# claims

claim_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad:claim:73643313410c296b6f09
claim_id: claim:73643313410c296b6f09
paper_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad
span_literal:
Regenerative epithelial cells co-expressed SPINK1, NXPH2, and TMEM213, and were transcriptionally enriched for vacuolar ATPases (ATP6V1B1, ATP6V0A4), ion channels (CLCNKA, CLCNKB), and FOXI1, a master regulator of intercalated cell identity.

summary:
In Homo sapiens, regenerative epithelial cells co-express SPINK1, NXPH2, and TMEM213, and are enriched for ATP6V1B1, ATP6V0A4, CLCNKA, CLCNKB, and FOXI1.


claim_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad:claim:57deb41d5f14bd309cf5
claim_id: claim:57deb41d5f14bd309cf5
paper_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad
span_literal: DUSP15⁺ cells are predominantly localized to a rare regenerative epithelial cluster.
summary:
In Homo sapiens, DUSP15 is a positive marker of a rare regenerative epithelial cell cluster in chromophobe renal cell carcinoma.


claim_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad:claim:1fd29c09441b66a0a81e
claim_id: claim:1fd29c09441b66a0a81e
paper_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad
span_literal:
DUSP15 expression was confined to a rare regenerative epithelial subset comprising ∼3.2% of tumour cells, nearly half of which were localized to an acid-base-handling epithelial cluster expressing FOXI1, ATP6V1B1, ATP6V0A4, and CLCNKB.

summary:
In Homo sapiens, DUSP15 expression is confined to a rare regenerative epithelial cell subset, localized to an acid-base-handling epithelial cluster expressing FOXI1, ATP6V1B1, ATP6V0A4, and CLCNKB.


claim_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad:claim:97071990f512fb9a0d36
claim_id: claim:97071990f512fb9a0d36
paper_key: biorxiv:001efeeb-7491-1014-a82f-ef19de5990ad
span_literal:
These cells co-expressed acid-base handling genes such as ATP6V1B1, CLCNKA, and FOXI1, and were devoid of immune effector transcripts or checkpoint ligands, directly linking the DUSP15-driven bulk tumour phenotype to a metabolically specialized, immune-silent epithelial niche.

summary:
In Homo sapiens, regenerative epithelial cells co-express ATP6V1B1, CLCNKA, and FOXI1, linking the DUSP15-driven phenotype to a metabolically specialized, immune-silent epithelial niche.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:c1efcd1fb91d6d773f82
claim_id: claim:c1efcd1fb91d6d773f82
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
In Dendritic Cells in Th1/Th2 Development, it is genes within TC that drive the prediction, concretely, IL13 shows the strongest upregulation, along with IL5 and CSF2/GM-CSF, while TLR7 shows a downregulation.

summary:
In Homo sapiens atopic dermatitis, T-cells in the Dendritic Cells in Th1/Th2 Development pathway show strongest upregulation of IL13, along with IL5 and CSF2, while TLR7 shows downregulation.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:dd128765a5856188f5ee
claim_id: claim:dd128765a5856188f5ee
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
summary: In Homo sapiens atopic dermatitis, melanocytes show upregulation of IL10, ITGAX, CD7, and CD33.
span_literal:
ANP/CD13 shows a strong upregulation in both APCs, while for MC it is an upregulation of IL10 that drives the prediction, as well as the upregulation of antigen coding genes: ITGAX/CD11c, CD7 and CD33.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:819ac7aeaee8fe62c8c3
claim_id: claim:819ac7aeaee8fe62c8c3
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
ANP/CD13 shows a strong upregulation in both APCs, while for MC it is an upregulation of IL10 that drives the prediction, as well as the upregulation of antigen coding genes: ITGAX/CD11c, CD7 and CD33.

summary:
In Homo sapiens atopic dermatitis, antigen presenting cells show strong upregulation of ANPEP (CD13).


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:2fc9e991a74dbc7bf01b
claim_id: claim:2fc9e991a74dbc7bf01b
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
In TC higher expression in AD samples compared to HC of interleukins dominate IL13, IL26, IL2RA, IL7, as well as IFNGR1.

summary:
In Homo sapiens atopic dermatitis, T-cells show higher expression of IL13, IL26, IL2RA, IL7, and IFNGR1 compared to healthy controls in the JAK-STAT signaling pathway.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:5a0408df482bbbd55696
claim_id: claim:5a0408df482bbbd55696
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
MC from AD samples show a simultaneous upregulation of CCND3 and CCND1, and so do receptors IFNGR2 and IL10RA.

summary:
In Homo sapiens atopic dermatitis, melanocytes show simultaneous upregulation of CCND3, CCND1, IFNGR2, and IL10RA.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:dc959bddf273c8a8ba85
claim_id: claim:dc959bddf273c8a8ba85
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
KC are characterized by overexpression of IL15 and its receptor IL15RA, on the contrary we observe a downregulation of SPRIY1.

summary:
In Homo sapiens atopic dermatitis, keratinocytes are characterized by overexpression of IL15 and IL15RA, and downregulation of SPRY1.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:01a3d1e2a3e4d0600394
claim_id: claim:01a3d1e2a3e4d0600394
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
Further, IL23A and IFNL1/IL-29 are downregulated in DC, while SPRED1, SOCS1 and OSM are upregulated.

summary:
In Homo sapiens atopic dermatitis, dendritic cells show downregulation of IL23A and IFNL1, and upregulation of SPRED1, SOCS1, and OSM.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:40b1c591983049c05ded
claim_id: claim:40b1c591983049c05ded
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
For LC a downregulation of genes IL22RA2, JAK1 and CCND1 is estimated, on the contrary there is a downregulation of CCND2 and STAT6.

summary:
In Homo sapiens atopic dermatitis, Langerhans cells show downregulation of IL22RA2, JAK1, CCND1, CCND2, and STAT6.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:2904175a899f0ad71a6f
claim_id: claim:2904175a899f0ad71a6f
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
Precisely, for DC chemokine receptor and ligands CCR6, CCL5/RANTES and CCL3L1 were all supressed in AD, and Herpesvirus entry mediator gene TNFRSF14 was upregulated.

summary:
In Homo sapiens atopic dermatitis, dendritic cells show suppression of CCR6, CCL5, and CCL3L1, and upregulation of TNFRSF14.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:524aa02a98be3a7f8352
claim_id: claim:524aa02a98be3a7f8352
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
summary: In Homo sapiens atopic dermatitis, keratinocytes show upregulation of CCL20, CCL7, and CCR2.
span_literal:
Common chemokine AD markers are observed; CCL20/LARC, CCL7/MCP1 and CCR2 upregulatione in KC; upregulated CCL17/TARC, CRR1 and CXCR4 in LC; CCL13 in DC.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:47256a3421e7abb8439f
claim_id: claim:47256a3421e7abb8439f
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
It is reported that simultaneous activation of CCND3/Cyclin-D3 and CCND1/Cyclin-D1 in melanocytic skin lesions promotes cell-cycle regulation (Alekseenko et al., 2010).

summary:
In Homo sapiens, simultaneous activation of CCND3 and CCND1 in melanocytes in skin lesions promotes cell-cycle regulation.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:7ff5f0cd4886b26fe283
claim_id: claim:7ff5f0cd4886b26fe283
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
Similarly, upregulation in KC of IL15RA/IL15Rα and IL15 in skin lesions has been associated to inflammatory processes.

summary:
In Homo sapiens, upregulation of IL15RA and IL15 in keratinocytes in skin lesions has been associated with inflammatory processes.


claim_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab:claim:5a02127f5b23cc68ebd5
claim_id: claim:5a02127f5b23cc68ebd5
paper_key: biorxiv:01e5e65d-751c-1014-a8e3-b5f1d7a951ab
span_literal:
Particularly, CCL5 expression in human skin AD lesions is upregulated in the acute phase but suppressed in chronic AD wounds (Tsoi et al., 2020), here we observe a downregulation of CCL5 in human AD.

summary:
In Homo sapiens, CCL5 expression in skin atopic dermatitis lesions is upregulated in the acute phase but suppressed in chronic atopic dermatitis wounds, with downregulation observed in human atopic dermatitis.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:f7dd4935b48fc0e800d9
claim_id: claim:f7dd4935b48fc0e800d9
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary: In Homo sapiens, T cells are marked by CD3E and IL7R in esophageal squamous cell carcinoma.
span_literal:
Annotation was supported by the expression of canonical markers such as CD3E, IL7R for T cells, MS4A1, CD79A for B cells, IGHG4, JCHAIN for plasma cells, LYZ, CD68 for myeloid cells, TPSAB1, KIT for mast cells, EPCAM, KRT18 for epithelial cells, VWF, PECAM1 for endothelial cells, DCN, COL1A1 for fibroblasts, and MYL9, MYH11 for smooth muscle cells


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:6b68da135b18653d4aed
claim_id: claim:6b68da135b18653d4aed
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, epithelial cells are marked by EPCAM and KRT18 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:f9069a7ebad27f846ef7
claim_id: claim:f9069a7ebad27f846ef7
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, endothelial cells are marked by VWF and PECAM1 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:08c2d4801fe22ebbff9a
claim_id: claim:08c2d4801fe22ebbff9a
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, smooth muscle cells are marked by MYL9 and MYH11 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:193cfb553f72420faddf
claim_id: claim:193cfb553f72420faddf
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary: In Homo sapiens, naïve T cells are marked by LEF1 and SELL in esophageal squamous cell carcinoma.
span_literal:
These subgroups encompassed CD4+ and CD8+ naïve T cells (TN) (LEF1, SELL), CD4+ memory T cells (TM) (ANXA1, LMNA), CD4+ tissue resident memory T cells (TRM) (CXCR6, CD69, ITGAE), CD4+ regulatory T cells (TREG) (FOXP3, CTLA4), CD4+ follicular helper like T cells (TFH-like) (CXCL13, SH2D1A), CD4+ stressed T cells (TSTR) (HSPA6, BAG3) [12], CD4+ IGF1R+ T cells, CD8+ effector memory T cells (TEM) (GZMK, GZMA), CD8+ terminally differentiated effector memory and effector cells (TEMRA) (CX3CR1), CD8+ ZNF683+ and ZNF683- TRM populations, CD8+ IFNG-AS1+ T cells, CD8+ exhausted T cells (TEXH) (PDCD1, LAG3, HAVCR2), CD8+ proliferating exhausted T cells (HAVCR2, MKI67, TOP2A), CD117+ T cells, mitochondria high T cells (MT-high) (MT-CO1, MT-ND6), and NK cells (NCAM1, KIR2DL4).


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:a161759a5bd6f4cdd94e
claim_id: claim:a161759a5bd6f4cdd94e
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
These subgroups encompassed CD4+ and CD8+ naïve T cells (TN) (LEF1, SELL), CD4+ memory T cells (TM) (ANXA1, LMNA), CD4+ tissue resident memory T cells (TRM) (CXCR6, CD69, ITGAE), CD4+ regulatory T cells (TREG) (FOXP3, CTLA4), CD4+ follicular helper like T cells (TFH-like) (CXCL13, SH2D1A), CD4+ stressed T cells (TSTR) (HSPA6, BAG3) [12], CD4+ IGF1R+ T cells, CD8+ effector memory T cells (TEM) (GZMK, GZMA), CD8+ terminally differentiated effector memory and effector cells (TEMRA) (CX3CR1), CD8+ ZNF683+ and ZNF683- TRM populations, CD8+ IFNG-AS1+ T cells, CD8+ exhausted T cells (TEXH) (PDCD1, LAG3, HAVCR2), CD8+ proliferating exhausted T cells (HAVCR2, MKI67, TOP2A), CD117+ T cells, mitochondria high T cells (MT-high) (MT-CO1, MT-ND6), and NK cells (NCAM1, KIR2DL4).

summary:
In Homo sapiens, CD4+ memory T cells are marked by ANXA1 and LMNA in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:4f0386539167dae7b57f
claim_id: claim:4f0386539167dae7b57f
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
These subgroups encompassed CD4+ and CD8+ naïve T cells (TN) (LEF1, SELL), CD4+ memory T cells (TM) (ANXA1, LMNA), CD4+ tissue resident memory T cells (TRM) (CXCR6, CD69, ITGAE), CD4+ regulatory T cells (TREG) (FOXP3, CTLA4), CD4+ follicular helper like T cells (TFH-like) (CXCL13, SH2D1A), CD4+ stressed T cells (TSTR) (HSPA6, BAG3) [12], CD4+ IGF1R+ T cells, CD8+ effector memory T cells (TEM) (GZMK, GZMA), CD8+ terminally differentiated effector memory and effector cells (TEMRA) (CX3CR1), CD8+ ZNF683+ and ZNF683- TRM populations, CD8+ IFNG-AS1+ T cells, CD8+ exhausted T cells (TEXH) (PDCD1, LAG3, HAVCR2), CD8+ proliferating exhausted T cells (HAVCR2, MKI67, TOP2A), CD117+ T cells, mitochondria high T cells (MT-high) (MT-CO1, MT-ND6), and NK cells (NCAM1, KIR2DL4).

summary:
In Homo sapiens, CD4+ tissue resident memory T cells are marked by CXCR6, CD69, and ITGAE in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:c22db9b639560c78666c
claim_id: claim:c22db9b639560c78666c
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD4+ regulatory T cells are marked by FOXP3 and CTLA4 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:9ac1789df501eefb389e
claim_id: claim:9ac1789df501eefb389e
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD4+ follicular helper-like T cells are marked by CXCL13 and SH2D1A in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:2460de700ff3c08bfea0
claim_id: claim:2460de700ff3c08bfea0
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD4+ stressed T cells are marked by HSPA6 and BAG3 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:922a2e79e784b6ab6b40
claim_id: claim:922a2e79e784b6ab6b40
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD8+ effector memory T cells are marked by GZMK and GZMA in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:dce457c1f02bd385d5d0
claim_id: claim:dce457c1f02bd385d5d0
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD8+ terminally differentiated effector memory and effector cells are marked by CX3CR1 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:908eb75991571b880ccb
claim_id: claim:908eb75991571b880ccb
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD8+ exhausted T cells are marked by PDCD1, LAG3, and HAVCR2 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:39ea6ba231ae95dc7cf7
claim_id: claim:39ea6ba231ae95dc7cf7
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CD8+ proliferating exhausted T cells are marked by HAVCR2, MKI67, and TOP2A in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:d5f65faa8679aec34ef7
claim_id: claim:d5f65faa8679aec34ef7
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, natural killer cells are marked by NCAM1 and KIR2DL4 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:362199de2e09868fbbd0
claim_id: claim:362199de2e09868fbbd0
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary: In Homo sapiens, naïve B cells are marked by IGHD and S1PR1 in esophageal squamous cell carcinoma.
span_literal:
we analyzed 85,482 B lineage cells and identified 10 transcriptionally distinct subgroups, including naïve (IGHD, S1PR1), activated (TNFRSF13B, GPR183), stressed (DNAJB1, DUSP1) [15], MT-high (MT-CO1, MT-ND6), CD3⁺ B cells (CD3D, CD3E), plasma cells (JCHAIN, MZB1, IGHG4), and two germinal center–like populations corresponding to light-zone (GC1) (RGS13, NEIL1, BCL6) and dark-zone (GC2) (MKI67, TOP2A) phenotypes


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:b9b28881b1d13cf8a2cf
claim_id: claim:b9b28881b1d13cf8a2cf
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
we analyzed 85,482 B lineage cells and identified 10 transcriptionally distinct subgroups, including naïve (IGHD, S1PR1), activated (TNFRSF13B, GPR183), stressed (DNAJB1, DUSP1) [15], MT-high (MT-CO1, MT-ND6), CD3⁺ B cells (CD3D, CD3E), plasma cells (JCHAIN, MZB1, IGHG4), and two germinal center–like populations corresponding to light-zone (GC1) (RGS13, NEIL1, BCL6) and dark-zone (GC2) (MKI67, TOP2A) phenotypes

summary:
In Homo sapiens, activated B cells are marked by TNFRSF13B and GPR183 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:907dd831ed09a5fc8ead
claim_id: claim:907dd831ed09a5fc8ead
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
we analyzed 85,482 B lineage cells and identified 10 transcriptionally distinct subgroups, including naïve (IGHD, S1PR1), activated (TNFRSF13B, GPR183), stressed (DNAJB1, DUSP1) [15], MT-high (MT-CO1, MT-ND6), CD3⁺ B cells (CD3D, CD3E), plasma cells (JCHAIN, MZB1, IGHG4), and two germinal center–like populations corresponding to light-zone (GC1) (RGS13, NEIL1, BCL6) and dark-zone (GC2) (MKI67, TOP2A) phenotypes

summary:
In Homo sapiens, stressed B cells are marked by DNAJB1 and DUSP1 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:d617d569412af0122780
claim_id: claim:d617d569412af0122780
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, plasma cells are marked by JCHAIN, MZB1, and IGHG4 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:70b21940cc92f1776218
claim_id: claim:70b21940cc92f1776218
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, germinal center light-zone B cells are marked by RGS13, NEIL1, and BCL6 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:6926f4fa245d6f54befd
claim_id: claim:6926f4fa245d6f54befd
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, germinal center dark-zone B cells are marked by MKI67 and TOP2A in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:62f59df2944e17848681
claim_id: claim:62f59df2944e17848681
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary: In Homo sapiens, monocytes are marked by VCAN and APOBEC3A in esophageal squamous cell carcinoma.
span_literal:
including monocytes (VCAN, APOBEC3A), TREM2low (APOE, C1QA, C1QC) and TREM2high macrophages (TREM2, APOE, C1QA), STRAD13⁺ macrophages (STARD13, CD163, MRC1), conventional dendritic cells (cDCs) (CD86, CD1C, CLEC10), CCR7⁺ DCs (CD86, CCR7), plasmacytoid DCs (pDCs) (PTCRA, CLEC4C), neutrophils (FCGR3B, S100A8), and mast cells (TPSAB1, TPSB2)


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:bfa7cef5c0aaed329d6c
claim_id: claim:bfa7cef5c0aaed329d6c
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
including monocytes (VCAN, APOBEC3A), TREM2low (APOE, C1QA, C1QC) and TREM2high macrophages (TREM2, APOE, C1QA), STRAD13⁺ macrophages (STARD13, CD163, MRC1), conventional dendritic cells (cDCs) (CD86, CD1C, CLEC10), CCR7⁺ DCs (CD86, CCR7), plasmacytoid DCs (pDCs) (PTCRA, CLEC4C), neutrophils (FCGR3B, S100A8), and mast cells (TPSAB1, TPSB2)

summary:
In Homo sapiens, TREM2low macrophages are marked by APOE, C1QA, and C1QC in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:ef736093e1a8aabe7c27
claim_id: claim:ef736093e1a8aabe7c27
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
including monocytes (VCAN, APOBEC3A), TREM2low (APOE, C1QA, C1QC) and TREM2high macrophages (TREM2, APOE, C1QA), STRAD13⁺ macrophages (STARD13, CD163, MRC1), conventional dendritic cells (cDCs) (CD86, CD1C, CLEC10), CCR7⁺ DCs (CD86, CCR7), plasmacytoid DCs (pDCs) (PTCRA, CLEC4C), neutrophils (FCGR3B, S100A8), and mast cells (TPSAB1, TPSB2)

summary:
In Homo sapiens, TREM2high macrophages are marked by TREM2, APOE, and C1QA in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:61aab38858b18607f840
claim_id: claim:61aab38858b18607f840
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, STARD13-positive macrophages are marked by STARD13, CD163, and MRC1 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:0caa81195c7ebb17628b
claim_id: claim:0caa81195c7ebb17628b
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, conventional dendritic cells are marked by CD86, CD1C, and CLEC10 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:6e1277a467d1b288dfe7
claim_id: claim:6e1277a467d1b288dfe7
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, CCR7-positive dendritic cells are marked by CD86 and CCR7 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:7fb33c6f594b8fa35347
claim_id: claim:7fb33c6f594b8fa35347
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, plasmacytoid dendritic cells are marked by PTCRA and CLEC4C in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:784435cb0daa4710da2d
claim_id: claim:784435cb0daa4710da2d
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
we subclustered 19,052 stromal cells into seven subsets: normal fibroblasts (NF) (PLA2G2A, IGFBP6), inflammatory cancer-assosicated fibroblasts (iCAFs) (CXCL1, PDGFRA, DCN), myofibroblast-like CAFs (myCAFs) (COL1A1, MFAP2, POSTN), antigen-presenting CAFs (apCAFs) (CD74, HLA-DRA), EFNA5⁺ CAFs (EFNA5, DDR2), smooth muscle cells (SMCs) (MYH11, CNN1), and pericytes (RGS5, PDGFRB)

summary:
In Homo sapiens, normal fibroblasts are marked by PLA2G2A and IGFBP6 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:c559f833808f0ea52474
claim_id: claim:c559f833808f0ea52474
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
we subclustered 19,052 stromal cells into seven subsets: normal fibroblasts (NF) (PLA2G2A, IGFBP6), inflammatory cancer-assosicated fibroblasts (iCAFs) (CXCL1, PDGFRA, DCN), myofibroblast-like CAFs (myCAFs) (COL1A1, MFAP2, POSTN), antigen-presenting CAFs (apCAFs) (CD74, HLA-DRA), EFNA5⁺ CAFs (EFNA5, DDR2), smooth muscle cells (SMCs) (MYH11, CNN1), and pericytes (RGS5, PDGFRB)

summary:
In Homo sapiens, inflammatory cancer-associated fibroblasts are marked by CXCL1, PDGFRA, and DCN in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:05b8221073d80a6b47d6
claim_id: claim:05b8221073d80a6b47d6
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
we subclustered 19,052 stromal cells into seven subsets: normal fibroblasts (NF) (PLA2G2A, IGFBP6), inflammatory cancer-assosicated fibroblasts (iCAFs) (CXCL1, PDGFRA, DCN), myofibroblast-like CAFs (myCAFs) (COL1A1, MFAP2, POSTN), antigen-presenting CAFs (apCAFs) (CD74, HLA-DRA), EFNA5⁺ CAFs (EFNA5, DDR2), smooth muscle cells (SMCs) (MYH11, CNN1), and pericytes (RGS5, PDGFRB)

summary:
In Homo sapiens, myofibroblast-like cancer-associated fibroblasts are marked by COL1A1, MFAP2, and POSTN in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:8b7363e8bd6145e2e54e
claim_id: claim:8b7363e8bd6145e2e54e
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, antigen-presenting cancer-associated fibroblasts are marked by CD74 and HLA-DRA in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:a81de422cc39c81b7e22
claim_id: claim:a81de422cc39c81b7e22
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, EFNA5-positive cancer-associated fibroblasts are marked by EFNA5 and DDR2 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:9f2ee245aad1cf0c27f3
claim_id: claim:9f2ee245aad1cf0c27f3
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
summary:
In Homo sapiens, smooth muscle cells are marked by MYH11 and CNN1 in esophageal squamous cell carcinoma.


