ASPCs were identified in a PDGFRA -positive cluster, comprising 26% of the nuclei (Fig. 6a ), and could be divided into five subclusters, ASPC1–5, marked by known ASPC subtype markers (Fig. 6b-c ).

summary:
In Homo sapiens subcutaneous adipose tissue, adipose stem and progenitor cells were identified by positive expression of PDGFRA.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:c28f247b0a225745e00e
claim_id: claim:c28f247b0a225745e00e
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
ASPC1 (32% of the ASPCs) expressed markers of highly proliferative multipotent progenitor cells 9 , including DPP-4 (ref. 23 ) and CD55 (ref. 10 ) and was F3 negative 23 (referred to as adipose stem cells in ref. 8 ).

summary:
In Homo sapiens, adipose stem and progenitor cell 1 expressed DPP4 and CD55 as positive markers and was negative for F3.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:5b9fa9e5dd71beb9c8a6
claim_id: claim:5b9fa9e5dd71beb9c8a6
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
ASPC2 (55%) expressed peroxisome proliferator-activated receptor-γ (PPARG) most highly and was CD9 low , suggesting its commitment to adipocyte fate 24 .

summary:
In Homo sapiens, adipose stem and progenitor cell 2 expressed peroxisome proliferator-activated receptor-gamma (PPARG) most highly and was CD9 low.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:8e3f7cc36eb0ecfa2d76
claim_id: claim:8e3f7cc36eb0ecfa2d76
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
ASPC3 (9%) expressed markers of profibrotic progenitor cells (CD9 high ), previously observed and designated myofibrogenic progenitors in humans and mice 23 , 24 .

summary:
In Homo sapiens, adipose stem and progenitor cell 3 expressed CD9 at high levels, marking it as a profibrotic progenitor cell.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:101ec65c588db86068b4
claim_id: claim:101ec65c588db86068b4
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
We chose PTPRB, PDE4D, SKAP1 and ANK2 as markers to identify SA2–5/VA2–5, respectively ( Methods and Fig. 5a–d ).

summary:
In Homo sapiens, PTPRB was used as a marker to identify angiogenic adipocytes (SA2/VA2) in subcutaneous and visceral adipose tissue.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:7d753e182e4ad411970b
claim_id: claim:7d753e182e4ad411970b
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
We chose PTPRB, PDE4D, SKAP1 and ANK2 as markers to identify SA2–5/VA2–5, respectively ( Methods and Fig. 5a–d ).

summary:
In Homo sapiens, PDE4D was used as a marker to identify immune-related adipocytes (SA3/VA3) in subcutaneous and visceral adipose tissue.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:868d83d0f7743a5e7ab7
claim_id: claim:868d83d0f7743a5e7ab7
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
We chose PTPRB, PDE4D, SKAP1 and ANK2 as markers to identify SA2–5/VA2–5, respectively ( Methods and Fig. 5a–d ).

summary:
In Homo sapiens, SKAP1 was used as a marker to identify immune-related (adaptive) adipocytes (SA4/VA4) in subcutaneous and visceral adipose tissue.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:b305853df80c6076cc0d
claim_id: claim:b305853df80c6076cc0d
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
summary:
In Homo sapiens, ANK2 was used as a marker to identify extracellular matrix adipocytes (SA5/VA5) in subcutaneous and visceral adipose tissue.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:2ac119f2c89780f9e67f
claim_id: claim:2ac119f2c89780f9e67f
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
summary: In Homo sapiens, the extracellular matrix adipocyte subtype (SA5/VA5) expressed PDGFRB.
span_literal:
The ECM subtype, SA5/VA5, enriched in ECM genes, also expressed PDGFRB , possibly relating it to fibroinflammatory progenitors previously reported in mice 32 .


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:4dbf9a4c2ae24bd70653
claim_id: claim:4dbf9a4c2ae24bd70653
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
Immunostaining hVAT for the VA6 mitochondrial marker protein, MT-CO2 (Fig. 5j ), revealed rare MT-CO2-positive adipocytes (positively stained for CD36 instead of perilipin, for technical reasons; Fig. 5k and Extended Data Figs. 2e and 3d ).

summary:
In Homo sapiens visceral adipose tissue, mito-ribosomal adipocytes (VA6) were identified by positive expression of the mitochondrial marker MT-CO2.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:d63255325e0263756fe8
claim_id: claim:d63255325e0263756fe8
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
In both depots, ADIPOR1 was largely absent from all adipocyte subtypes, ADIPOR2 was ubiquitous, CDH13 was expressed uniquely by angiogenic adipocytes (SA2/VA2) and LEPR was expressed in most subtypes (Extended Data Fig. 6a ).

summary:
In Homo sapiens, ADIPOR1 was largely absent from all adipocyte subtypes, ADIPOR2 was ubiquitously expressed, CDH13 was uniquely expressed by angiogenic adipocytes (SA2/VA2), and LEPR was expressed in most adipocyte subtypes.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:43c4212e0360eb7ce648
claim_id: claim:43c4212e0360eb7ce648
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
In both depots, ADIPOR1 was largely absent from all adipocyte subtypes, ADIPOR2 was ubiquitous, CDH13 was expressed uniquely by angiogenic adipocytes (SA2/VA2) and LEPR was expressed in most subtypes (Extended Data Fig. 6a ).