claim_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97:claim:b627f95c455cb1c12eaa
claim_id: claim:b627f95c455cb1c12eaa
paper_key: biorxiv:03092aac-75a4-1014-b9cc-d44d468fbd97
span_literal:
Consistent with their earlier differentiation status, TPRE-EXH cells in TLN expressed markedly higher levels of TCF7, a defining marker of progenitor-like exhausted CD8+ T cells

summary:
In Homo sapiens, pre-exhausted CD8+ T cells express TCF7, a defining marker of progenitor-like exhausted CD8+ T cells, in esophageal squamous cell carcinoma.


claim_key: biorxiv:03a1691c-70ce-1014-bf1a-b6bd63c41968:claim:b7026df8ddbdfb684169
claim_id: claim:b7026df8ddbdfb684169
paper_key: biorxiv:03a1691c-70ce-1014-bf1a-b6bd63c41968
span_literal:
porcine cytotoxic ILCs were primarily predicted as human FCGR3A+ NK cells, and porcine NCR1+EOMES+ ILCs were primarily predicted as CD160+ NK cells

summary:
In Homo sapiens, FCGR3A-positive natural killer cells are marked by FCGR3A expression in the spleen.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:b93f2e0240f51da199a9
claim_id: claim:b93f2e0240f51da199a9
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal: testicular germ cell marker Melanoma Antigen family A 4, MAGEA4
summary:
In Homo sapiens, melanoma antigen family A 4 (MAGEA4) is a positive marker of testicular germ cells.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:b879109710a40a85bcdb
claim_id: claim:b879109710a40a85bcdb
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal: Sertoli cell markers SRY-BOX9, SOX9 (AB5535; Merck; dilution 1:200) and anti-Vimentin VHH-Atto488
summary:
In Homo sapiens, SRY-box transcription factor 9 (SOX9) and vimentin are positive markers of Sertoli cells.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:70d5996281b19b97bd29
claim_id: claim:70d5996281b19b97bd29
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
spermatogonia (melanoma-associated antigen 4), least differentiated spermatogonia (Piwi-like protein 4), Sertoli cells (vimentin and SRY-Box transcription Factor 9), peritubular myoid cells and vasculature (alpha-smooth muscle actin), and NucSpot as a nuclear dye.

summary:
In Homo sapiens, melanoma-associated antigen 4 (MAGEA4) is a positive marker of spermatogonia, Piwi-like protein 4 (PIWIL4) is a positive marker of least differentiated spermatogonia, vimentin and SRY-box transcription factor 9 are positive markers of Sertoli cells, and alpha-smooth muscle actin is a positive marker of peritubular myoid cells.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:d91947a600ce603ad973
claim_id: claim:d91947a600ce603ad973
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
spermatogonia (melanoma-associated antigen 4), least differentiated spermatogonia (Piwi-like protein 4), Sertoli cells (vimentin and SRY-Box transcription Factor 9), peritubular myoid cells and vasculature (alpha-smooth muscle actin), and NucSpot as a nuclear dye.

summary:
In Homo sapiens, Piwi-like protein 4 (PIWIL4) is a positive marker of least differentiated spermatogonia.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:8e07783d7d48097fb320
claim_id: claim:8e07783d7d48097fb320
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
This was indicated by MAGEA4-positive spermatogonia (Fig 1A), SOX9- and Vimentin-positive Sertoli cells and alpha-SMA expression in peritubular myoid cells (Fig 1B-E) and the vasculature (Figs 1C and 1E).

summary:
In Homo sapiens, MAGEA4 is a positive marker of spermatogonia, SOX9 and vimentin are positive markers of Sertoli cells, and alpha-smooth muscle actin is a positive marker of peritubular myoid cells.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:254043255660c54e687e
claim_id: claim:254043255660c54e687e
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
This was indicated by MAGEA4-positive spermatogonia (Fig 1A), SOX9- and Vimentin-positive Sertoli cells and alpha-SMA expression in peritubular myoid cells (Fig 1B-E) and the vasculature (Figs 1C and 1E).

summary:
In Homo sapiens, alpha-smooth muscle actin (alpha-SMA) is a positive marker of peritubular myoid cells.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:3ea14ba79a54dc4d9b6f
claim_id: claim:3ea14ba79a54dc4d9b6f
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
Additionally, there was predominant basal localization of MAGEA4-positive spermatogonia and SOX9-positive Sertoli cells, indicating maturity of the testis.

summary:
In Homo sapiens, MAGEA4 is a positive marker of spermatogonia and SOX9 is a positive marker of Sertoli cells in the mature testis.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:9218a4d1e61a72cb7efa
claim_id: claim:9218a4d1e61a72cb7efa
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
Comparable to MAGEA4-positive spermatogonia, PIWIL4-positive spermatogonia, which are the least differentiated, were predominantly localized at the basement membrane of the ITTS, but they occurred rarely compared to MAGEA4-positive spermatogonia across the three species.

summary:
In Homo sapiens, PIWIL4 is a positive marker of the least differentiated spermatogonia, and MAGEA4 is a positive marker of spermatogonia in the testis.


claim_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312:claim:917bab09c41954dd8f2c
claim_id: claim:917bab09c41954dd8f2c
paper_key: biorxiv:03bcb34d-755c-1014-ade5-9b7bdb3d9312
span_literal:
We observed fewer PIWIL4-positive spermatogonia, the least differentiated, compared to MAGEA4-positive spermatogonia across all species.

summary:
In Homo sapiens, PIWIL4 is a positive marker of the least differentiated spermatogonia, and MAGEA4 is a positive marker of spermatogonia.


claim_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92:claim:d884f8f1c40439ef5cde
claim_id: claim:d884f8f1c40439ef5cde
paper_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92
span_literal:
Employing lysozyme expression and Paneth cell module scores (Pangalo database) as criteria, we have identified LYZ+ cancer cells harboring Paneth cell properties across 5 clusters

summary:
In Homo sapiens, lysozyme-positive cancer cells harboring Paneth cell properties are identified by LYZ expression in colorectal cancer.


claim_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92:claim:cc0c8d0fb0358583e96f
claim_id: claim:cc0c8d0fb0358583e96f
paper_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92
span_literal:
Notably, key players in glycolysis such as ALDOB and KDELR3 genes are increased in LYZ+ cancer cells (Fig. 5B).

summary:
In Homo sapiens, lysozyme-positive cancer cells show increased expression of ALDOB and KDELR3 compared to lysozyme-negative cancer cells.


claim_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92:claim:9f2258b318b3d5b44162
claim_id: claim:9f2258b318b3d5b44162
paper_key: biorxiv:0900c414-6db3-1014-86e7-ea4583587c92
span_literal:
Further analyses for human colorectal cancer scRNA-seq data revealed that HNF4A regulation activity is reduced in LYZ+ human colon cancer cells compared to the LYZ- cancer cells while SOX9 regulation activity is significantly increased (Fig. 6J-6K and S5) suggesting the key roles of HNF4A and SOX9 in LYZ+ cancer cell formation in human.

summary:
In Homo sapiens, lysozyme-positive colon cancer cells show reduced hepatocyte nuclear factor 4-alpha regulation activity and increased SOX9 regulation activity compared to lysozyme-negative cancer cells.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:f5eba5dd9bd556c31801
claim_id: claim:f5eba5dd9bd556c31801
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
In fact, only about 2% of the cells (cluster 5) represented other cell types and showed expression of well-known markers for endothelial/epithelial and immune cells (DCN, CD74, ZEB2 and TCF4; Figures S1C-S1D, and Table S1), which we excluded from further analysis.

summary:
In Homo sapiens, endothelial/epithelial and immune cells express DCN, CD74, ZEB2, and TCF4 as markers.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:edd935f40406d86fc424
claim_id: claim:edd935f40406d86fc424
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
Genes most prominently enriched in cluster 1 include SDS and ASS1, while CYP1A2, CYP3A4, GLUL are enriched in cluster 3 (Figure S1D), all representing markers known to be associated with liver zonation.

summary:
In Homo sapiens, periportal hepatocytes (cluster 1) are marked by SDS and ASS1, while pericentral hepatocytes (cluster 3) are marked by CYP1A2, CYP3A4, and GLUL, all associated with liver zonation.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:8a75b4c754216e561858
claim_id: claim:8a75b4c754216e561858
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
Genes most prominently enriched in cluster 1 include SDS and ASS1, while CYP1A2, CYP3A4, GLUL are enriched in cluster 3 (Figure S1D), all representing markers known to be associated with liver zonation.

summary:
In Homo sapiens, pericentral hepatocytes (cluster 3) are marked by CYP1A2, CYP3A4, and GLUL, associated with liver zonation.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:ddbfd640828e6704e091
claim_id: claim:ddbfd640828e6704e091
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
In line with previous reports (6,26), we detected a down-regulation of WNT target gene LGR5 and progenitor/cholangiocyte marker SOX9, and up-regulation of hepatocyte markers (ALB, CYP3A4, GLUL and GC) (Figures S4D-S4F).

summary:
In Homo sapiens, differentiated intrahepatic cholangiocyte organoids show down-regulation of the progenitor/cholangiocyte marker SOX9 and WNT target gene LGR5, and up-regulation of hepatocyte markers ALB, CYP3A4, GLUL, and GC.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:ce3de5337bae7693b602
claim_id: claim:ce3de5337bae7693b602
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
In line with previous reports (6,26), we detected a down-regulation of WNT target gene LGR5 and progenitor/cholangiocyte marker SOX9, and up-regulation of hepatocyte markers (ALB, CYP3A4, GLUL and GC) (Figures S4D-S4F).

summary:
In Homo sapiens, SOX9 is a marker of progenitor/cholangiocyte cells, and LGR5 is a WNT target gene expressed in expansion-medium intrahepatic cholangiocyte organoids.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:23ab394cba577305d218
claim_id: claim:23ab394cba577305d218
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
summary: In Homo sapiens, cholangiocytes are marked by TFF1, TFF3, MUC5B, EPCAM, KRT7, and KRT19.
span_literal:
Expression of cholangiocyte markers (TFF1, TFF3, and MUC5B) in DM-ICOs decreased compared to EM-ICOs, while other cholangiocyte markers such as EPCAM, KRT7 and KRT19 remained largely similar (Figure S4F), indicating that ICOs under hepatocyte differentiation condition still retain cholangiocyte features.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:dccb05339aecac72328d
claim_id: claim:dccb05339aecac72328d
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
On the other hand, we identified ELF3 and EHF as main regulons in ICOs (EM and DM) that are absent in PHHs.

summary:
In Homo sapiens, ELF3 and EHF are transcription factors specifically active in intrahepatic cholangiocyte organoids and absent in primary human hepatocytes.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:b632703dde51de58f96c
claim_id: claim:b632703dde51de58f96c
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
For example, MLX Interacting Protein Like (MLXIPL), also known as ChREBP, is a glucose-sensitive transcription factor that is crucial for glucose metabolisms and de novo lipogenesis (29).

summary:
In Homo sapiens, MLX Interacting Protein Like (MLXIPL) is a glucose-sensitive transcription factor enriched in primary human hepatocytes.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:facee0dcddd64e4d409e
claim_id: claim:facee0dcddd64e4d409e
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) is required for nutrient metabolism in the liver (30,31).

summary:
In Homo sapiens, peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) is enriched in primary human hepatocytes and required for nutrient metabolism in the liver.


claim_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b:claim:55a857b2080924ee008e
claim_id: claim:55a857b2080924ee008e
paper_key: biorxiv:09d40fbc-6c3d-1014-b39f-eee50a07ad3b
span_literal:
Violin plots showing expression of representative zonal markers (periportal: ALB, ALDOB, and SDS; pericentral: CYP3A4, CYP1A2, and GLUL) across hepatocyte clusters.

summary:
In Homo sapiens, periportal hepatocytes are marked by ALB, ALDOB, and SDS, while pericentral hepatocytes are marked by CYP3A4, CYP1A2, and GLUL.


claim_key: biorxiv:0a6d6372-6dad-1014-aa2c-84eb1d405c37:claim:01400ec950da0be6d2a3
claim_id: claim:01400ec950da0be6d2a3
paper_key: biorxiv:0a6d6372-6dad-1014-aa2c-84eb1d405c37
span_literal:
Additionally, we observed a small cluster of Goblet-Ionocyte cells with high expression of markers of Goblet (MUC5AC) and Ionocytes (CFTR), which have not been previously described to our knowledge.

summary:
In Homo sapiens nasal epithelial cells, goblet-ionocyte cells express high levels of the goblet cell marker MUC5AC and the ionocyte marker CFTR.


claim_key: biorxiv:0a6d6372-6dad-1014-aa2c-84eb1d405c37:claim:29f03f5daeeab51d3657
claim_id: claim:29f03f5daeeab51d3657
paper_key: biorxiv:0a6d6372-6dad-1014-aa2c-84eb1d405c37
summary: In Homo sapiens, Vimentin (VIM) is a mesenchymal marker.
span_literal:
When the mesenchymal marker Vimentin (VIM) in mock-control cells of donor 6 was compared with mock-control samples in all other donors, VIM was up-regulated (padj < 0.05, Figure S7a).


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:ccd5197f5718fabdb7d8
claim_id: claim:ccd5197f5718fabdb7d8
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
OSCC cells were identified both by the presence of copy number variations (CNVs) inferred from scRNAseq data as well as the expression of epithelial markers including S100A2, S100A14, cytokeratins (KRT5, KRT14, KRT17) and stratifin (SFN)

summary:
In Homo sapiens, oral squamous cell carcinoma cells were identified by expression of epithelial markers including S100A2, S100A14, KRT5, KRT14, KRT17, and stratifin (SFN).


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:8e3e7ea527c457d9199f
claim_id: claim:8e3e7ea527c457d9199f
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
515 cells exhibited a pEMT phenotype by expressing a mixture of epithelial and mesenchymal genes such as matrix metallopeptidases (MMPs), caveolin-1 (CAV1) and CXCL14 that were previously described in pEMT signatures and are enriched in the EMT hallmark gene set from the molecular signatures database (MSigDB)

summary:
In Homo sapiens, oral squamous cell carcinoma cells with a partial epithelial-mesenchymal transition phenotype express matrix metallopeptidases, caveolin-1 (CAV1), and CXCL14.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:5d3be19acdb02914211c
claim_id: claim:5d3be19acdb02914211c
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
385 cells showed higher expression of genes associated with epithelial differentiation such as S100A7/A8/A9, the keratinocyte envelope protein cornifin-B (SPRR1B), and various cytokeratins (e.g., KRT6B and KRT16).

summary:
In Homo sapiens, epithelial differentiated oral squamous cell carcinoma cells show higher expression of S100A7, S100A8, S100A9, cornifin-B (SPRR1B), KRT6B, and KRT16.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:70c5907394dcf0196fe2
claim_id: claim:70c5907394dcf0196fe2
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
268 cells exhibited an immune-regulatory phenotype enriched for genes associated with cytokine-mediated responses and higher expression of the chemokines CXCL1/2/3/8 and CCL20

summary:
In Homo sapiens, oral squamous cell carcinoma cells with an immune-regulatory phenotype show higher expression of CXCL1, CXCL2, CXCL3, CXCL8, and CCL20.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:4057c342bd6cc8a64783
claim_id: claim:4057c342bd6cc8a64783
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal: 51 cells had higher expression of transcription factors FOS and JUN suggesting a stress response.
summary:
In Homo sapiens, oral squamous cell carcinoma cells with a stress response phenotype show higher expression of FOS and JUN.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:95916b625850672d3a3d
claim_id: claim:95916b625850672d3a3d
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
310 cells can be assumed to respond to hypoxic conditions in the tumor based on the higher expression of NDRG1 and EGLN3 both of which are regulated by oxygen levels

summary:
In Homo sapiens, oral squamous cell carcinoma cells responding to hypoxic conditions show higher expression of NDRG1 and EGLN3.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:290a0bc917a163be3775
claim_id: claim:290a0bc917a163be3775
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
The upregulated genes ASNS, PSAT1 and PHGDH integrate the metabolites of serine and glycine metabolism into glycolysis and therefore fuel glycolysis with amino acids

summary:
In Homo sapiens, oral squamous cell carcinoma cells adapted to low-glucose conditions show upregulation of ASNS, PSAT1, and PHGDH.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:860418ed3a2a9138652e
claim_id: claim:860418ed3a2a9138652e
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
pEMT-1 is enriched for genes involved in coagulation and play a role in angiogenesis as THBS1, CYR61 and F3

summary:
In Homo sapiens, partial epithelial-mesenchymal transition 1 oral squamous cell carcinoma cells are enriched for THBS1, CYR61, and F3.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:3d3a8daf91a7a13e25ee
claim_id: claim:3d3a8daf91a7a13e25ee
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
pEMT-2 also higher expressed cytokeratin KRT15 and chemokine CXCL14 while pEMT-3 higher expressed the serine protease inhibitor SERPINA1 and podoplanin (PDPN) which mediates efficient ECM degradation by controlling invadopodia

summary:
In Homo sapiens, partial epithelial-mesenchymal transition 2 oral squamous cell carcinoma cells show higher expression of KRT15 and CXCL14, while partial epithelial-mesenchymal transition 3 cells show higher expression of SERPINA1 and podoplanin (PDPN).


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:74f6c57edd1fb6517d01
claim_id: claim:74f6c57edd1fb6517d01
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
pEMT-2 also higher expressed cytokeratin KRT15 and chemokine CXCL14 while pEMT-3 higher expressed the serine protease inhibitor SERPINA1 and podoplanin (PDPN) which mediates efficient ECM degradation by controlling invadopodia

summary:
In Homo sapiens, partial epithelial-mesenchymal transition 3 oral squamous cell carcinoma cells show higher expression of SERPINA1 and podoplanin (PDPN).


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:8faa27dd2a98e405bd1c
claim_id: claim:8faa27dd2a98e405bd1c
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
Epi-3 showed higher expression of S100A7 and KRTDAP, whereas epi-4 has higher expression of kallikreins (KLK6/7), prostate stem cell antigen (PSCA) and adipogenesis regulatory factor (ADIRF).

summary:
In Homo sapiens, epithelial differentiated 3 oral squamous cell carcinoma cells show higher expression of S100A7 and KRTDAP, whereas epithelial differentiated 4 cells show higher expression of KLK6, KLK7, prostate stem cell antigen (PSCA), and adipogenesis regulatory factor (ADIRF).


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:7fb4646e81c4ac6a7075
claim_id: claim:7fb4646e81c4ac6a7075
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
Epi-3 showed higher expression of S100A7 and KRTDAP, whereas epi-4 has higher expression of kallikreins (KLK6/7), prostate stem cell antigen (PSCA) and adipogenesis regulatory factor (ADIRF).

summary:
In Homo sapiens, epithelial differentiated 4 oral squamous cell carcinoma cells show higher expression of KLK6, KLK7, prostate stem cell antigen (PSCA), and adipogenesis regulatory factor (ADIRF).


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:c90e5e58aacce44bf065
claim_id: claim:c90e5e58aacce44bf065
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
In epithelial differentiated cells, the most upregulated genes are S100A8 and S100A9, encoding calprotectin, and SPRR1B, all members of the epidermal differentiation complex

summary:
In Homo sapiens, epithelial differentiated oral squamous cell carcinoma cells show upregulation of S100A8, S100A9, and SPRR1B.


claim_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd:claim:bb2a212ff470e2dbebc3
claim_id: claim:bb2a212ff470e2dbebc3
paper_key: biorxiv:0bd28b37-6e2e-1014-871e-a496f0a6bacd
span_literal:
Consistent with the fact that one of the main functions of ZEB1 is the downregulation of E-cadherin (46) (CDH1), OSCC cells generally showed low expression of CDH1

summary:
In Homo sapiens, oral squamous cell carcinoma cells generally show low expression of CDH1 (E-cadherin), consistent with ZEB1-mediated downregulation.


claim_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954:claim:c0ccd18ea6eec7b99fd5
claim_id: claim:c0ccd18ea6eec7b99fd5
paper_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954
span_literal:
Finally, cyclin-dependent kinase inhibitor p21 (CDKN1A), a member of the p53 pathway, is a well-established marker of cellular senescence, DNA damage, and tumor progression78,79.

summary:
In Homo sapiens, cyclin-dependent kinase inhibitor p21 (CDKN1A) is a well-established positive marker of senescent cells, associated with DNA damage and tumor progression.


claim_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954:claim:bd6a009026571f3b6e1d
claim_id: claim:bd6a009026571f3b6e1d
paper_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954
span_literal:
Thus, glycoprotein nonmetastatic melanoma protein B (GPNMB), involved in regulation of cell differentiation, regeneration and inflammation72, was shown to have elevated levels in patients with neurodegenerative diseases, including Alzheimer’s disease73, Gaucher disease74, and amyotrophic lateral sclerosis75.

summary:
In Homo sapiens, glycoprotein nonmetastatic melanoma protein B (GPNMB) has elevated levels in patients with neurodegenerative diseases, serving as a positive marker in neurodegenerative disease cells.


claim_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954:claim:e20c8a9e8a26384be1ef
claim_id: claim:e20c8a9e8a26384be1ef
paper_key: biorxiv:0c36d8d8-6cad-1014-ad28-fa021d92b954
span_literal:
Cystatin F regulates cell cytotoxicity, while its induction is also associated with development of brain pathologies, such as a prion disease76 and AD in mice and humans77, presumably through the impairment of lysosomal function in microglia.

summary:
In Homo sapiens, Cystatin F (CST7) induction is associated with Alzheimer's disease, presumably through impairment of lysosomal function in microglia.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:6cf626a9d8b612b19373
claim_id: claim:6cf626a9d8b612b19373
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
This population, labelled as vascular immature, was defined by increased abundance of PCNA and CEBPE (Fig. 4C) with concurrent increased abundance of mitochondrial metabolic enzymes including PDHB, IDH3A and ACAT1, mitochondrial membrane proteins including TOMM5 and IMMT (Fig. 4D), and overall ribosomal proteins including RPL4, RPL7 and RPL15 (Fig. 4E).

summary:
In Homo sapiens glioblastoma, vascular immature neutrophils are defined by increased abundance of PCNA, CEBPE, PDHB, IDH3A, ACAT1, TOMM5, IMMT, RPL4, RPL7, and RPL15.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:8f21aab50d11c468f4f8
claim_id: claim:8f21aab50d11c468f4f8
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
The most abundant population, the armed neutrophils, have a signature consistent with recent extravasation with the highest abundance of cytoskeletal and motility related proteins (Fig. 5A) including ITGB2 (CD18) and ITGAM (Cd11b), vital integrins forming the MAC1 complex.

summary:
In Homo sapiens glioblastoma, armed neutrophils have the highest abundance of ITGB2 and ITGAM, vital integrins forming the MAC1 complex.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:7837013132d6f72ad602
claim_id: claim:7837013132d6f72ad602
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
Engaged neutrophils demonstrate signs of granule release, exemplified by reductions in myeloperoxidase (MPO) and calprotectin subunit S100A8 content, and a trajectory towards vital NETosis (Fig. 5 D&E) where loss of granule proteins and secretory vesicles (Fig. 5F) is associated with a reduction in histones (Fig. 5G&H) and nuclear and cell membrane proteins (Fig. 5I).

summary:
In Homo sapiens glioblastoma, engaged neutrophils demonstrate reductions in myeloperoxidase (MPO) and calprotectin subunit S100A8.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:167ac13a011a5136ca43
claim_id: claim:167ac13a011a5136ca43
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
These cells have a significant reduction in proteins involved in vital metabolic processes including glycolysis, glycogenolysis and the pentose phosphate pathway (Fig. 5J), exemplified by low level expression of the key regulatory proteins glucose transporter GLUT 3 (SLC2A3) and glycogen phosphorylase (PYGL) (Fig. 5K&L).

summary:
In Homo sapiens glioblastoma, exhausted neutrophils have low level expression of glucose transporter GLUT 3 (SLC2A3) and glycogen phosphorylase (PYGL).


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:da623238a4177fde5f1f
claim_id: claim:da623238a4177fde5f1f
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
In keeping with a reduced capacity to respond, this dysfunction also extends to regulators of neutrophil function including the NADPH oxidase regulator RAC2 (Fig. 5M), and the calcium binding protein calmodulin (Fig. 5N).

summary:
In Homo sapiens glioblastoma, exhausted neutrophils have reduced abundance of the NADPH oxidase regulator RAC2 and the calcium binding protein calmodulin.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:27183039541505873843
claim_id: claim:27183039541505873843
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
Interestingly this population was also defined by high abundance of GABBR1,a Gabba receptor associated with innate lymphoid cell inhibition29 (Fig. 5O) and CD2BP2, a CD2 binding protein with unknown neutrophil effector functions (Fig. 5P).

summary:
In Homo sapiens glioblastoma, exhausted neutrophils are defined by high abundance of GABBR1 and CD2BP2.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:e915e53194918816016f
claim_id: claim:e915e53194918816016f
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
The proteomic data also uncovered the presence of a distinct neutrophil state within the tumour that displayed an immunosuppressive signature30, with high abundance of Arginase 1 (ARG1) and S100A7 (Fig. 6A&B).

summary:
In Homo sapiens glioblastoma, immunosuppressive and angiogenic neutrophils display high abundance of Arginase 1 (ARG1) and S100A7.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:59a613ebf029454ecb9d
claim_id: claim:59a613ebf029454ecb9d
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
This cluster was further defined by an increase in abundance of the pro-angiogenic factors ECM1 (extracellular matrix protein 1) (Fig. 6C) and S100A10 (Fig. 6D) thus we have termed these immunosuppressive and angiogenic (I&A) neutrophils.

summary:
In Homo sapiens glioblastoma, immunosuppressive and angiogenic neutrophils are defined by increased abundance of ECM1 (extracellular matrix protein 1) and S100A10.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:e44c0ee4128af5d26aad
claim_id: claim:e44c0ee4128af5d26aad
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal: A reduction in the matrix metalloproteinases, MMP8 (Fig. 6E) & MMP9 (Fig. 6F) was also revealed.
summary:
In Homo sapiens glioblastoma, immunosuppressive and angiogenic neutrophils display a reduction in MMP8 and MMP9.


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:1ca696474e98edb845f1
claim_id: claim:1ca696474e98edb845f1
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
In addition, immunosuppressive and angiogenic neutrophils displayed evidence of enhanced lysosomal capacity with increased abundance of core lysosomal proteins (Fig. 6G), including Cathepsin D (CTSD), lysosomal associated membrane protein 1 (LAMP1) and scavenger receptor class B member 2 (SCARB2).

summary:
In Homo sapiens glioblastoma, immunosuppressive and angiogenic neutrophils display increased abundance of Cathepsin D (CTSD), lysosomal associated membrane protein 1 (LAMP1), and scavenger receptor class B member 2 (SCARB2).


claim_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002:claim:6928c3a2d1cd4ef6530e
claim_id: claim:6928c3a2d1cd4ef6530e
paper_key: biorxiv:0c5b4463-70b4-1014-b7ae-f953f2710002
span_literal:
A higher abundance of proteins reported to associate with increased neutrophil maturation status was observed, including core components of the NADPH oxidase, granule proteins MMP8, MMP9, S100A8, S100A9 (Fig. 2K) and the cell surface markers CD11b, CD18, CD16 and SLC2A3 (Fig. 2L).

summary:
In Homo sapiens, mature normal density neutrophils have higher abundance of MMP8, MMP9, S100A8, S100A9, CD11b, CD18, CD16, and SLC2A3 compared to immature low density neutrophils.


claim_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44:claim:5a8e26926ad5ff8acb53
claim_id: claim:5a8e26926ad5ff8acb53
paper_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44
span_literal:
The appearance of Tbr2/EOMES positive cells (Fig. S2A) indicated that some basal progenitors were present and confirmed forebrain tissue identity, while Beta-Tubulin labelling (Fig. S2B) established neuron generation.

summary:
In Homo sapiens, basal progenitors are marked by positive expression of TBR2/EOMES, confirming forebrain tissue identity, while neurons are identified by Beta-Tubulin labelling.


claim_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44:claim:7e6e2fb3a4a48987d2d1
claim_id: claim:7e6e2fb3a4a48987d2d1
paper_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44
span_literal:
their subsequent differentiation into SOX2 expressing neural progenitors, which self-organise into neural rosettes exhibiting localised expression of apico-basal polarity markers such as NCAD/CDH2 by Day 6 (D6) following NMP-L cell plating

summary:
In Homo sapiens, neural progenitors express SOX2, and neural rosettes exhibit localised expression of NCAD/CDH2 as an apico-basal polarity marker.


claim_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44:claim:6af590289257b7a3b52a
claim_id: claim:6af590289257b7a3b52a
paper_key: biorxiv:0c7fdd53-755f-1014-abd5-c154158d9e44
span_literal:
Two passages after thawing cells were checked for uniform expression of pluripotency markers (OCT4, SOX2, NANOG, SSEA-3, SSEA-4 TRA-1-60 and TRA-1-81), absence of differentiation markers (SSEA-1, HNF3-beta, beta-III-tubulin and smooth muscle alpha actinin) by immunofluorescence.

summary:
In Homo sapiens, pluripotent stem cells are characterized by positive expression of OCT4, SOX2, NANOG, SSEA-3, SSEA-4, TRA-1-60, and TRA-1-81, and by absence of SSEA-1, HNF3-beta, beta-III-tubulin, and smooth muscle alpha actinin.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:2a86bc55fbb5a2400b47
claim_id: claim:2a86bc55fbb5a2400b47
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
Cell identities were annotated based on their expression of previously reported signatures (ISC: LGR5, ASCL2, OLFM4, SMOC2, OLFM414; TA: MKI67, TOP2A15; EC: APOA4, ANPEP, FABP216; GC: MUC217; EEC: PAX4, INSM1, CHGA, CHGB18) in healthy human intestinal epithelial cells (Fig. 1B, E).

summary:
In Homo sapiens, intestinal stem cells are marked by LGR5, ASCL2, OLFM4, and SMOC2 in healthy human intestinal epithelial cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:04b710334a4100af460c
claim_id: claim:04b710334a4100af460c
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
Cell identities were annotated based on their expression of previously reported signatures (ISC: LGR5, ASCL2, OLFM4, SMOC2, OLFM414; TA: MKI67, TOP2A15; EC: APOA4, ANPEP, FABP216; GC: MUC217; EEC: PAX4, INSM1, CHGA, CHGB18) in healthy human intestinal epithelial cells (Fig. 1B, E).

summary:
In Homo sapiens, transit amplifying cells are marked by MKI67 and TOP2A in healthy human intestinal epithelial cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:8bf7f68e7b078ed4bf2e
claim_id: claim:8bf7f68e7b078ed4bf2e
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
Cell identities were annotated based on their expression of previously reported signatures (ISC: LGR5, ASCL2, OLFM4, SMOC2, OLFM414; TA: MKI67, TOP2A15; EC: APOA4, ANPEP, FABP216; GC: MUC217; EEC: PAX4, INSM1, CHGA, CHGB18) in healthy human intestinal epithelial cells (Fig. 1B, E).

summary:
In Homo sapiens, enterocytes are marked by APOA4, ANPEP, and FABP2 in healthy human intestinal epithelial cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:c15cb1868c1c1d721189
claim_id: claim:c15cb1868c1c1d721189
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary:
In Homo sapiens, enteroendocrine cells are marked by PAX4, INSM1, CHGA, and CHGB in healthy human intestinal epithelial cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:b56ebf67dad62f4d4231
claim_id: claim:b56ebf67dad62f4d4231
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
PLA2G2A, a phospholipase A2 family member that is highly expressed in fetal ISC24 and adult human Paneth cells (PC)25.

summary:
In Homo sapiens, PLA2G2A (phospholipase A2 group IIA) is highly expressed in fetal intestinal stem cells and adult Paneth cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:5dca1f2b747e77ae7d36
claim_id: claim:5dca1f2b747e77ae7d36
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary: In Homo sapiens, Paneth cells are marked by LYZ, DEFA4, DEFA5, and PRSS2.
span_literal:
However, ISCLC 1 did not express PC markers LYZ27, DEFA4/527, or PRSS228 (Fig. S2C), so it was unlikely to be adult PC-like cells or the stem-like that have been reported to appear after inflammation in a previous study29.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:eccca6e38549a8399ee3
claim_id: claim:eccca6e38549a8399ee3
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary: In Homo sapiens, adult intestinal stem cells are marked by OLFM4, RARRES2, and CD44.
span_literal:
Although LGR5 and SMOC2 were expressed, there was no active transcription of human adult ISC marker genes OLFM4, RARRES2, or CD44 (Fig. 2B, Fig. 2D).


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:35b93bc13db87ff3cf3b
claim_id: claim:35b93bc13db87ff3cf3b
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary: In Homo sapiens, the immature fetal intestine is characterized by the lack of OLFM4 expression.
span_literal:
Interestingly, the lack of OLFM4 is a feature of the immature fetal intestine, strengthening the fetal-like features of the co-culture52.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:988ddfb122ddf2a7793a
claim_id: claim:988ddfb122ddf2a7793a
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary: In Homo sapiens, mature enterocytes are defined by the expression of APOA4, ANPEP, and FABP2.
span_literal:
Their ECLC identity was defined by the expression of major mature enterocyte transporters APOA4, ANPEP, and FABP253, 55, 56.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:565bb1c7ead595d67cc4
claim_id: claim:565bb1c7ead595d67cc4
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
BMP4 is a bone morphogenetic protein that is reported to restrict the stemness of LGR5+ ISCs71 and enhance the differentiation72.

summary:
In Homo sapiens, BMP4 is expressed in cells that restrict the stemness of LGR5-positive intestinal stem cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:e2a33daeb965e15fdc0b
claim_id: claim:e2a33daeb965e15fdc0b
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
Lysozyme (LYZ), a well-studied antimicrobial agent, is transcribed in BEST4+ enterocytes, PCs, tuft cells, and follicle-associated epithelial cells, which seemingly supports the hypothesis that those cells being Paneth-like cells.

summary:
In Homo sapiens, LYZ (lysozyme) is transcribed in BEST4-positive enterocytes, Paneth cells, tuft cells, and follicle-associated epithelial cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:6dbdc820d02986bf2104
claim_id: claim:6dbdc820d02986bf2104
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary: In Homo sapiens, Paneth cells are marked by DEFA4, DEFA5, and ITLN2.
span_literal:
However, the lack of other Paneth markers DEFA4/5 or ITLN2 (Fig. S2C) undermined the possibility that this population being full-fledged PC- like cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:164d20d5f03f76126350
claim_id: claim:164d20d5f03f76126350
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
summary: In Homo sapiens, MUC2 is a putative marker of intestinal goblet cells.
span_literal:
The GCLC strongly and uniquely expressed gel-forming mucin MUC279, a putative marker of the intestinal goblet cells and the building block of the mucus layer (Fig. 4B-C).


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:a857d64de98c6fd8f8d3
claim_id: claim:a857d64de98c6fd8f8d3
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
Besides, part of the DEGs in human goblet cells were also present in the GCLC, such as IgGFc-binding protein FCGBP, SLC12A2, trefoil factor TFF3, and SPDEF (Fig. 4D).

summary:
In Homo sapiens, goblet cells express differentially expressed genes including FCGBP, SLC12A2, TFF3, and SPDEF.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:7a348f08c8b88e3b6b86
claim_id: claim:7a348f08c8b88e3b6b86
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
EECLC-1 uniquely expressed GCG, UCN3, ETV1 (EEC subtype L-cells), SST (EEC subtype D-cells)23, whereas EECLC-2 expressed PROX1 (EEC subtype L-cells) and a high-level of STMN1 (Fig. 4B).

summary:
In Homo sapiens, enteroendocrine L-cells express GCG, UCN3, ETV1, and PROX1, while enteroendocrine D-cells express SST. In Homo sapiens, enteroendocrine L-cells express PROX1.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:a912d2d2b525d8657aa6
claim_id: claim:a912d2d2b525d8657aa6
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
Most of the mature human EEC DEGs such as CHGA and CHGB were missing in both EECLC groups (Fig. 4F), yet some EECLC DEGs were expressed in human EECs (Fig. S4 D).

summary:
In Homo sapiens, mature enteroendocrine cells express differentially expressed genes including CHGA and CHGB.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:143291116ca4edabd0a1
claim_id: claim:143291116ca4edabd0a1
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
it expressed ASCL2 and RARRES2, a gene transcribed mainly in colon ISCs and in colon goblet cells56 (Fig. 4B, Fig. 4I).

summary:
In Homo sapiens, RARRES2 is transcribed mainly in colon intestinal stem cells and in colon goblet cells.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:28d600d26c9cfac5fef3
claim_id: claim:28d600d26c9cfac5fef3
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
KRT20 has long been used to identify the differentiated cells in the primary epithelium74, yet its role in CRC cells is controversial.

summary:
In Homo sapiens, KRT20 (keratin 20) has long been used to identify differentiated epithelial cells in the primary epithelium.


claim_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181:claim:e42a7f4d0817c48a15f5
claim_id: claim:e42a7f4d0817c48a15f5
paper_key: biorxiv:0e94bf21-6c7c-1014-b6a7-bcc9b09c8181
span_literal:
TLR4 is primarily responsible for initiating the defense-related NF-κB signaling pathway in cells when it binds to the LPS of gram-negative bacteria98.

summary:
In Homo sapiens, TLR4 (Toll-like receptor 4) is expressed on epithelial cells and is primarily responsible for initiating the NF-κB signaling pathway upon lipopolysaccharide binding.


claim_key: biorxiv:0ea346cb-7048-1014-a5d3-d23c8828e500:claim:889fea3032a43c55b941
claim_id: claim:889fea3032a43c55b941
paper_key: biorxiv:0ea346cb-7048-1014-a5d3-d23c8828e500
span_literal: The kit removes cells expressing CD2, CD3, CD14, CD16, CD56, CD61, CD66b.
summary:
In Homo sapiens, chronic lymphocytic leukemia B cells are isolated by negative selection, removing cells expressing CD2, CD3, CD14, CD16, CD56, CD61, and CD66b, which are markers of non-chronic lymphocytic leukemia cell populations.