summary:
In Homo sapiens, ADIPOR1 was largely absent from all adipocyte subtypes while ADIPOR2 was ubiquitously expressed across adipocyte subtypes.


claim_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5:claim:2b8a7915658dbca4cc16
claim_id: claim:2b8a7915658dbca4cc16
paper_key: hca:0174_10.1038_s41588-024-02048-3_7311b9bde5
span_literal:
It is interesting that CDH13 expression characterized endothelial cells in both depots (although lymphatic endothelial cells expressed CDH13 only in hSAT), suggesting that adiponectin may similarly affect angiogenic adipocytes and endothelial cells.

summary:
In Homo sapiens, CDH13 expression characterized endothelial cells in both subcutaneous and visceral adipose tissue depots.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:377e8f9eb81a789be17e
claim_id: claim:377e8f9eb81a789be17e
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal:
Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1

summary:
In Homo sapiens, macrophages of patients with hypertension exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:5d983045916cfb48208b
claim_id: claim:5d983045916cfb48208b
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal:
neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1

summary:
In Homo sapiens, neutrophils of patients with hypertension exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:3d7f2f3402d55f6a0afa
claim_id: claim:3d7f2f3402d55f6a0afa
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: CCR1 , the receptor bound by CCL3 and CCL4 , increased in nrMa
summary:
In Homo sapiens, expression of CCR1, the receptor bound by CCL3 and CCL4, increased in non-resident macrophages concomitantly with severity of COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:218960dce874a277fabb
claim_id: claim:218960dce874a277fabb
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: CCR1 . Shown are mean expression levels per patient in nrMA and Neu
summary:
In Homo sapiens, expression of CCR1, the receptor bound by CCL3 and CCL4, increased in neutrophils concomitantly with severity of COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:27950d25bf2a825c3316
claim_id: claim:27950d25bf2a825c3316
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: CCL4 derived from nrMa
summary:
In Homo sapiens, CCL4 expression derived from non-resident macrophages was significantly positively associated with an increased risk for critical COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:c8af5cf257617887bbf7
claim_id: claim:c8af5cf257617887bbf7
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: CCL3 expressed by Neu
summary:
In Homo sapiens, CCL3 expression by neutrophils was significantly positively associated with an increased risk for critical COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:699c98226bd4acfab607
claim_id: claim:699c98226bd4acfab607
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal:
secretory cells (Fig. 3a , Extended Data Fig. 5a and Supplementary Table 4a ), including CXCL1 , CXCL6 and IL-8 , which recruit and activate neutrophils (Neu), and CXCL17

summary:
In Homo sapiens, secretory cells expressed CXCL1, CXCL6, IL-8 and CXCL17 genes involved in chemotaxis and inflammatory response under ARB treatment in COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:80e3ffc3b070b8ce10f7
claim_id: claim:80e3ffc3b070b8ce10f7
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: macrophage subtypes, CCL3 and CCL4
summary:
In Homo sapiens, CCL3 and CCL4 expression was increased in all macrophage subtypes of ARB-treated hypertensive patients compared to ACEI-treated hypertensive patients with COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:c297faad32d1f9e39ba1
claim_id: claim:c297faad32d1f9e39ba1
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: Neu ( ITGAM and ICAM1
summary:
In Homo sapiens, the infiltrative potential markers ITGAM and ICAM1 were increased in neutrophils of ARB-treated hypertensive patients compared to ACEI-treated hypertensive patients with COVID-19.


claim_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48:claim:7f1957791e854d32a9ed
claim_id: claim:7f1957791e854d32a9ed
paper_key: hca:0175_10.1038_s41587-020-00796-1_81545d4d48
span_literal: ACE2 receptor, expressed on epithelial cells in the respiratory system
summary:
In Homo sapiens, ACE2 receptor is expressed on epithelial cells in the respiratory system and is exploited by SARS-CoV-2 for cellular attachment and entry.


claim_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2:claim:88a4ab35f34287d1d0e8
claim_id: claim:88a4ab35f34287d1d0e8
paper_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2
span_literal: Group 1 cells selectively expressed DPP4 , CD55 , and WNT2 , comparable to murine group 1 cells
summary:
In Homo sapiens subcutaneous adipose tissue, group 1 interstitial progenitor cells selectively express DPP4, CD55, and WNT2.


claim_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2:claim:70f63516f72ebf9e6f40
claim_id: claim:70f63516f72ebf9e6f40
paper_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2
span_literal: Group 2 cells expressed ICAM1 , PPARg , and GGT5 , comparable to murine group 2 cells.
summary:
In Homo sapiens subcutaneous adipose tissue, group 2 committed preadipocyte cells express ICAM1, PPARG, and GGT5.