claim_key: biorxiv:0ea346cb-7048-1014-a5d3-d23c8828e500:claim:ab878991d8683fe64ddb
claim_id: claim:ab878991d8683fe64ddb
paper_key: biorxiv:0ea346cb-7048-1014-a5d3-d23c8828e500
span_literal:
B-memory cell populations (CD19+ and CD27+), and B-naive cell populations (CD19+ and CD27−), were reported to have purities between 90-98%.

summary:
In Homo sapiens, B-memory cells are positive for CD19 and CD27, while B-naive cells are positive for CD19 and negative for CD27.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:5ba1b01cd96ceebc38df
claim_id: claim:5ba1b01cd96ceebc38df
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
we plotted the median-scaled MS-based protein abundance of the main pancreatic peptide hormones glucagon (GCG), insulin (INS), somatostatin (SST) and pancreatic polypeptide (PPY) across the single cells analyzed from healthy 1 (Figure 1D). These hormones are specific to alpha, beta, delta, and gamma cells, respectively.

summary:
In Homo sapiens pancreatic islets, glucagon (GCG) is a specific marker of alpha cells, insulin (INS) is a specific marker of beta cells, somatostatin (SST) is a specific marker of delta cells, and pancreatic polypeptide (PPY) is a specific marker of gamma cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:5be1018c80bd75931c2d
claim_id: claim:5be1018c80bd75931c2d
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
summary:
In Homo sapiens pancreatic islets, pancreatic polypeptide (PPY) is a specific marker of gamma cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:3f4fcd8ecdfa4b2f876b
claim_id: claim:3f4fcd8ecdfa4b2f876b
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
summary: In Homo sapiens pancreatic islets, ghrelin (GHRL) is a marker of epsilon cells.
span_literal:
The epsilon cell marker Ghrelin (GHRL) was also detected but at very low abundance and in very few cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:f6ec35af085accc234bb
claim_id: claim:f6ec35af085accc234bb
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
For instance, PCSK, the gene that encodes for the enzyme prohormone-convertase 1, is often used as a marker of delta cells including in Azimuth but is also involved in proinsulin processing and present at similar levels in beta cells (Supplementary Figure 2).

summary:
In Homo sapiens pancreatic islets, PCSK1 encoding prohormone-convertase 1 is often used as a marker of delta cells but is also present at similar levels in beta cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:9a1328ced8e0c4f914ab
claim_id: claim:9a1328ced8e0c4f914ab
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal: Only retinol-binding protein 4 (RBP4) matched cells with high levels of somatostatin.
summary:
In Homo sapiens pancreatic islets, retinol-binding protein 4 (RBP4) is a marker of delta cells as it matched cells with high levels of somatostatin.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:9672dbfb4850657cadbc
claim_id: claim:9672dbfb4850657cadbc
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
Four markers were detected in alpha cells, with transthyretin (TTR) and prohormone-convertase 2 (PCSK2) showing good agreement with glucagon (GLUC) expression levels, which was not the case for protein phosphatase 1 regulatory subunit 1A (PPP1R1A).

summary:
In Homo sapiens pancreatic islets, transthyretin (TTR) and prohormone-convertase 2 (PCSK2) are markers of alpha cells showing good agreement with glucagon expression levels.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:aaf5694fd0b4119ae6a1
claim_id: claim:aaf5694fd0b4119ae6a1
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
For beta cells, the detected markers seemed in agreement with insulin abundance including the levels for hydroxyacyl-coenzyme A dehydrogenase (HADH), gelsolin (GSN), glucose-6-phosphatase 2 (G6PC2), neuronal pentraxin-2 (NPTX2) and islet amyloid polypeptide (IAPP).

summary:
In Homo sapiens pancreatic islets, hydroxyacyl-coenzyme A dehydrogenase (HADH), gelsolin (GSN), glucose-6-phosphatase 2 (G6PC2), neuronal pentraxin-2 (NPTX2), and islet amyloid polypeptide (IAPP) are markers of beta cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:0103eb885c24d1d2f3a4
claim_id: claim:0103eb885c24d1d2f3a4
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
Ductal cells were mostly characterized by the expression of annexin A4 (ANXA4), and other detected markers were expressed in other cell types.

summary:
In Homo sapiens pancreatic islets, ductal cells are mostly characterized by the expression of annexin A4 (ANXA4).


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:4cefab746f66c36d716c
claim_id: claim:4cefab746f66c36d716c
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
Acinar cells had three markers present at high abundance in other cell types including carboxypeptidase A1 (CPA1), chymotrypsinogen B2 (CTRB2) and chymotrypsin-like elastase 3A (CELA3A).

summary:
In Homo sapiens pancreatic islets, carboxypeptidase A1 (CPA1), chymotrypsinogen B2 (CTRB2), and chymotrypsin-like elastase 3A (CELA3A) are markers of acinar cells, though also present at high abundance in other cell types.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:40345bd66e922fd61d9a
claim_id: claim:40345bd66e922fd61d9a
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
We hereby confirmed that aldehyde dehydrogenase 1A1 (ALDH1A1) and gelsolin (GSN) showed higher levels in alpha cells, and hydroxyacyl-coenzyme A dehydrogenase (HADH), ERO1-like protein beta (ERO1B), syntaxin-1A (STX1A) and neuroendocrine secretory protein 55 (GNAS) were higher in beta cells compared to other cell types.

summary:
In Homo sapiens pancreatic islets, aldehyde dehydrogenase 1A1 (ALDH1A1) and gelsolin (GSN) showed higher levels in alpha cells compared to other cell types.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:673679a155e449e4c0eb
claim_id: claim:673679a155e449e4c0eb
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
We hereby confirmed that aldehyde dehydrogenase 1A1 (ALDH1A1) and gelsolin (GSN) showed higher levels in alpha cells, and hydroxyacyl-coenzyme A dehydrogenase (HADH), ERO1-like protein beta (ERO1B), syntaxin-1A (STX1A) and neuroendocrine secretory protein 55 (GNAS) were higher in beta cells compared to other cell types.

summary:
In Homo sapiens pancreatic islets, hydroxyacyl-coenzyme A dehydrogenase (HADH), ERO1-like protein beta (ERO1B), syntaxin-1A (STX1A), and neuroendocrine secretory protein 55 (GNAS) were higher in beta cells compared to other cell types.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:4fd85ec96c705648f3de
claim_id: claim:4fd85ec96c705648f3de
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
while the calmodulin regulator protein PCP4 (PCP4) showed high abundance in delta cells, it was also highly abundant in beta cells.

summary:
In Homo sapiens pancreatic islets, calmodulin regulator protein PCP4 showed high abundance in delta cells, though it was also highly abundant in beta cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:236352d59f67a7a204e4
claim_id: claim:236352d59f67a7a204e4
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
Those include clusterin (CLU), sulfide quinone oxidoreductase (SQOR), aromatic-L-amino-acid decarboxylase (DDC), and dipeptidyl peptidase 4 (DPP4) for alpha cells; palmitoyl-protein thioesterase ABHD10 (ABHD10), ankyrin repeat and SOCS box protein 9 (ASB9), DNA dC->dU-editing enzyme APOBEC-2 (APOBEC2), Synaptic vesicular amine transporter (SLC18A2), carboxypeptidase E (CPE), ganglioside-induced differentiation-associated protein 1 (GDAP1), retinol dehydrogenase 14 (RDH14), cell adhesion molecule 1 (CADM1), complexin-2 (CPLX2), cytoplasmic glycerol-3-phosphate dehydrogenase (GPD1), alpha-1,3/1,6-mannosyltransferase ALG2 (ALG2), and golgi-resident adenosine 3’,5’-bisphosphate 3’-phosphatase (BPNT2) for beta cells; embryonal fyn-associated substrate (EFS) for delta cells; nesprin-2 (SYNE2), insulin-like growth factor-binding protein 7 (IGFBP7) and glutathione peroxidase 1 (GPX1) for gamma cells (Supplementary Figure 4).

summary:
In Homo sapiens pancreatic islets, clusterin (CLU), sulfide quinone oxidoreductase (SQOR), aromatic-L-amino-acid decarboxylase (DDC), and dipeptidyl peptidase 4 (DPP4) are markers for alpha cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:791502ca7219d4792dbb
claim_id: claim:791502ca7219d4792dbb
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
Those include clusterin (CLU), sulfide quinone oxidoreductase (SQOR), aromatic-L-amino-acid decarboxylase (DDC), and dipeptidyl peptidase 4 (DPP4) for alpha cells; palmitoyl-protein thioesterase ABHD10 (ABHD10), ankyrin repeat and SOCS box protein 9 (ASB9), DNA dC->dU-editing enzyme APOBEC-2 (APOBEC2), Synaptic vesicular amine transporter (SLC18A2), carboxypeptidase E (CPE), ganglioside-induced differentiation-associated protein 1 (GDAP1), retinol dehydrogenase 14 (RDH14), cell adhesion molecule 1 (CADM1), complexin-2 (CPLX2), cytoplasmic glycerol-3-phosphate dehydrogenase (GPD1), alpha-1,3/1,6-mannosyltransferase ALG2 (ALG2), and golgi-resident adenosine 3’,5’-bisphosphate 3’-phosphatase (BPNT2) for beta cells; embryonal fyn-associated substrate (EFS) for delta cells; nesprin-2 (SYNE2), insulin-like growth factor-binding protein 7 (IGFBP7) and glutathione peroxidase 1 (GPX1) for gamma cells (Supplementary Figure 4).

summary:
In Homo sapiens pancreatic islets, palmitoyl-protein thioesterase ABHD10, ankyrin repeat and SOCS box protein 9 (ASB9), DNA dC->dU-editing enzyme APOBEC-2 (APOBEC2), synaptic vesicular amine transporter (SLC18A2), carboxypeptidase E (CPE), ganglioside-induced differentiation-associated protein 1 (GDAP1), retinol dehydrogenase 14 (RDH14), cell adhesion molecule 1 (CADM1), complexin-2 (CPLX2), cytoplasmic glycerol-3-phosphate dehydrogenase (GPD1), alpha-1,3/1,6-mannosyltransferase ALG2, and golgi-resident adenosine 3',5'-bisphosphate 3'-phosphatase (BPNT2) are markers for beta cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:f2df3712ee0fb83bcde8
claim_id: claim:f2df3712ee0fb83bcde8
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
span_literal:
Those include clusterin (CLU), sulfide quinone oxidoreductase (SQOR), aromatic-L-amino-acid decarboxylase (DDC), and dipeptidyl peptidase 4 (DPP4) for alpha cells; palmitoyl-protein thioesterase ABHD10 (ABHD10), ankyrin repeat and SOCS box protein 9 (ASB9), DNA dC->dU-editing enzyme APOBEC-2 (APOBEC2), Synaptic vesicular amine transporter (SLC18A2), carboxypeptidase E (CPE), ganglioside-induced differentiation-associated protein 1 (GDAP1), retinol dehydrogenase 14 (RDH14), cell adhesion molecule 1 (CADM1), complexin-2 (CPLX2), cytoplasmic glycerol-3-phosphate dehydrogenase (GPD1), alpha-1,3/1,6-mannosyltransferase ALG2 (ALG2), and golgi-resident adenosine 3’,5’-bisphosphate 3’-phosphatase (BPNT2) for beta cells; embryonal fyn-associated substrate (EFS) for delta cells; nesprin-2 (SYNE2), insulin-like growth factor-binding protein 7 (IGFBP7) and glutathione peroxidase 1 (GPX1) for gamma cells (Supplementary Figure 4).

summary:
In Homo sapiens pancreatic islets, embryonal fyn-associated substrate (EFS) is a marker for delta cells.


claim_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022:claim:892715a405508f5a1c1f
claim_id: claim:892715a405508f5a1c1f
paper_key: biorxiv:10f6f17d-749e-1014-bdcf-fe1d1407f022
summary:
In Homo sapiens pancreatic islets, nesprin-2 (SYNE2), insulin-like growth factor-binding protein 7 (IGFBP7), and glutathione peroxidase 1 (GPX1) are markers for gamma cells.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:2b78de61caad6eb5d502
claim_id: claim:2b78de61caad6eb5d502
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
CD11c+CD14+ GVHD cells expressed common macrophage antigens (CD163, CD64 CD206 and CD209) but showed upregulation of monocyte-associated antigens (CD172a, S100A8/9, CD16

summary:
In Homo sapiens, CD11c+CD14+ graft versus host disease macrophages express common macrophage antigens CD163, CD64, CD206, and CD209, and show upregulation of monocyte-associated antigens CD172a, S100A8/9, and CD16.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:da3335713ceb30cbae5f
claim_id: claim:da3335713ceb30cbae5f
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
Nanostring gene expression analysis confirmed transcription of a core set of macrophage-related genes including MAF, MERTK, F13A1, CD163 and CD14.

summary:
In Homo sapiens, graft versus host disease macrophages express a core set of macrophage-related genes including MAF, MERTK, F13A1, CD163, and CD14.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:6bce07d5c1c27a34957f
claim_id: claim:6bce07d5c1c27a34957f
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
Additional staining demonstrated high expression of monocyte antigens S100A8/A9 and SIRPA (CD172), consistent with recent emigration of monocytes from the blood (35, 36).

summary:
In Homo sapiens, graft versus host disease macrophages show high expression of monocyte antigens S100A8/A9 and SIRPA, consistent with recent emigration of monocytes from the blood.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:ea6cd4b695555e831c25
claim_id: claim:ea6cd4b695555e831c25
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
Gene expression profiling of 2,000-5,000 sorted cells, revealed upregulation of allo-stimulatory functions included antigen presentation (HLA, TAP1), recruitment (CCL24) and stimulation of lymphocytes (CD82), stimulation of pro-inflammatory cytokines (SPP1), and leukocyte extravasation (SELPLG)

summary:
In Homo sapiens, graft versus host disease macrophages show upregulation of HLA, TAP1, CCL24, CD82, SPP1, and SELPLG compared with steady-state monocyte-derived macrophages.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:f0a894f321b1338a2ede
claim_id: claim:f0a894f321b1338a2ede
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
A donor-derived population of CD11c+CD14+ cells was the dominant population of all leukocytes in GVHD.

summary:
In Homo sapiens, a donor-derived population of CD11c+CD14+ macrophages was the dominant leukocyte population in graft versus host disease.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:a43840773de410d0a64d
claim_id: claim:a43840773de410d0a64d
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
In GVHD, however, there was upregulation of monocyte antigens SIRPα and S100A8/9, and transcripts associated with leukocyte trafficking, pattern recognition, antigen presentation, and co-stimulation.

summary:
In Homo sapiens, graft versus host disease macrophages show upregulation of monocyte antigens SIRPα and S100A8/9.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:819b7886912160f52d4b
claim_id: claim:819b7886912160f52d4b
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
MLR-activated macrophages also expressed cytotoxic molecules perforin, granzyme A, granulolysin and TRAIL, similarly to GVHD macrophages (Figure 5b-d).

summary:
In Homo sapiens, mixed leukocyte reaction-activated macrophages and graft versus host disease macrophages express cytotoxic molecules perforin, granzyme A, granulolysin, and TRAIL.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:830372e8a398eafa7640
claim_id: claim:830372e8a398eafa7640
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
MLR-activated macrophages also expressed cytotoxic molecules perforin, granzyme A, granulolysin and TRAIL, similarly to GVHD macrophages (Figure 5b-d).

summary:
In Homo sapiens, graft versus host disease macrophages express cytotoxic molecules perforin, granzyme A, granulolysin, and TRAIL.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:37df6e0f7f01abecee39
claim_id: claim:37df6e0f7f01abecee39
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
span_literal:
This GVHD-related subset lacked CD1c expression and mapped to parameter space containing monocyte-macrophages in the steady-state (25).

summary:
In Homo sapiens, the graft versus host disease-related CD11c+CD14+ macrophage subset lacks CD1c expression.


claim_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14:claim:94cc0c1844671d88e82a
claim_id: claim:94cc0c1844671d88e82a
paper_key: biorxiv:11b72b7e-6c1b-1014-84e4-aaf6df161d14
summary: In Homo sapiens, resident macrophages in the CD14+CD11c- gate express FXIIIA and CD163.
span_literal:
Cells in the CD14+ CD11c-gate contained FXIIIA+ CD163+ macrophages with high melanin content and auto-fluorescence, representing ‘fixed’ or resident macrophages (22, 29, 30).


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:91e8328fb07b6c834dc5
claim_id: claim:91e8328fb07b6c834dc5
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: Th1 classic: CD3+CD4+CxCR3+CCR6-CD161-
summary:
In Homo sapiens, classic T helper 1 cells are positive for CD3, CD4, and CXCR3, and negative for CCR6 and CD161.


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:632b7953278872614c77
claim_id: claim:632b7953278872614c77
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: Th17: CD3+CD4+CxCR3+CCR6-CD161+CCR4+
summary:
In Homo sapiens, Th17 cells are positive for CD3, CD4, CXCR3, CD161, and CCR4, and negative for CCR6.


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:4aec6eabc20af57aead5
claim_id: claim:4aec6eabc20af57aead5
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: Th1/17: CD3+CD4+CCR6-CD161+CxCR3highCCR4low
summary:
In Homo sapiens, Th1/17 cells are positive for CD3, CD4, CD161, and CXCR3, negative for CCR6, and low for CCR4.


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:ab8e594829f79e4fb7bd
claim_id: claim:ab8e594829f79e4fb7bd
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: CD3+CD8+: T reg CD28-and T naive CD28-CD45RA+
summary:
In Homo sapiens, CD8-positive regulatory T cells are positive for CD3 and CD8 and negative for CD28.


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:c67969fc98d86cba7b1a
claim_id: claim:c67969fc98d86cba7b1a
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: CD3+CD8+: T reg CD28-and T naive CD28-CD45RA+
summary:
In Homo sapiens, CD8-positive naive T cells are positive for CD3, CD8, and CD45RA, and negative for CD28.


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:6d6b9b3f8939d6eab194
claim_id: claim:6d6b9b3f8939d6eab194
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: B mature: CD19+CD14-CD24+CD38low
summary:
In Homo sapiens, mature B cells are positive for CD19 and CD24, negative for CD14, and low for CD38.


claim_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed:claim:02b728736f9ea0f57884
claim_id: claim:02b728736f9ea0f57884
paper_key: biorxiv:1219c420-6c6a-1014-afb9-e13c88e111ed
span_literal: NK cells: Effector: CD3-CD14-CD56dim: Regulatory: CD3-CDCD56bright (reg)
summary:
In Homo sapiens, effector natural killer cells are negative for CD3 and CD14 and dim for CD56, while regulatory natural killer cells are negative for CD3 and bright for CD56.


claim_key: biorxiv:13c39b66-72f2-1014-9c8c-e313c291b504:claim:92d24f868ad7dbf95758
claim_id: claim:92d24f868ad7dbf95758
paper_key: biorxiv:13c39b66-72f2-1014-9c8c-e313c291b504
span_literal: all the cell lines demonstrated strong expression of the pericyte marker COX4I2
summary:
In Homo sapiens kidney, COX4I2 is a positive marker of pericytes, as defined by single-cell RNA sequencing analysis of human adult kidney samples.


claim_key: biorxiv:15360e56-7361-1014-9683-c96cb33ab32f:claim:a3657569959e329e2a2a
claim_id: claim:a3657569959e329e2a2a
paper_key: biorxiv:15360e56-7361-1014-9683-c96cb33ab32f
summary: In Homo sapiens, neuroprotective A2 reactive astrocytes express S100A10 as a specific marker.
span_literal:
Reactive astrocytes express specific markers (S100A10 for A2 astrocytes, complement 3 for A1 astrocytes) allowing their identification35, 36.


claim_key: biorxiv:15360e56-7361-1014-9683-c96cb33ab32f:claim:929aef98f4a41ffe0b00
claim_id: claim:929aef98f4a41ffe0b00
paper_key: biorxiv:15360e56-7361-1014-9683-c96cb33ab32f
span_literal:
We next investigated the effect of infection on astrogliosis by measurement of the expression of complement 3 (C3, a neurotoxic reactive astrocyte marker) and S100A10 (a neuroprotective marker).

summary:
In Homo sapiens, complement 3 (C3) is a marker of neurotoxic reactive astrocytes, and S100A10 is a marker of neuroprotective reactive astrocytes.


claim_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e:claim:5f413e25e21318b62e44
claim_id: claim:5f413e25e21318b62e44
paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
span_literal:
A MRC2high HSC subtype was identified in human (Figure S4D-S4F). MRC2high HSCs also exhibited enrichment of apoptosis-related terms, p53 signaling pathway activation, and high expression of orthologous activation suppressors (WT1, GATA6, NR4A1, and NR4A2)

summary:
In Homo sapiens, MRC2-high hepatic stellate cells exhibit high expression of WT1, GATA6, NR4A1, and NR4A2, which are activation suppressors, along with enrichment of apoptosis-related pathways and p53 signaling pathway activation.


claim_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e:claim:5b82247087b5e1d9bcbb
claim_id: claim:5b82247087b5e1d9bcbb
paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
span_literal:
Immunofluorescence staining of human liver tissue confirmed MRC2-positive or WT1-positive HSCs significantly co-expressed p53

summary:
In Homo sapiens, MRC2-positive hepatic stellate cells significantly co-express p53 protein, as confirmed by immunofluorescence staining of human liver tissue. In Homo sapiens, WT1-positive hepatic stellate cells significantly co-express p53 protein, as confirmed by immunofluorescence staining of human liver tissue.


claim_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e:claim:2acebb01b00c4b282cbd
claim_id: claim:2acebb01b00c4b282cbd
paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
span_literal:
The abundance of S100a6high and Acta2high aHSCs correlated with fibrosis severity and effectively discriminated F3 and F4 from F0-F2 patients.

summary:
In Homo sapiens, the abundance of S100A6-high activated hepatic stellate cells correlated with fibrosis severity and effectively discriminated advanced fibrosis from early fibrosis stages.


claim_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e:claim:76ea6f8eeba0661c3d4a
claim_id: claim:76ea6f8eeba0661c3d4a
paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
span_literal:
The abundance of S100a6high and Acta2high aHSCs correlated with fibrosis severity and effectively discriminated F3 and F4 from F0-F2 patients.

summary:
In Homo sapiens, the abundance of ACTA2-high activated hepatic stellate cells correlated with fibrosis severity and effectively discriminated advanced fibrosis from early fibrosis stages.


claim_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e:claim:434875de82686fdb3bf7
claim_id: claim:434875de82686fdb3bf7
paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
span_literal:
Flow cytometry analysis revealed that each of HBP1, TBX20, ATOH8, and PLAGL1 significantly promoted the apoptosis of LX-2 cells, showing more than a two-fold change increase relative to the empty vector

summary:
In Homo sapiens, overexpression of HBP1, TBX20, ATOH8, and PLAGL1 significantly promoted apoptosis of LX-2 hepatic stellate cells.


claim_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e:claim:991b749a87f2533a9748
claim_id: claim:991b749a87f2533a9748
paper_key: biorxiv:166eb232-7528-1014-af8e-ff8db1c08d2e
span_literal:
Notably, none of these four TFs increased COL1A1 or COL3A1 expression, and PLAGL1 even suppressed collagen levels

summary:
In Homo sapiens, PLAGL1 overexpression suppressed COL1A1 and COL3A1 collagen expression in LX-2 hepatic stellate cells.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:aff2cffae758f7297cc8
claim_id: claim:aff2cffae758f7297cc8
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical MSN markers were conserved across species, with DRD1 and TAC1 enriched in D1 MSNs, DRD2 and PENK enriched in D2 MSNs, and RXFP1 marking eccentric MSNs

summary:
In Homo sapiens, D1 medium spiny neurons in the basal ganglia are marked by enriched expression of DRD1 and TAC1.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:ea9a4622655802bbffec
claim_id: claim:ea9a4622655802bbffec
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical MSN markers were conserved across species, with DRD1 and TAC1 enriched in D1 MSNs, DRD2 and PENK enriched in D2 MSNs, and RXFP1 marking eccentric MSNs

summary:
In Homo sapiens, D2 medium spiny neurons in the basal ganglia are marked by enriched expression of DRD2 and PENK.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:14bd92a81067f924b3ad
claim_id: claim:14bd92a81067f924b3ad
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical MSN markers were conserved across species, with DRD1 and TAC1 enriched in D1 MSNs, DRD2 and PENK enriched in D2 MSNs, and RXFP1 marking eccentric MSNs

summary:
In Homo sapiens, eccentric medium spiny neurons in the basal ganglia are marked by RXFP1 expression.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:14d59834c259ca2bd64d
claim_id: claim:14d59834c259ca2bd64d
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical primate markers of both striosome and matrix MSNs, including KCNIP1 and STXBP6, were co-expressed, alongside shared expression of COCH with classical D1 and D2 MSNs and selective sharing of KCNT2 with eccentric MSNs, but notably lacking expression of the eccentric marker RXFP1

summary:
In Homo sapiens, the STRd D2 StrioMat Hybrid medium spiny neuron co-expresses the striosome and matrix markers KCNIP1 and STXBP6, shares COCH expression with classical D1 and D2 medium spiny neurons, shares KCNT2 with eccentric medium spiny neurons, but lacks expression of the eccentric marker RXFP1.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:6a09e91ebd124c1090a8
claim_id: claim:6a09e91ebd124c1090a8
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal: Expression of SMYD2 was selectively enriched in this population
summary:
In Homo sapiens, SMYD2 expression is selectively enriched in the STRd D2 StrioMat Hybrid medium spiny neuron population.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:7a81ce9218a9716d28c4
claim_id: claim:7a81ce9218a9716d28c4
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
TBR1 and ONECUT1 separated GPi core and shell neurons, each defining transcriptomic and spatially coherent populations

summary:
In Homo sapiens, TBR1 and ONECUT1 distinguish globus pallidus internus core neuron from globus pallidus internus shell neuron populations.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:04de0ad68d2fddba435b
claim_id: claim:04de0ad68d2fddba435b
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
TBR1 and ONECUT1 separated GPi core and shell neurons, each defining transcriptomic and spatially coherent populations

summary:
In Homo sapiens, TBR1 and ONECUT1 distinguish globus pallidus internus shell neuron from globus pallidus internus core neuron populations.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:ece87ab8f31b2576838c
claim_id: claim:ece87ab8f31b2576838c
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Enrichment of DPF3, which shapes Group-specific enhancer landscapes, together with PRDM8, a determinant of GABAergic Group identity, suggests that TAC-expressing interneurons are defined by a distinct regulatory architecture not shared with other BG interneurons.

summary:
In Homo sapiens, TAC-expressing interneurons in the basal ganglia are marked by enrichment of DPF3 and PRDM8.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:f5f6b829fb907f67ac57
claim_id: claim:f5f6b829fb907f67ac57
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Dopaminergic neurons were partitioned into SN SOX6, SN-VTR GAD2, and SN-VTR CALB1 Groups, characterized by divergent TF signatures including TWIST1, POU3F2, and EN1.

summary:
In Homo sapiens, dopaminergic neuron groups in the substantia nigra, including SN SOX6, SN-VTR GAD2, and SN-VTR CALB1, are characterized by transcription factor signatures including TWIST1, POU3F2, and EN1.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:3f4fd1b113d9b0ac1321
claim_id: claim:3f4fd1b113d9b0ac1321
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical regulators such as BCL11B marked the LGE-derived MSNs while RARB and POU3F1 distinguished ventral and eccentric MSNs

summary:
In Homo sapiens, BCL11B marks lateral ganglionic eminence-derived medium spiny neurons, while RARB and POU3F1 distinguish ventral and eccentric medium spiny neurons.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:1b92803d96feb4a38ea8
claim_id: claim:1b92803d96feb4a38ea8
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical regulators such as BCL11B marked the LGE-derived MSNs while RARB and POU3F1 distinguished ventral and eccentric MSNs

summary:
In Homo sapiens, RARB and POU3F1 distinguish ventral medium spiny neurons from other medium spiny neuron populations.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:8d1d5efa87912e961d1d
claim_id: claim:8d1d5efa87912e961d1d
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
Canonical regulators such as BCL11B marked the LGE-derived MSNs while RARB and POU3F1 distinguished ventral and eccentric MSNs

summary:
In Homo sapiens, RARB and POU3F1 distinguish eccentric medium spiny neurons from other medium spiny neuron populations.


claim_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67:claim:b7122f44efcd814ea50e
claim_id: claim:b7122f44efcd814ea50e
paper_key: biorxiv:1819420a-7028-1014-9d82-b8532c727b67
span_literal:
OB Dopa-GABA shares PAX6, TH, SCGN, and SP8 markers with previously identified STR laureatum neurons

summary:
In Homo sapiens, OB Dopa-GABA neurons share the markers PAX6, TH, SCGN, and SP8 with previously identified striatum laureatum neurons.


claim_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496:claim:090bf26d469bd4336e75
claim_id: claim:090bf26d469bd4336e75
paper_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496
span_literal:
Further clustering of an SMC cluster (marker: ACTA2) in the previous study identified three subclusters; ACTA2-expressing cluster as myofibroblasts (MFBs), CNN1-expressing cluster as SMCs, and RGS5- and LBH-expressing clusters as pericytes (Fig. 5B and Supplementary Fig. 12A-B).

summary:
In Homo sapiens corpus cavernosum, ACTA2 is a marker of myofibroblasts, CNN1 is a marker of smooth muscle cells, and RGS5 and LBH (Limb-bud and Heart) are markers of pericytes.


claim_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496:claim:d4c0c7cac2f15bcbbe9a
claim_id: claim:d4c0c7cac2f15bcbbe9a
paper_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496
span_literal:
Further clustering of an SMC cluster (marker: ACTA2) in the previous study identified three subclusters; ACTA2-expressing cluster as myofibroblasts (MFBs), CNN1-expressing cluster as SMCs, and RGS5- and LBH-expressing clusters as pericytes (Fig. 5B and Supplementary Fig. 12A-B).

summary:
In Homo sapiens corpus cavernosum, CNN1 is a marker of smooth muscle cells, distinguishing them from myofibroblasts and pericytes.


claim_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496:claim:f784cf5080a3f8beb0ab
claim_id: claim:f784cf5080a3f8beb0ab
paper_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496
summary: In Homo sapiens corpus cavernosum, LBH (Limb-bud and Heart) is a marker of pericytes.
span_literal:
The newly identified pericyte marker, LBH is also a marker of pericytes in the human corpus cavernosum, and LBH expression was significantly reduced in human cavernous tissues from patients with diabetes-induced ED compared to age-matched controls (Fig. 5D, F).


claim_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496:claim:f8f16db1e2211e562a78
claim_id: claim:f8f16db1e2211e562a78
paper_key: biorxiv:1898c531-75b0-1014-a18a-e291a49d1496
span_literal:
LBH was identified as a pericyte-positive and SMC-negative marker that was also highly expressed in human cavernous pericytes (Fig. 5) and was validated through IF staining in many vascular tissues and cell types (Fig. 2).

summary:
In Homo sapiens, LBH (Limb-bud and Heart) is a positive marker of pericytes and a negative marker of smooth muscle cells in cavernous tissue.


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:d559933744ecaab43e48
claim_id: claim:d559933744ecaab43e48
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal:
VSMC) contractility controls vessel tone, but the cells display a remarkable phenotypic plasticity characterized by downregulation of the contractile machinery (e.g. MYH11, ACTA2 and CNN1), concomitant increased expression of extracellular matrix (ECM) components (e.g. Matrix gla protein, MGP

summary:
In Homo sapiens, vascular smooth muscle cells undergoing phenotypic switching show downregulation of MYH11, ACTA2, and CNN1 (contractile markers) and increased expression of MGP (extracellular matrix marker).


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:fa592c72ebaf2b9a6893
claim_id: claim:fa592c72ebaf2b9a6893
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal:
Most cells expressed a contractile MYH11+ signature, consistent with the absence of signs of vascular disease, but reduced levels of contractile genes were observed in cell cluster 3 and a subset of cells in cluster 0.

summary:
In Homo sapiens, most medial vascular smooth muscle cells from healthy aorta express a contractile MYH11-positive signature.


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:888633f0b242b4c93dd8
claim_id: claim:888633f0b242b4c93dd8
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal:
Anti-correlating with MYH11, gradually higher expression of COL8A1, MGP and other synthetic genes was detected through clusters 2, 0 and 3, suggesting that different extents of phenotypic switching exist in human vessels

summary:
In Homo sapiens, vascular smooth muscle cells undergoing phenotypic switching in healthy vessels show increased expression of COL8A1 and MGP, anti-correlating with MYH11.


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:90a4bec0e0af27621d10
claim_id: claim:90a4bec0e0af27621d10
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal:
Transcripts for orthologues of injury-induced proliferation-associated genes, including FBLN2 and LUM, were also detected in Cluster 0 and 3

summary:
In Homo sapiens, phenotypically switched vascular smooth muscle cells in healthy aorta (clusters 0 and 3) express FBLN2 and LUM.


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:c7de70f357d17f48417b
claim_id: claim:c7de70f357d17f48417b
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal:
pseudotime-induced genes included growth factor binding proteins (LTBP2, HTRA1) and CXCL12 that encodes stromal cell-derived factor 1 (SDF1) and is linked genetically to cardiovascular disease

summary:
In Homo sapiens, primed vascular smooth muscle cells in healthy arteries show pseudotime-induced expression of LTBP2, HTRA1, and CXCL12 (encoding stromal cell-derived factor 1).


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:3b3b7a5697b77eace6cd
claim_id: claim:3b3b7a5697b77eace6cd
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal: Importantly, FBLN2 was detected in αSMA-stained cells in human carotid artery plaques
summary:
In Homo sapiens, FBLN2 is expressed in alpha-smooth muscle actin-positive vascular smooth muscle cells in carotid artery plaques.


claim_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72:claim:548ed4ac13da104b8f73
claim_id: claim:548ed4ac13da104b8f73
paper_key: biorxiv:1b938bfc-6db4-1014-bcdd-aff1924d9f72
span_literal:
of the 23 genes associated with the SNP-27 coronary artery disease risk score panel38 that were included in our dataset, 11 showed differential expression along the trajectory; including TCF21, CXCL12 and ADAMTS7

summary:
In Homo sapiens, primed vascular smooth muscle cells in healthy arteries show differential expression of coronary artery disease-associated genes including TCF21, CXCL12, and ADAMTS7 along the pseudotime trajectory.


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:7b08a0dd6d33f3bff2a2
claim_id: claim:7b08a0dd6d33f3bff2a2
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
span_literal:
Most control NPCs expressed transcription factors involved in NPC maintenance and identity such as POU3F1, SOX21, LHX5, and HES5 (Figure 3E, 4C).

summary:
In Homo sapiens, neural progenitor cells express POU3F1, SOX21, LHX5, and HES5 as markers of neural progenitor cell maintenance and identity.


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:560857764c2b10f96cb7
claim_id: claim:560857764c2b10f96cb7
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
span_literal:
Similarly, control NPCs expressed CDH8, a cell surface marker of neurogenic progenitors in the developing brain37 (Figure 3F).

summary:
In Homo sapiens, neurogenic progenitor cells in the developing brain express CDH8 as a cell surface marker.


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:e62a6b8b803e49c13512
claim_id: claim:e62a6b8b803e49c13512
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
summary: In Homo sapiens, CDH6 is a marker of gliogenic progenitor cells.
span_literal:
Most BRG1KD NPCs lacked CDH8 expression and instead expressed CDH6, a marker of gliogenic progenitors (Figure 3F)37.


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:b7a54cc2eebc46701289
claim_id: claim:b7a54cc2eebc46701289
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
summary: In Homo sapiens, neural crest cells are marked by expression of FOXD3, TFAP2B, and NGFR.
span_literal:
Indeed, markers of neural crest cells such as FOXD3, TFAP2B, and NGFR were strongly enriched in cluster 5 (Figure 4E).


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:eafacefdc73a3375415e
claim_id: claim:eafacefdc73a3375415e
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
summary: In Homo sapiens, SOX10 is a marker of neural crest-derived lineage cells.
span_literal:
A subset of cluster 5 cells were also enriched for SOX10, a marker of further neural crest-derived lineages (Figure 4E).


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:87d0da4946ca100f314c
claim_id: claim:87d0da4946ca100f314c
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
summary: In Homo sapiens, MITF is a marker gene of melanocytes and MPZ is a marker gene of Schwann cells.
span_literal:
Strikingly, some BRG1KD cells in cluster 5 also expressed MITF and MPZ, marker genes of melanocytes and Schwann cells, respectively (Figure 4F).


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:9e3c940e7f03e2dcb2c7
claim_id: claim:9e3c940e7f03e2dcb2c7
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
summary: In Homo sapiens, neuronal lineage cells are marked by expression of NHLH1, STMN2, and ELAVL3.
span_literal:
Both clusters were specifically enriched for a variety of neuronal lineage markers such as NHLH1, STMN2, and ELAVL3 (Figure S4C).


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:0e694a68d10aa5da64cc
claim_id: claim:0e694a68d10aa5da64cc
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
summary: In Homo sapiens, ciliated cells are marked by expression of CCNO, CDC20B, and RSPH1.
span_literal:
Comprised of 88 day 9 and 2 day 6 cells, this cluster was uniquely enriched for markers of cilia development and morphogenesis such as CCNO, CDC20B, RSPH1, and several genes in the CFAP family (Figure S5A, B).


claim_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510:claim:b74fed52790e6298ebe5
claim_id: claim:b74fed52790e6298ebe5
paper_key: biorxiv:1d26f338-6e4a-1014-b712-c54808557510
span_literal:
A neural crest cell population marked by expression of the transcription factors SOX10, FOXD3, ETS1, and TFAP2A/B/C also arose from BRG1-depleted NPCs.

summary:
In Homo sapiens, neural crest cells are marked by expression of the transcription factors SOX10, FOXD3, ETS1, TFAP2A, TFAP2B, and TFAP2C.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:960cd187f4d3704561b3
claim_id: claim:960cd187f4d3704561b3
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
Most of the top DEGs for SSA+SjD were ISGs with the most frequently upregulated DEGs being IFI44L, IFI27, and MX1, which are markers of IFN-I response.

summary:
In Homo sapiens, IFI44L, IFI27, and MX1 are markers of type I interferon response, upregulated across cell types in SSA-positive Sjögren's disease peripheral blood mononuclear cells.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:15f730ebb172c407ec8e
claim_id: claim:15f730ebb172c407ec8e
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
Unsupervised B cell clustering identified 23 populations, revealing significant diversity within transitional B cells, which were defined by canonical markers (IGHD, CD24, CD38) and the expression of the pre-BCR component VPREB3

summary:
In Homo sapiens, transitional B cells are defined by canonical markers IGHD, CD24, CD38, and expression of the pre-B cell receptor component VPREB3.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:e114b9f04d3e88e2db80
claim_id: claim:e114b9f04d3e88e2db80
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
Four monocyte populations were significantly enriched in SSA+SjD specimens, exhibiting high ISG expression (ISG15, IFI6, IFI44L, MX1, MX2) compared to all other cell clusters: ISG+ AP1low classical monocytes (4.1-fold increase compared to SjD-, pfdr=6e-52)), ISG+ AP1 high classical monocytes (2.9-fold increase compared to SjD-, pfdr=9e-20), HLA-DR-high intermediate monocytes, and ISG+ non-classical monocytes (3.3-fold increase compared to SjD-, pfdr=9e-27)

summary:
In Homo sapiens, interferon-stimulated gene-positive classical monocytes exhibit high expression of ISG15, IFI6, IFI44L, MX1, and MX2.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:a65fd92804529162cd0b
claim_id: claim:a65fd92804529162cd0b
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
Four monocyte populations were significantly enriched in SSA+SjD specimens, exhibiting high ISG expression (ISG15, IFI6, IFI44L, MX1, MX2) compared to all other cell clusters: ISG+ AP1low classical monocytes (4.1-fold increase compared to SjD-, pfdr=6e-52)), ISG+ AP1 high classical monocytes (2.9-fold increase compared to SjD-, pfdr=9e-20), HLA-DR-high intermediate monocytes, and ISG+ non-classical monocytes (3.3-fold increase compared to SjD-, pfdr=9e-27)

summary:
In Homo sapiens, interferon-stimulated gene-positive AP1 high classical monocytes exhibit high expression of ISG15, IFI6, IFI44L, MX1, and MX2.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:41bbc381605f5ddec958
claim_id: claim:41bbc381605f5ddec958
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
Four monocyte populations were significantly enriched in SSA+SjD specimens, exhibiting high ISG expression (ISG15, IFI6, IFI44L, MX1, MX2) compared to all other cell clusters: ISG+ AP1low classical monocytes (4.1-fold increase compared to SjD-, pfdr=6e-52)), ISG+ AP1 high classical monocytes (2.9-fold increase compared to SjD-, pfdr=9e-20), HLA-DR-high intermediate monocytes, and ISG+ non-classical monocytes (3.3-fold increase compared to SjD-, pfdr=9e-27)

summary:
In Homo sapiens, interferon-stimulated gene-positive non-classical monocytes exhibit high expression of ISG15, IFI6, IFI44L, MX1, and MX2.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:97e3a8cc7604551eb288
claim_id: claim:97e3a8cc7604551eb288
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal: ISG+ GZMK+ effector memory CD8+ T cells upregulating IFIT1, IFIT2, IFIT3, ISG15, and OASL
summary:
In Homo sapiens, interferon-stimulated gene-positive GZMK-positive effector memory CD8-positive T cells upregulate IFIT1, IFIT2, IFIT3, ISG15, and OASL.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:4a50ff5306db62501019
claim_id: claim:4a50ff5306db62501019
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
ISG+ naive CD4+ T cells (3.2-fold increase in abundance compared to SjD-) upregulating IFI44L, IFI6, and ISG15

summary:
In Homo sapiens, interferon-stimulated gene-positive naive CD4-positive T cells upregulate IFI44L, IFI6, and ISG15.


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:63cdd168b4886ae9aec6
claim_id: claim:63cdd168b4886ae9aec6
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
apart from the ISG-enriched monocyte populations, most other monocyte subsets were decreased in SSA+SjD samples, regardless of their polarization as M1 (CD163-, pro-inflammatory) or M2 (CD163+, anti-inflammatory)

summary:
In Homo sapiens, M1 monocytes are CD163-negative (pro-inflammatory) and M2 monocytes are CD163-positive (anti-inflammatory).


claim_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616:claim:ea33117e89aab2be0dea
claim_id: claim:ea33117e89aab2be0dea
paper_key: biorxiv:1e0a6787-73c3-1014-991b-bc3d9c192616
span_literal:
Previous studies have reported an increased proportion of transitional B cells in SjD 51–53, but these analyses were limited in power and primarily defined transitional B cells based on surface markers (CD27-CD24highCD38high), mainly capturing the T2 stage of development.

summary:
In Homo sapiens, transitional B cells are defined by surface markers CD27-negative, CD24 high, and CD38 high.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:be2a40abd6afca45ef92
claim_id: claim:be2a40abd6afca45ef92
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal: Cells in cluster 2 were predominately CD45RA+ and expressed high levels of granzyme B
summary:
In Homo sapiens, CD8+ T cells in cluster 2 are characterized by CD45RA and high expression of granzyme B.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:00d81099cc3bc60e9568
claim_id: claim:00d81099cc3bc60e9568
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
summary: In Homo sapiens, CD8+ T cell cluster 3 is characterized by high levels of CD28, CD127, and TCF-1.
span_literal:
Cluster 3 was present in the circulating and tumor compartments and was comprised of heterogenous PD-1− and PD-1dim cells with high levels of CD28, CD127, and TCF-1


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:3bbbbd61784e333ba76d
claim_id: claim:3bbbbd61784e333ba76d
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cells in clusters 4 and 5 both expressed CD69, consistent with tissue residence and their predominance in the tumor

summary:
In Homo sapiens, CD8+ T cells in cluster 4 express CD69, consistent with tissue residence in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:b515fb2f37855ff66e27
claim_id: claim:b515fb2f37855ff66e27
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cells in clusters 4 and 5 both expressed CD69, consistent with tissue residence and their predominance in the tumor

summary:
In Homo sapiens, CD8+ T cells in cluster 5 express CD69, consistent with tissue residence in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:71d3429c20c2a12be885
claim_id: claim:71d3429c20c2a12be885
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cells in both clusters 4 and 5 also expressed CD38 and were low for TCF-1 and CD127; expression of these latter two markers on CD8+ T cells within the tumor was primarily restricted to cluster 3, a cluster shared between the tumor and circulating compartments

summary:
In Homo sapiens, CD8+ T cells in cluster 4 express CD38 and have low expression of TCF-1 and CD127 in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:51e9c6c6bcdc5ea20733
claim_id: claim:51e9c6c6bcdc5ea20733
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cells in both clusters 4 and 5 also expressed CD38 and were low for TCF-1 and CD127; expression of these latter two markers on CD8+ T cells within the tumor was primarily restricted to cluster 3, a cluster shared between the tumor and circulating compartments

summary:
In Homo sapiens, CD8+ T cells in cluster 5 express CD38 and have low expression of TCF-1 and CD127 in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:d0cf3ad2ed65a3abb972
claim_id: claim:d0cf3ad2ed65a3abb972
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cluster 5 appears to be an exhausted, terminally-differentiated population of CD8+ T cells, expressing PD-1 as well as other co-inhibitory molecules including CTLA-4, CD39 and TIM-3

summary:
In Homo sapiens, terminally-differentiated exhausted CD8+ T cells (cluster 5) express PD-1, CTLA-4, CD39, and TIM-3 in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:bf6bf9d77753278fd899
claim_id: claim:bf6bf9d77753278fd899
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal: Most cells in cluster 5 also expressed TOX and were TCF-1−
summary:
In Homo sapiens, most terminally-differentiated CD8+ T cells (cluster 5) express TOX and lack TCF-1 expression in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:48d7a7e14adfdef43e3d
claim_id: claim:48d7a7e14adfdef43e3d
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cells in cluster 6 are dividing (KI-67+) and express activation markers such as HLA-DR and CD38, as well as exhaustion markers such as PD-1

summary:
In Homo sapiens, dividing CD8+ T cells (cluster 6) express KI-67, HLA-DR, CD38, and PD-1 in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:8bf40322fd496cf19479
claim_id: claim:8bf40322fd496cf19479
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal: Cluster 6 cells express CD28 but low levels of TCF-1 and CD127
summary:
In Homo sapiens, dividing CD8+ T cells (cluster 6) express CD28 but have low levels of TCF-1 and CD127 in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:5f47af448a4dfd847930
claim_id: claim:5f47af448a4dfd847930
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Tumor-infiltrating PD-1+ CD8+ T cells in metaclusters A and D had a terminally-differentiated phenotype similar to that of FlowSOM cluster 5, characterized by high expression of genes encoding co-inhibitory molecules such as CTLA4, ENTPD1 (CD39), HAVCR2 (TIM-3), and LAG3, consistent with this population containing tumor-reactive cells

summary:
In Homo sapiens, terminally-differentiated PD-1+ CD8+ T cells (metaclusters A and D) in brain metastases are characterized by high expression of CTLA4, ENTPD1 (CD39), HAVCR2 (TIM-3), and LAG3.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:dde299c93f6604f4213a
claim_id: claim:dde299c93f6604f4213a
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Cells in the Dividing metacluster were additionally defined by high expression of cell cycle genes, such as MKI67 (KI-67) and TOP2A

summary:
In Homo sapiens, dividing PD-1+ CD8+ T cells (Dividing metacluster) in brain metastases are defined by high expression of MKI67 (KI-67) and TOP2A.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:ef3412d6abeb9f9e9d39
claim_id: claim:ef3412d6abeb9f9e9d39
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
They were distinguished from each other by higher expression of tissue residence genes, such as CD69, in metacluster C

summary:
In Homo sapiens, PD-1+ CD8+ T cells in metacluster C are distinguished from metacluster B by higher expression of the tissue residence gene CD69 in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:0deb22208e657f75bc5e
claim_id: claim:0deb22208e657f75bc5e
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Together, metaclusters B and C contained PD-1+ CD8+ T cells with higher expression of the progenitor markers TCF7 (TCF-1) and IL7R (CD127) compared to terminally-differentiated and dividing cells.

summary:
In Homo sapiens, PD-1+ CD8+ T cells in metaclusters B and C express higher levels of the progenitor markers TCF7 (TCF-1) and IL7R (CD127) compared to terminally-differentiated and dividing cells in brain metastases.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:2e99c5219b562fe1c391
claim_id: claim:2e99c5219b562fe1c391
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
Importantly, some of these experimentally-validated bystander cells had a transcriptional phenotype similar to tumor-specific progenitor PD-1+ CD8+ T cells characterized in other studies,41 marked by expression of IL7R (CD127), TOX, and TCF7 (TCF-1)

summary:
In Homo sapiens, bystander CD8+ T cells infiltrating brain metastases express IL7R (CD127), TOX, and TCF7 (TCF-1), resembling tumor-specific progenitor PD-1+ CD8+ T cells.


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:00ee30a02cd30b8bae99
claim_id: claim:00ee30a02cd30b8bae99
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
expression of genes associated with the terminally-differentiated phenotype of CD8+ T cells such as HAVCR2 (TIM-3), LAG3, CXCL13 and GZMB, was highest in the tumor parenchyma adjacent to inflammation, while expression of the progenitor markers TCF7 (TCF-1) and IL7R (CD127) was highest in the inflammatory stroma suggesting that immune cell phenotype determines its location within the diverse TME

summary:
In Homo sapiens, terminally-differentiated CD8+ T cells in brain metastases express HAVCR2 (TIM-3), LAG3, CXCL13, and GZMB, while progenitor-like CD8+ T cells express TCF7 (TCF-1) and IL7R (CD127).


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:b91bb542131d12159db8
claim_id: claim:b91bb542131d12159db8
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
expression of genes associated with the terminally-differentiated phenotype of CD8+ T cells such as HAVCR2 (TIM-3), LAG3, CXCL13 and GZMB, was highest in the tumor parenchyma adjacent to inflammation, while expression of the progenitor markers TCF7 (TCF-1) and IL7R (CD127) was highest in the inflammatory stroma suggesting that immune cell phenotype determines its location within the diverse TME

summary:
In Homo sapiens, progenitor-like CD8+ T cells in brain metastases express the progenitor markers TCF7 (TCF-1) and IL7R (CD127).


claim_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad:claim:6df004c61e58485d9de7
claim_id: claim:6df004c61e58485d9de7
paper_key: biorxiv:1e500b21-6c04-1014-adde-c104b14bbdad
span_literal:
bystander CD8+ T cells specific for microbial antigens; these cells infiltrated brain metastases and expressed genes shared with exhausted progenitor CD8+ T cells, such as TCF7 and IL7R

summary:
In Homo sapiens, bystander CD8+ T cells specific for microbial antigens infiltrate brain metastases and express TCF7 and IL7R, genes shared with exhausted progenitor CD8+ T cells.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:dec06a22ffac4fc507b1
claim_id: claim:dec06a22ffac4fc507b1
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
Interleukin-receptor (IL-R) markers dominated this ratio, CD127 (IL7Rα), CD123 (IL3Rα) (IL-R triad, IL-RT), and CD25 (IL2Rα), with CD25 particularly highlighting TeLEV-positive monocytes and mDCs, including IL-RT positive cells (Figure S2).

summary:
In Homo sapiens, CD25 (interleukin-2 receptor alpha) is a marker highlighting malignant B-cell-derived extracellular vesicle-positive monocytes distinguished from matched secreted protein recipient cells.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:c5cba402d198882d3c5d
claim_id: claim:c5cba402d198882d3c5d
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
Interleukin-receptor (IL-R) markers dominated this ratio, CD127 (IL7Rα), CD123 (IL3Rα) (IL-R triad, IL-RT), and CD25 (IL2Rα), with CD25 particularly highlighting TeLEV-positive monocytes and mDCs, including IL-RT positive cells (Figure S2).

summary:
In Homo sapiens, CD25 (interleukin-2 receptor alpha), CD127 (interleukin-7 receptor alpha), and CD123 (interleukin-3 receptor alpha) are markers highlighting malignant B-cell-derived extracellular vesicle-positive myeloid dendritic cells.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:614bb7bb38484efeb533
claim_id: claim:614bb7bb38484efeb533
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
Some IL-RT-positive monocytes also showed increased CD197 expression, indicating a transition toward a monocyte-derived dendritic cell-like state.

summary:
In Homo sapiens, interleukin receptor triad-positive monocytes showing increased CD197 expression indicate a transition toward a monocyte-derived dendritic cell-like state.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:ec5061a82b4f907de847
claim_id: claim:ec5061a82b4f907de847
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
These cells had lower HLA-DR than conventional myeloid dendritic cells, reduced CD14, and lacked CD183 (CXCR3)30.

summary:
In Homo sapiens, monocyte-derived dendritic cell-like cells had lower HLA-DR than conventional myeloid dendritic cells, reduced CD14, and lacked CD183 (CXCR3).


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:bee2a9e309ff2d63fd77
claim_id: claim:bee2a9e309ff2d63fd77
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
In monocytes, CD123 and CD127 rose within 15–30 minutes, dipped toward baseline by ∼1 hour, and then entered a second phase in which CD127 peaked near eight hours while CD123 continued to increase through 48 hours; CD25 exhibited a delayed induction that lagged CD127 by ∼8 hours and remained elevated thereafter (Figure 5e-f).

summary:
In Homo sapiens, monocytes exposed to malignant B-cell-derived extracellular vesicles showed biphasic expression of CD123 (interleukin-3 receptor alpha) and CD127 (interleukin-7 receptor alpha) followed by delayed CD25 (interleukin-2 receptor alpha) induction.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:61f7bc9c350e434b5467
claim_id: claim:61f7bc9c350e434b5467
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
pDCs and mDCs showed analogous but lineage-specific kinetics, with earlier and higher CD123 in pDCs and more sustained CD25 in mDCs (Figure 5g).

summary:
In Homo sapiens, plasmacytoid dendritic cells showed earlier and higher CD123 (interleukin-3 receptor alpha) expression upon malignant B-cell-derived extracellular vesicle uptake.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:387ceb42fa2c694f7d05
claim_id: claim:387ceb42fa2c694f7d05
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
pDCs and mDCs showed analogous but lineage-specific kinetics, with earlier and higher CD123 in pDCs and more sustained CD25 in mDCs (Figure 5g).

summary:
In Homo sapiens, myeloid dendritic cells showed more sustained CD25 (interleukin-2 receptor alpha) expression upon malignant B-cell-derived extracellular vesicle uptake.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:421d80fc8b600bef4444
claim_id: claim:421d80fc8b600bef4444
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
MBC-EVs also increased PD-L1 and BCL-2 in myeloid and dendritic cell subsets, monocytes, mo-derived DCs, mDCs, and pDCs, with these changes heightened by STAT3 degradation and diminished by STAT5 degradation (Figure 6l,m).

summary:
In Homo sapiens, malignant B-cell-derived extracellular vesicles increased PD-L1 and BCL-2 expression in monocytes.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:3aa6950f332d0b824676
claim_id: claim:3aa6950f332d0b824676
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
MBC-EVs also increased PD-L1 and BCL-2 in myeloid and dendritic cell subsets, monocytes, mo-derived DCs, mDCs, and pDCs, with these changes heightened by STAT3 degradation and diminished by STAT5 degradation (Figure 6l,m).

summary:
In Homo sapiens, malignant B-cell-derived extracellular vesicles increased PD-L1 and BCL-2 expression in monocyte-derived dendritic cells.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:6470b40b5d29c33c3324
claim_id: claim:6470b40b5d29c33c3324
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
MBC-EVs also increased PD-L1 and BCL-2 in myeloid and dendritic cell subsets, monocytes, mo-derived DCs, mDCs, and pDCs, with these changes heightened by STAT3 degradation and diminished by STAT5 degradation (Figure 6l,m).

summary:
In Homo sapiens, malignant B-cell-derived extracellular vesicles increased PD-L1 and BCL-2 expression in myeloid dendritic cells.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:819a8f088098b90ea30c
claim_id: claim:819a8f088098b90ea30c
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
summary:
In Homo sapiens, malignant B-cell-derived extracellular vesicles increased PD-L1 and BCL-2 expression in plasmacytoid dendritic cells.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:7bfd46ee59dab7b0e50f
claim_id: claim:7bfd46ee59dab7b0e50f
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal: MBC-EVs pushed populations toward higher CD25, whereas few non-B sources favored CD127.
summary:
In Homo sapiens, malignant B-cell-derived extracellular vesicle recipient cells showed higher CD25 expression, while non-B-cell extracellular vesicle recipient cells favored CD127 expression.


claim_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb:claim:dff325a8e31dcfaad550
claim_id: claim:dff325a8e31dcfaad550
paper_key: biorxiv:1efd9fbe-6f02-1014-8df4-f37a8d806beb
span_literal:
A subset of triad-positive monocytes acquired CD197 and features of a monocyte-derived dendritic-like state with lower HLA-DR and absent CD183.

summary:
In Homo sapiens, a subset of interleukin receptor triad-positive monocytes acquired CD197 and features of a monocyte-derived dendritic-like state with lower HLA-DR and absent CD183.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:2ab06229ea8841203ca0
claim_id: claim:2ab06229ea8841203ca0
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
summary: In Homo sapiens, IL7R is a marker gene of CD4 T cells in peripheral blood mononuclear cells.
span_literal:
IL7R (CD4 T cells), CD8A and CD8B (CD8 T cells), CD14, LYZ, LGALS3, and S100A8 (CD14+ monocytes), MS4A1 and CD79A (B cells), GNLY, NKG7, and KLRB1 (natural killer cells), FCGR3A and MS4A7 (FCGR3A+ monocytes), FCER1A and CST3 (dendritic cells), and PPBP (megakaryocytes).


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:51f926ee670c73a7071a
claim_id: claim:51f926ee670c73a7071a
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
span_literal:
IL7R (CD4 T cells), CD8A and CD8B (CD8 T cells), CD14, LYZ, LGALS3, and S100A8 (CD14+ monocytes), MS4A1 and CD79A (B cells), GNLY, NKG7, and KLRB1 (natural killer cells), FCGR3A and MS4A7 (FCGR3A+ monocytes), FCER1A and CST3 (dendritic cells), and PPBP (megakaryocytes).

summary:
In Homo sapiens, CD8A and CD8B are marker genes of CD8 T cells in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:aa11bae27396677cd00d
claim_id: claim:aa11bae27396677cd00d
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
span_literal:
IL7R (CD4 T cells), CD8A and CD8B (CD8 T cells), CD14, LYZ, LGALS3, and S100A8 (CD14+ monocytes), MS4A1 and CD79A (B cells), GNLY, NKG7, and KLRB1 (natural killer cells), FCGR3A and MS4A7 (FCGR3A+ monocytes), FCER1A and CST3 (dendritic cells), and PPBP (megakaryocytes).

summary:
In Homo sapiens, CD14, LYZ, LGALS3, and S100A8 are marker genes of CD14+ monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:d6ce73d6ef37d30ccc29
claim_id: claim:d6ce73d6ef37d30ccc29
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
summary:
In Homo sapiens, GNLY, NKG7, and KLRB1 are marker genes of natural killer cells in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:98f7f61adb149959d3ae
claim_id: claim:98f7f61adb149959d3ae
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
summary:
In Homo sapiens, FCGR3A and MS4A7 are marker genes of FCGR3A+ monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:a60d7108c2f0bc1db973
claim_id: claim:a60d7108c2f0bc1db973
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
summary:
In Homo sapiens, FCER1A and CST3 are marker genes of dendritic cells in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:e1cc9f80d3a42ac4dfb8
claim_id: claim:e1cc9f80d3a42ac4dfb8
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
summary: In Homo sapiens, IL7R is a marker gene of CD4 T cells in peripheral blood mononuclear cells.
span_literal:
These include, for example, IL7R (CD4 T cells), CD8A and CD8B (CD8 T cells), and CD14 (CD14+ monocytes).


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:29da01b4d4a5b5445dcb
claim_id: claim:29da01b4d4a5b5445dcb
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
span_literal:
REOCDE v2 can detect all the marker genes and only RECODE v2 is able to capture key marker genes such as IL7R, CD8A, CD8B, and CD14, while Seurat and Seurat v3 fail to detect them (Figure 2c).

summary:
In Homo sapiens, IL7R is a key marker gene of CD4 T cells, CD8A and CD8B are key marker genes of CD8 T cells, and CD14 is a key marker gene of CD14+ monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:cf16a9fc3f58e61b4d0c
claim_id: claim:cf16a9fc3f58e61b4d0c
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
span_literal:
REOCDE v2 can detect all the marker genes and only RECODE v2 is able to capture key marker genes such as IL7R, CD8A, CD8B, and CD14, while Seurat and Seurat v3 fail to detect them (Figure 2c).

summary:
In Homo sapiens, CD8A and CD8B are key marker genes of CD8 T cells in peripheral blood mononuclear cells.


claim_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec:claim:c502c4e1ee9c8413ba0c
claim_id: claim:c502c4e1ee9c8413ba0c
paper_key: biorxiv:1f87890c-7e00-1014-91de-cf40554be0ec
span_literal:
REOCDE v2 can detect all the marker genes and only RECODE v2 is able to capture key marker genes such as IL7R, CD8A, CD8B, and CD14, while Seurat and Seurat v3 fail to detect them (Figure 2c).

summary:
In Homo sapiens, CD14 is a key marker gene of CD14+ monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:856f29eca9e205efaa24
claim_id: claim:856f29eca9e205efaa24
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
Immune checkpoint molecules were mainly expressed in regulatory T cells (CD4-c10-FOXP3), pre-exhaustion T cells (CD8-c6-CXCL13), and exhaustion T cells (CD8-c5-PDCD1) as shown in Figure 4B.

summary:
In Homo sapiens liver cancer, regulatory T cells (CD4-c10-FOXP3) express immune checkpoint molecules, with FOXP3 serving as a marker of this subtype.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:096328528e2f3287efc7
claim_id: claim:096328528e2f3287efc7
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
Immune checkpoint molecules were mainly expressed in regulatory T cells (CD4-c10-FOXP3), pre-exhaustion T cells (CD8-c6-CXCL13), and exhaustion T cells (CD8-c5-PDCD1) as shown in Figure 4B.

summary:
In Homo sapiens liver cancer, pre-exhaustion T cells (CD8-c6-CXCL13) express immune checkpoint molecules, with CXCL13 serving as a marker of this subtype.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:048b40bc164b4177adf4
claim_id: claim:048b40bc164b4177adf4
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
Immune checkpoint molecules were mainly expressed in regulatory T cells (CD4-c10-FOXP3), pre-exhaustion T cells (CD8-c6-CXCL13), and exhaustion T cells (CD8-c5-PDCD1) as shown in Figure 4B.

summary:
In Homo sapiens liver cancer, exhaustion T cells (CD8-c5-PDCD1) express immune checkpoint molecules, with PDCD1 serving as a marker of this subtype.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:8af10973362825b5dd2b
claim_id: claim:8af10973362825b5dd2b
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
Large proportions of memory T cells of CD4-c2-CD69, CD8-c4-GZMK, and CD8-c3-IL7R, as well as a group of cytotoxic T cells of CD8-c9-GNLY were observed in BI-A.

summary:
In Homo sapiens liver cancer, memory T cells (CD4-c2-CD69) are marked by CD69, memory T cells (CD8-c4-GZMK) are marked by GZMK, memory T cells (CD8-c3-IL7R) are marked by IL7R, and cytotoxic T cells (CD8-c9-GNLY) are marked by GNLY.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:8875c9136017991f4bf7
claim_id: claim:8875c9136017991f4bf7
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
In contrast, proliferative pre-exhaustion T cells of CD4/CD8-c6/c7-MKI67-CXCL13 and pre-exhaustion T cells of CD8-c6-CXCL13 were enriched in BI-B&C.

summary:
In Homo sapiens liver cancer, proliferative pre-exhaustion T cells (CD4/CD8-c6/c7-MKI67-CXCL13) are marked by MKI67 and CXCL13.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:71a50b8b110c179647ea
claim_id: claim:71a50b8b110c179647ea
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
summary: In Homo sapiens, naïve T cells are marked by CCR7, LEF1, SELL, and TCF7.
span_literal:
We also evaluated each T cell subtype by using the 4 well-defined naïve T cell markers (CCR7, LEF1, SELL, TCF7), 12 cytotoxic markers (PRF1, IFNG, GNLY, NKG7, GZMB, GZMA, GZMH, KLRK1, KLRB1, KLRD1, CTSW, CST7) as well as T-cell exhaustion marker genes (Figures S4D and S4G) (Guo et al., 2018).


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:312f5fadade33bcd6580
claim_id: claim:312f5fadade33bcd6580
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
We also evaluated each T cell subtype by using the 4 well-defined naïve T cell markers (CCR7, LEF1, SELL, TCF7), 12 cytotoxic markers (PRF1, IFNG, GNLY, NKG7, GZMB, GZMA, GZMH, KLRK1, KLRB1, KLRD1, CTSW, CST7) as well as T-cell exhaustion marker genes (Figures S4D and S4G) (Guo et al., 2018).

summary:
In Homo sapiens, cytotoxic T cells are marked by PRF1, IFNG, GNLY, NKG7, GZMB, GZMA, GZMH, KLRK1, KLRB1, KLRD1, CTSW, and CST7.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:aabab1cfccb6a8de37da
claim_id: claim:aabab1cfccb6a8de37da
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
summary: In Homo sapiens, T cells are identified by expression of CD3D, CD3E, or CD3G.
span_literal:
To ensure a pure population of T cells, we calculated the proportion of T cells expressing CD3D, CD3E, or CD3G in each cluster generated from a graph-based clustering algorithm with default parameter settings (Waltman and Van Eck, 2013).


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:958ad901fb8a84b6b9c2
claim_id: claim:958ad901fb8a84b6b9c2
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
To confidently identify T cell subtypes, we first extracted CD4+ (expressing CD4, n = 2,275) T cells and CD8+ (expressing CD8A or CD8B, n = 6,686) T cells, respectively.

summary:
In Homo sapiens, CD4-positive T cells are identified by expression of CD4, while CD8-positive T cells are identified by expression of CD8A or CD8B.


claim_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1:claim:36c8ccab5cf0d5ffefea
claim_id: claim:36c8ccab5cf0d5ffefea
paper_key: biorxiv:1fa7b83f-6da7-1014-a69d-d257852e8dd1
span_literal:
We excluded CD4-c10-FOXP3 (regulatory T cells) and CD8-c10-NCR3 (largely composed of mucosal associated invariant T cells) from the trajectory analysis due to their distinct characteristics, following a strategy used in a recent study (Guo et al., 2018).

summary:
In Homo sapiens, regulatory T cells (CD4-c10-FOXP3) are marked by FOXP3, and mucosal associated invariant T cells (CD8-c10-NCR3) are marked by NCR3.


claim_key: biorxiv:200cf446-75b0-1014-a31c-a786c6d74a08:claim:efa6aad99774f443ed1c
claim_id: claim:efa6aad99774f443ed1c
paper_key: biorxiv:200cf446-75b0-1014-a31c-a786c6d74a08
span_literal:
We next evaluated the expression of the well-described markers of brown and white adipose identity UCP1, PPARGCA, CITED1, PRDM16, CIDEA (all BAT) and HOXC8 (WAT).

summary:
In Homo sapiens, UCP1, PPARGC1A, CITED1, PRDM16, and CIDEA are markers of brown adipose tissue identity.


claim_key: biorxiv:200cf446-75b0-1014-a31c-a786c6d74a08:claim:65cfe4661c9f10592b89
claim_id: claim:65cfe4661c9f10592b89
paper_key: biorxiv:200cf446-75b0-1014-a31c-a786c6d74a08
summary: In Homo sapiens, UCP1, PPARGC1A, PRDM16, CIDEA, and CITED1 are brown adipose tissue marker genes.
span_literal:
no statistically significant overall trends emerged for any of the five BAT marker genes (UCP1, PPARGC1A, PRDM16, CIDEA, CITED1), nor for the WAT marker HOXC8.


claim_key: biorxiv:200cf446-75b0-1014-a31c-a786c6d74a08:claim:9dd70588362e0746ab24
claim_id: claim:9dd70588362e0746ab24
paper_key: biorxiv:200cf446-75b0-1014-a31c-a786c6d74a08
span_literal:
Cell death inducing DFFA like effector a (CIDEA) is a well-established brown adipose tissue mRNA marker

summary:
In Homo sapiens, cell death inducing DFFA like effector a (CIDEA) is a well-established brown adipose tissue marker.


claim_key: biorxiv:20db10ff-6d71-1014-91a5-bffabd7bad90:claim:2bbc7f0462b63778de39
claim_id: claim:2bbc7f0462b63778de39
paper_key: biorxiv:20db10ff-6d71-1014-91a5-bffabd7bad90
span_literal:
For this, we extracted the gene expression signature from single cell RNAseq39 and confirmed COL1A is expressed by MAFs (Extended Data Fig. 4h).

summary:
In Homo sapiens, collagen type I alpha 1 (COL1A1) is expressed by melanoma-associated fibroblasts, as confirmed by single cell RNA sequencing.


claim_key: biorxiv:20db10ff-6d71-1014-91a5-bffabd7bad90:claim:73827cdcb1fa21d6eca1
claim_id: claim:73827cdcb1fa21d6eca1
paper_key: biorxiv:20db10ff-6d71-1014-91a5-bffabd7bad90
span_literal:
Finally, we confirmed that human fibroblasts, and not melanoma cells, are the main source of MMP1; and the melanoma cell lines do not express COL1A1 or COL1A239 (Extended Data Fig. 2l).

summary:
In Homo sapiens, fibroblasts are the main source of matrix metalloproteinase-1 (MMP1), while melanoma cells do not express collagen type I alpha 1 (COL1A1) or collagen type I alpha 2 (COL1A2).


claim_key: biorxiv:20db10ff-6d71-1014-91a5-bffabd7bad90:claim:26f5a0237c0db40bfaed
claim_id: claim:26f5a0237c0db40bfaed
paper_key: biorxiv:20db10ff-6d71-1014-91a5-bffabd7bad90
span_literal:
Finally, we confirmed that human fibroblasts, and not melanoma cells, are the main source of MMP1; and the melanoma cell lines do not express COL1A1 or COL1A239 (Extended Data Fig. 2l).

summary:
In Homo sapiens, melanoma cells do not express collagen type I alpha 1 (COL1A1) or collagen type I alpha 2 (COL1A2), and are not the main source of matrix metalloproteinase-1 (MMP1).


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:741c351f25e414e53418
claim_id: claim:741c351f25e414e53418
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
summary: In Homo sapiens coronary arteries, pericytes are marked by RGS5, STEAP4, and CD36.
span_literal:
These cell states included pericytes (RGS5, STEAP4, CD36), four SMC subtypes (SMC1: RERGL, PHLDA2, BCAM; SMC2; MYH11, CNN1, PLN; SMC3: ACTG2, MYH10, ITGA8; SMC4: IFI44L, IFIT3, MX1), and 2 modulated SMC subtypes (fibromyocytes/FMCs: IGFBP2, VCAN, TNFRSF11B; chondromyocytes/CMCs: CCL19, COMP, POSTN).


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:f5c4803bdfb447e3c231
claim_id: claim:f5c4803bdfb447e3c231
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
summary: In Homo sapiens coronary arteries, fibroblast 1 is marked by PLA2G2A, MFAP5, and PCOLCE2.
span_literal:
Additionally, we identified seven fibroblast subtypes (Fib1: PLA2G2A, MFAP5, PCOLCE2; Fib2: CFD, C7, FBLN1; Fib3: VWF, EGFL7, ACKR1; Fib4: CXCL14, LEPR, RARRES2; Fib5: ANGPTL7, APOD, PTGDS; Fib6: SLC2A1, KRT19, ITGA6; Fib7: ABCA8, ABCA10, CDH19)


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:4fa322f1ff5673e94204
claim_id: claim:4fa322f1ff5673e94204
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
Notably, the FMC and CMC cell states exhibited high expression of the surface protein FAP (Fig. 2d).

summary:
In Homo sapiens coronary arteries, fibromyocyte and chondromyocyte cell states exhibited high expression of the surface protein fibroblast activation protein (FAP).


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:013a52840780df03869d
claim_id: claim:013a52840780df03869d
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
Notably, the FMC and CMC cell states exhibited high expression of the surface protein FAP (Fig. 2d).

summary:
In Homo sapiens coronary arteries, chondromyocyte cell states exhibited high expression of the surface protein fibroblast activation protein (FAP).


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:24ee0fa5f67d7e47c8b6
claim_id: claim:24ee0fa5f67d7e47c8b6
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal: Broadly, SMC1-3 exhibited an enrichment of contractile markers such as MYH11 and ACTA2
summary:
In Homo sapiens, smooth muscle cell 1 through smooth muscle cell 3 exhibited enrichment of the contractile markers MYH11 and ACTA2.


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:d61607d7fb1d1350905d
claim_id: claim:d61607d7fb1d1350905d
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
whereas FMCs and CMCs were characterized by synthetic and fibrotic gene signatures1,38,39 such as TNFRSF11B, MGP, and POSTN

summary:
In Homo sapiens, fibromyocytes and chondromyocytes were characterized by synthetic and fibrotic gene signatures including TNFRSF11B, MGP, and POSTN.


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:eff09b3c1a675bf410d1
claim_id: claim:eff09b3c1a675bf410d1
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
whereas FMCs and CMCs were characterized by synthetic and fibrotic gene signatures1,38,39 such as TNFRSF11B, MGP, and POSTN

summary:
In Homo sapiens, chondromyocytes were characterized by synthetic and fibrotic gene signatures including TNFRSF11B, MGP, and POSTN.


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:ffd3384152b4f1a0016e
claim_id: claim:ffd3384152b4f1a0016e
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
Surface protein analysis revealed that LILRA4 is enriched on tissue-resident macrophages, while CCR2 is predominantly expressed on monocytes, inflammatory macrophages (Mac1), and dendritic cells

summary:
In Homo sapiens, LILRA4 is enriched on tissue-resident macrophages, while CCR2 is predominantly expressed on monocytes, inflammatory macrophages (Mac1), and dendritic cells.


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:9f2c9f5424c78fc8b18e
claim_id: claim:9f2c9f5424c78fc8b18e
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
Notably, the Mac4 subset is enriched in genes involved in lipid metabolism, including FABP4, FABP5, GPNMB, CTSL, and SPP1 (Fig. 4c).

summary:
In Homo sapiens, the Mac4 macrophage subset is enriched in genes involved in lipid metabolism, including FABP4, FABP5, GPNMB, CTSL, and SPP1.


claim_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355:claim:330ebe402ed4753aec9e
claim_id: claim:330ebe402ed4753aec9e
paper_key: biorxiv:219b21d9-7007-1014-9157-ab439216a355
span_literal:
Our analysis identified fibroblast activation protein (FAP) as a marker of modulated VSMCs within the neo-intima.

summary:
In Homo sapiens, fibroblast activation protein (FAP) is a marker of modulated vascular smooth muscle cells within the neo-intima.


claim_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f:claim:0c2ea8b7607646c4cff9
claim_id: claim:0c2ea8b7607646c4cff9
paper_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f
span_literal:
The Cxcl10 14 gene cluster correlated highest, with 12 genes in common to IFN-γ differentiated M1-like macrophages that promote inflammation by secreting cytokines and chemokines (P = 3.70E-21).

summary:
In Homo sapiens, the CXCL10 gene cluster correlated highest with interferon gamma differentiated M1-like macrophages in COVID-19 bronchoalveolar lavage fluid, indicating CXCL10 as a positive marker of M1-like macrophages.


claim_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f:claim:b1aa213069e4319fcf9d
claim_id: claim:b1aa213069e4319fcf9d
paper_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f
span_literal:
Results from three independent scRNAseq studies using peripheral blood mononuclear cells from COVID-19 subjects revealed the Cxcl10 cluster correlated highest with i) 10 genes in common to CD163hi Monocytes-Cohort 1-Cluster 2 in (Schulte-Schrepping et al., 2020) (P = 1.90E-15), ii) 9 genes in common to the Severe COVID-19 up-regulated gene set in (Lee et al., 2020) (P = 2.3E-15) and iii) 6 genes in common to CD16 Monocyte-Cluster28 in (Wilk et al., 2020) (P = 1.70E-07).

summary:
In Homo sapiens, the CXCL10 gene cluster correlated highest with CD163hi monocytes (Cohort 1, Cluster 2) in peripheral blood mononuclear cells from COVID-19 subjects, indicating CXCL10 as a positive marker of CD163hi monocytes.


claim_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f:claim:0278f1c2e48096cb1987
claim_id: claim:0278f1c2e48096cb1987
paper_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f
span_literal:
Results from three independent scRNAseq studies using peripheral blood mononuclear cells from COVID-19 subjects revealed the Cxcl10 cluster correlated highest with i) 10 genes in common to CD163hi Monocytes-Cohort 1-Cluster 2 in (Schulte-Schrepping et al., 2020) (P = 1.90E-15), ii) 9 genes in common to the Severe COVID-19 up-regulated gene set in (Lee et al., 2020) (P = 2.3E-15) and iii) 6 genes in common to CD16 Monocyte-Cluster28 in (Wilk et al., 2020) (P = 1.70E-07).

summary:
In Homo sapiens, the CXCL10 gene cluster correlated with CD16 monocytes (Cluster 28) in peripheral blood mononuclear cells from COVID-19 subjects, indicating CXCL10 as a positive marker of CD16 monocytes.


claim_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f:claim:51391c5f69667c7b4766
claim_id: claim:51391c5f69667c7b4766
paper_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f
span_literal:
The interferon stimulated gene ISG15 stands out as having the highest fold change in severe COVID-19 patients and is strongly represented in the 3 other COVID-19 scRNAseq studies.

summary:
In Homo sapiens, the interferon stimulated gene ISG15 has the highest fold change in severe COVID-19 patients, serving as a positive marker in monocyte-macrophage lineages.


claim_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f:claim:8471a5302a6d136a012b
claim_id: claim:8471a5302a6d136a012b
paper_key: biorxiv:2351d19e-6c56-1014-8708-9339c5f1215f
span_literal:
The prevalence of up-regulated kinase genes highlights a prominent activation of intracellular signaling processes in late stage infection (Aurka, Aurkb, Cdk1, Tk1, Plk1, Pbk, Melk), as described previously in this article.

summary:
In Homo sapiens, aurora kinase A, aurora kinase B, cyclin dependent kinase 1, thymidine kinase 1, polo like kinase 1, PDZ binding kinase, and maternal embryonic leucine zipper kinase are up-regulated in proliferating T cells during late stage COVID-19 infection.


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:7a98d34c57872db4aa63
claim_id: claim:7a98d34c57872db4aa63
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
span_literal: positive for basal K14
summary:
In Homo sapiens, keratinocytes in the skin-on-a-chip model are positive for the basal marker keratin 14.


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:33c17ca9cfba997084f5
claim_id: claim:33c17ca9cfba997084f5
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
summary: In Homo sapiens, proliferative basal epidermal cells are positive for Ki67.
span_literal:
Infrequent proliferative cells (Ki67 positive) were observed in the basal epidermal layers of epidermal equivalents cultured submerged in medium (Figure 3).


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:6c3eb9c673a08f1f589a
claim_id: claim:6c3eb9c673a08f1f589a
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
span_literal:
However, relatively weak expression of the dermal fibroblast marker vimentin was observed in the dermal compartment of both cultures, and very weak staining for the epidermal differentiation marker transglutaminase 1 (TGM-1) was observed in the stratified layers of corresponding epidermal compartments (Figure 4B).

summary:
In Homo sapiens, vimentin is a marker of dermal fibroblasts, and transglutaminase 1 is a marker of differentiated epidermal cells.


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:79915e8dc9d2efdb5d5e
claim_id: claim:79915e8dc9d2efdb5d5e
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
summary: In Homo sapiens, endothelial cells are positive for CD31.
span_literal:
CD31 positive structures were obviously only observed in vascularized models, as would be expected from the presence of endothelial cells (Figure 5B).


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:df0931d5f553f43dc0c9
claim_id: claim:df0931d5f553f43dc0c9
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
span_literal:
the thickness of involucrin positive layers in chips containing either HUVECs alone or alongside pericytes (8 +/− 5.8 and 8 +/− 3.8 μm, respectively) compared to avascular models (3 +/− 2.2 μm, Figures A and D).

summary:
In Homo sapiens, the upper epidermal layers of skin equivalents express involucrin as a terminal differentiation marker.


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:e9e80e1d1cd9a3dec266
claim_id: claim:e9e80e1d1cd9a3dec266
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
span_literal:
expression of the terminal differentiation marker involucrin was observed in the upper-epidermal layers of both cultures, the thickness of the associated differentiated layer was significantly increased in submerged cultures (3.5 +/− 2.2 μm) compared to those kept at the air-liquid interface (0.5 +/− 0.2 μm, Figure 4).

summary:
In Homo sapiens, involucrin is a terminal differentiation marker expressed in the upper epidermal layers of skin equivalents.


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:a8bde607d349fd2b6f76
claim_id: claim:a8bde607d349fd2b6f76
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
span_literal:
Ki67 positive cells in the epidermis were confined to the basal layer in all conditions and their frequency was comparable (Figure 5D).

summary:
In Homo sapiens, Ki67-positive proliferative cells are confined to the basal layer of the epidermis.


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:0962a0a3365595f1dd29
claim_id: claim:0962a0a3365595f1dd29
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
summary: In Homo sapiens, CD31 and laminin are expressed in lumenated capillary endothelial cells.
span_literal:
CD31 and laminin stainings clearly established the formation of rosettes associated with the formation of lumenated capillaries (Figure 7D), in agreement with the recruitment of laminin at the basal membrane of micro-capillaries (Black et al., 1998, Schurr et al., 1999, Kubota et al., 1988).


claim_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382:claim:7c8e5eb3553b458a639b
claim_id: claim:7c8e5eb3553b458a639b
paper_key: biorxiv:23bc60ca-7289-1014-89a4-d91c9024f382
span_literal:
vascularization enhances stratification and differentiation (thickness, architecture and expression of terminal differentiation markers such as involucrin and transglutaminase 1), allowing formation of more mature skin equivalents in microfluidic chips.

summary:
In Homo sapiens, involucrin and transglutaminase 1 are terminal differentiation markers of epidermal cells in skin equivalents.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:fa5db5ea269dc258eb5f
claim_id: claim:fa5db5ea269dc258eb5f
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
The majority of cells expressed basal cell markers (Cytokeratin (KRT) 5 and 17, TP63), of which a fraction co-expressed mesenchymal cell markers (VIM, FN1, CDH2), alveolar (SLC34A2, ABCA3, LPCAT1, EMP2, HOPX) and/or secretory epithelial cell markers (SCGB1A1, MUC4).

summary:
In Homo sapiens, aberrant basal-like cells express basal cell markers cytokeratin 5 (KRT5), cytokeratin 17 (KRT17), and TP63. In Homo sapiens, a fraction of aberrant basal-like cells co-express mesenchymal cell markers vimentin (VIM), fibronectin 1 (FN1), and N-cadherin (CDH2).


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:95b07e381f5e7a54d84f
claim_id: claim:95b07e381f5e7a54d84f
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
We observed expression of mesenchymal stem cell markers, as described previously [15]: CD44 was highly expressed, whereas CD90 (THY1) and CD105 (ENG) were expressed at lower levels (Figure 2 A).

summary:
In Homo sapiens, fibrosis-enriched aberrant basal-like cells express mesenchymal stem cell markers CD44 (highly), CD90 (THY1), and CD105 (ENG).


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:b592ca3cb67cba7d21f5
claim_id: claim:b592ca3cb67cba7d21f5
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
Furthermore, other mesenchymal markers such as vimentin (VIM), N-cadherin (CDH2), or fibronectin (FN1) were also highly expressed.

summary:
In Homo sapiens, fibrosis-enriched aberrant basal-like cells highly express mesenchymal markers vimentin (VIM), N-cadherin (CDH2), and fibronectin 1 (FN1).


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:172223c57d076e6b33e1
claim_id: claim:172223c57d076e6b33e1
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
We observed moderate to high expression of the typical epithelial cell markers E-cadherin (CDH1), EPCAM, NKX2-1, SOX2, SOX9, basal cell markers p63 (TP63), cytokeratin 5 (KRT5) and 14 (KRT14), AT-1 markers EMP2, HOPX, AT2 markers SLC34A2, ABCA3, LPCAT1, and the club cell marker SCGB1A1 (Figure 2 A).

summary:
In Homo sapiens, alveolar epithelial cell type 1 markers EMP2 and HOPX are expressed in fibrosis-enriched aberrant basal-like cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:9b58ded3b921bb8a7e2e
claim_id: claim:9b58ded3b921bb8a7e2e
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
We observed moderate to high expression of the typical epithelial cell markers E-cadherin (CDH1), EPCAM, NKX2-1, SOX2, SOX9, basal cell markers p63 (TP63), cytokeratin 5 (KRT5) and 14 (KRT14), AT-1 markers EMP2, HOPX, AT2 markers SLC34A2, ABCA3, LPCAT1, and the club cell marker SCGB1A1 (Figure 2 A).

summary:
In Homo sapiens, alveolar epithelial cell type 2 markers SLC34A2, ABCA3, and LPCAT1 are expressed in fibrosis-enriched aberrant basal-like cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:3a3e39b2d16599ccf738
claim_id: claim:3a3e39b2d16599ccf738
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
We observed moderate to high expression of the typical epithelial cell markers E-cadherin (CDH1), EPCAM, NKX2-1, SOX2, SOX9, basal cell markers p63 (TP63), cytokeratin 5 (KRT5) and 14 (KRT14), AT-1 markers EMP2, HOPX, AT2 markers SLC34A2, ABCA3, LPCAT1, and the club cell marker SCGB1A1 (Figure 2 A).

summary:
In Homo sapiens, the club cell marker SCGB1A1 is expressed in fibrosis-enriched aberrant basal-like cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:644fab8770213d190640
claim_id: claim:644fab8770213d190640
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
The conducting airway is lined with p63+/KRT5+ basal cells and different secretory and ciliated cells.

summary:
In Homo sapiens, the conducting airway is lined with basal cells that are positive for TP63 and KRT5.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:7aac8a5d1ddba34a31a7
claim_id: claim:7aac8a5d1ddba34a31a7
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
Similarly, the co-expression of KRT17 and FOXJ1, a marker for ciliated epithelial cells, or EMP2, a marker for alveolar epithelial cells was detectable in a fraction of cultured cells (Figure 6 C, D).

summary:
In Homo sapiens, FOXJ1 is a marker for ciliated epithelial cells, and EMP2 is a marker for alveolar epithelial cells; both are co-expressed with KRT17 in a fraction of cultured aberrant basal-like cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:7e44e7a0b10d65042c20
claim_id: claim:7e44e7a0b10d65042c20
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
Similarly, the co-expression of KRT17 and FOXJ1, a marker for ciliated epithelial cells, or EMP2, a marker for alveolar epithelial cells was detectable in a fraction of cultured cells (Figure 6 C, D).

summary:
In Homo sapiens, EMP2 is a marker for alveolar epithelial cells and is co-expressed with KRT17 in a fraction of cultured aberrant basal-like cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:e9b0036ebaf34955be89
claim_id: claim:e9b0036ebaf34955be89
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
This was mirrored by the atypical co-expression of the mesenchymal markers FN1 and VIM in the majority of the KRT17 positive cells (Figure 4 E).

summary:
In Homo sapiens, the majority of KRT17-positive aberrant basal-like cells atypically co-express the mesenchymal markers FN1 and VIM.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:30d473d30cca2a4ae5ce
claim_id: claim:30d473d30cca2a4ae5ce
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
Two recent studies performing single-cell RNA-seq analysis of cells derived from dissociated human fibrotic and control lung tissue described a novel fibrosis-enriched aberrant basal-like cell population, named “aberrant basaloid” by Adams et al. [13] and “KRT5-/KRT17+” by Habermann et al. [14].

summary:
In Homo sapiens, the aberrant basaloid cell population is characterized as KRT5-negative and KRT17-positive.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:0f6d6093b9bc1f8f6a3c
claim_id: claim:0f6d6093b9bc1f8f6a3c
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
Similar to the aberrant basaloid cells virtually all of our cultured basal-like cells expressed KRT17.

summary:
In Homo sapiens, virtually all cultured aberrant basal-like cells express KRT17, similar to aberrant basaloid cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:14bc9ebfe5ff81989b30
claim_id: claim:14bc9ebfe5ff81989b30
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
The disease-specific presence of atypical epithelial cells in the peripheral IPF lung was observed before: ΔNP63 [12], KRT5 [10], or ΔNP63 and KRT5/6 [11] expressing cells as well as recently described KRT17+/KRT5-aberrant basal-like cells [13, 14] or KRT8+ alveolar epithelial progenitor cells [27, 36] were detected in the alveolar compartment of lung tissue derived from IPF patients, but were absent in tissue from control donors.

summary:
In Homo sapiens, KRT17-positive/KRT5-negative aberrant basal-like cells and KRT8-positive alveolar epithelial progenitor cells are detected in the alveolar compartment of idiopathic pulmonary fibrosis lung tissue.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:9bc8ff39568827e0cfb5
claim_id: claim:9bc8ff39568827e0cfb5
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
The disease-specific presence of atypical epithelial cells in the peripheral IPF lung was observed before: ΔNP63 [12], KRT5 [10], or ΔNP63 and KRT5/6 [11] expressing cells as well as recently described KRT17+/KRT5-aberrant basal-like cells [13, 14] or KRT8+ alveolar epithelial progenitor cells [27, 36] were detected in the alveolar compartment of lung tissue derived from IPF patients, but were absent in tissue from control donors.

summary:
In Homo sapiens, KRT8-positive alveolar epithelial progenitor cells are detected in the alveolar compartment of idiopathic pulmonary fibrosis lung tissue.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:dc6fc0124500076eb791
claim_id: claim:dc6fc0124500076eb791
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
This is in line with a recent study showing that cultured human AT2 cells trans-differentiate into KRT5 positive basal cells via a KRT17+/KRT8+ alveolar-basal intermediate when co-cultured with adult human lung mesenchyme in a 3D organoid system [39].

summary:
In Homo sapiens, cultured alveolar epithelial cell type 2 trans-differentiate into KRT5-positive basal cells via a KRT17-positive/KRT8-positive alveolar-basal intermediate cell.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:3b6689f7a6c57170a891
claim_id: claim:3b6689f7a6c57170a891
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
This is in line with a recent study showing that cultured human AT2 cells trans-differentiate into KRT5 positive basal cells via a KRT17+/KRT8+ alveolar-basal intermediate when co-cultured with adult human lung mesenchyme in a 3D organoid system [39].

summary:
In Homo sapiens, cultured alveolar epithelial cell type 2 trans-differentiate into KRT5-positive basal cells.


claim_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9:claim:f0a48a52d413e9eeeca3
claim_id: claim:f0a48a52d413e9eeeca3
paper_key: biorxiv:2439b48c-6d2d-1014-8b64-9f8fdc0d5fe9
span_literal:
The expression across cells of different clusters of the basal cell markers KRT5, KRT14, KRT17, ITGB4, and TP63; markers of transitional epithelial cells KRT8 and KRT18 [27]; the general epithelial marker KRT7 [28], mesenchymal markers FN1 and VIM; the transcription factors SOX4 and SOX9, IPF-related matrix metalloprotease (MMP)7 [29], and secretory cell markers MUC4 and SCGB1A1 can be seen in Figure 4 D.

summary:
In Homo sapiens, basal cell markers include KRT5, KRT14, KRT17, ITGB4, and TP63; transitional epithelial cell markers include KRT8 and KRT18; the general epithelial marker is KRT7; mesenchymal markers include FN1 and VIM; and secretory cell markers include MUC4 and SCGB1A1.


claim_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e:claim:8e3d6901f2178aa05994
claim_id: claim:8e3d6901f2178aa05994
paper_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e
span_literal: Cluster 8 was a small cluster that expressed IL7R, KLRB1, TXK, IL1R1, TNFRSF18, TLE1, and IL2RA.
summary:
In Homo sapiens, T cell cluster 8 in the choroid expresses IL7R, KLRB1, TXK, IL1R1, TNFRSF18, TLE1, and IL2RA.


claim_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e:claim:7a3cab34393e9a1ce9a3
claim_id: claim:7a3cab34393e9a1ce9a3
paper_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e
span_literal:
T cell cluster 0 expressed genes consistent with cytotoxic CD8+ T cells (CD8A, CD8B1, NKG7, GZMA, and KLRC1), whereas T cell cluster 1 expressed genes consistent with naïve T cells and CD4+ effector memory T cells, such as IL7R, KLF2, TCF7, and LEF1 and CD4.

summary:
In Homo sapiens choroid, T cell cluster 0 expresses CD8A, CD8B1, NKG7, GZMA, and KLRC1, consistent with cytotoxic CD8-positive T cells.


claim_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e:claim:33f3c33d3bb5d5774913
claim_id: claim:33f3c33d3bb5d5774913
paper_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e
span_literal:
T cell cluster 0 expressed genes consistent with cytotoxic CD8+ T cells (CD8A, CD8B1, NKG7, GZMA, and KLRC1), whereas T cell cluster 1 expressed genes consistent with naïve T cells and CD4+ effector memory T cells, such as IL7R, KLF2, TCF7, and LEF1 and CD4.

summary:
In Homo sapiens choroid, T cell cluster 1 expresses IL7R, KLF2, TCF7, LEF1, and CD4, consistent with naïve T cells and CD4-positive effector memory T cells.


claim_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e:claim:93725f4c8a606ef8e8ce
claim_id: claim:93725f4c8a606ef8e8ce
paper_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e
span_literal:
Whilst several MC/Mφ and DC clusters were identified in the mouse choroid, only one cluster (cluster 4) expressed genes characteristic of MC/Mφ (CD14, CD68) and DCs (FLT3) in the human choroid (Figure 7b-d).

summary:
In Homo sapiens choroid, the monocyte/macrophage and dendritic cell cluster (cluster 4) expresses CD14, CD68, and FLT3.


claim_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e:claim:0b4b8d202e76588b8ea3
claim_id: claim:0b4b8d202e76588b8ea3
paper_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e
span_literal:
This cluster was also characterised by expression of HLA-DMA, HLA-DRA, HLA-DRB1, HLA-DPB1, HLA-DPA1, and CD74, suggesting that cells within this cluster likely function in antigen processing and presentation.

summary:
In Homo sapiens choroid, the monocyte/macrophage and dendritic cell cluster expresses HLA-DMA, HLA-DRA, HLA-DRB1, HLA-DPB1, HLA-DPA1, and CD74, suggesting a role in antigen processing and presentation.


claim_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e:claim:8543a8e67e27a4ed7843
claim_id: claim:8543a8e67e27a4ed7843
paper_key: biorxiv:2696a317-6c07-1014-9562-d326b0aa508e
span_literal: In addition, S100A9 and S100A8 were upregulated in a part of this cluster.
summary:
In Homo sapiens choroid, S100A9 and S100A8 are upregulated in a subset of the monocyte/macrophage and dendritic cell cluster.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:8e3d251ad52a81854f80
claim_id: claim:8e3d251ad52a81854f80
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal:
AQP1 is mainly expressed in microvascular endothelium and tumor microvessels, and it plays a role in driving water transport in lamellipodia and facilitating lamellipodial extension and cell migration

summary:
In Homo sapiens, aquaporin 1 (AQP1) is positively expressed in microvascular endothelial cells and tumor microvascular endothelial cells.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:f16eef2eec2e889a08c9
claim_id: claim:f16eef2eec2e889a08c9
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal:
Our results also demonstrated that AQP1 was specifically expressed in ECs (including HUVECs and isolated human ECs), similar to the maker genes CD31 and CD144, but AQP8 expression was almost undetectable in ECs

summary:
In Homo sapiens, aquaporin 1 (AQP1) is positively expressed in endothelial cells, including human umbilical vein endothelial cells, similar to the marker genes CD31 and CD144, while aquaporin 8 (AQP8) expression is negative in endothelial cells.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:3f353b57c45287c62093
claim_id: claim:3f353b57c45287c62093
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal: In comparison to ECs, AQP1 and AQP8 were seldom expressed in human ESCs (H1 line)
summary:
In Homo sapiens, aquaporin 1 (AQP1) and aquaporin 8 (AQP8) are negatively expressed in human embryonic stem cells compared to endothelial cells.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:58742eaf03178c8d7229
claim_id: claim:58742eaf03178c8d7229
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal:
However, H1-derived ECs (H1-ECs) (from day 4 onwards) showed an increased expression of AQP1, but the AQP8 expression was not altered

summary:
In Homo sapiens, H1-derived endothelial cells show increased expression of aquaporin 1 (AQP1) but not aquaporin 8 (AQP8).


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:bce2505812d5e1d418c6
claim_id: claim:bce2505812d5e1d418c6
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal: human AQP1 is specifically and strongly expressed in most microvascular endothelial cells
summary:
In Homo sapiens, aquaporin 1 (AQP1) is specifically and strongly expressed in microvascular endothelial cells.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:2f1d4dd5808b9741103e
claim_id: claim:2f1d4dd5808b9741103e
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal:
However, human AQP8 (zebrafish aqp8a.1 homologue) is mainly presented in epithelial cells of varied tissues but barely detected in endothelial cells

summary:
In Homo sapiens, aquaporin 8 (AQP8) is positively expressed in epithelial cells but is negative in endothelial cells.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:47ad05fb01a5e457ce35
claim_id: claim:47ad05fb01a5e457ce35
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal:
However, human AQP8 (zebrafish aqp8a.1 homologue) is mainly presented in epithelial cells of varied tissues but barely detected in endothelial cells

summary:
In Homo sapiens, aquaporin 8 (AQP8) is barely detected in endothelial cells, in contrast to epithelial cells.


claim_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c:claim:b8cb90e628a798283412
claim_id: claim:b8cb90e628a798283412
paper_key: biorxiv:2746af96-6da7-1014-ab14-859a63e4801c
span_literal:
Quantitative PCR analysis confirmed the loss of AQP1 in ΔAQP1-1H1-ECs and ΔAQP1-1H2-ECs, but the expressions of maker genes CD31 and CD144 were comparable in these three derived ECs

summary:
In Homo sapiens, the endothelial cell marker genes CD31 and CD144 are expressed in H1-derived endothelial cells.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:025d26135d6faa0e2b4a
claim_id: claim:025d26135d6faa0e2b4a
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
KLRG1, identified as a co-inhibitory receptor for natural killer (NK) cells and antigen-experienced T cells, has been implicated in immune regulation in patients with non-small cell lung cancer.

summary:
In Homo sapiens, killer cell lectin-like receptor G1 (KLRG1) is identified as a co-inhibitory receptor expressed on natural killer cells and antigen-experienced T cells, implicated in immune regulation in patients with non-small cell lung cancer.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:1a3ffba18b064feeeeee
claim_id: claim:1a3ffba18b064feeeeee
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
KLRG1, identified as a co-inhibitory receptor for natural killer (NK) cells and antigen-experienced T cells, has been implicated in immune regulation in patients with non-small cell lung cancer.

summary:
In Homo sapiens, killer cell lectin-like receptor G1 (KLRG1) is identified as a co-inhibitory receptor expressed on antigen-experienced T cells, implicated in immune regulation in patients with non-small cell lung cancer.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:79b3bccf23fffa86f277
claim_id: claim:79b3bccf23fffa86f277
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
This observation aligns with previous studies that the percentage of PD-1+ CD8 T cells that were KLRG1-negative was strongly associated with response in both pre-treatment and 2-week on-treatment blood samples58.

summary:
In Homo sapiens, the percentage of PD-1-positive CD8 T cells that were KLRG1-negative was strongly associated with treatment response, indicating KLRG1 as a negative marker of responding PD-1-positive CD8 T cells.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:8831a32f42f610076cd1
claim_id: claim:8831a32f42f610076cd1
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
Previous research has identified CD127 as a crucial factor in the dynamic regulation of the T-cell compartment, playing a key role in the maintenance of memory T cells60.

summary:
In Homo sapiens, CD127 has been identified as a crucial factor in the maintenance of memory T cells.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:8cde9d20cde042aecce9
claim_id: claim:8cde9d20cde042aecce9
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
CD197, on the other hand, is predominantly expressed in naive and memory cells, highlighting its importance in these populations61.

summary:
In Homo sapiens, CD197 is predominantly expressed in naive T cells, highlighting its importance in these populations.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:0d382b29eb3a52e57d7d
claim_id: claim:0d382b29eb3a52e57d7d
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
CD197, on the other hand, is predominantly expressed in naive and memory cells, highlighting its importance in these populations61.

summary:
In Homo sapiens, CD197 is predominantly expressed in memory T cells, highlighting its importance in these populations.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:4baec1691d8b0897f0fd
claim_id: claim:4baec1691d8b0897f0fd
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
HLADR is a significant marker involved in antigen presentation to T-cell receptors (TCRs) on T-helper cells, which subsequently leads to antibody production62.

summary:
In Homo sapiens, HLADR is a significant marker involved in antigen presentation to T-cell receptors on T-helper cells.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:09e401708316fc488b5c
claim_id: claim:09e401708316fc488b5c
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
A study by Ishiyama et al.68 showed that CMV-infected patients exhibit increased expression of proliferation and cytotoxicity markers, such as Ki67, Granzyme B, NKG2C, and CD57, largely due to the adaptive response of natural killer (NK) cells and CD8+ T cells in controlling viral replication.

summary:
In Homo sapiens, CMV-infected patients exhibit increased expression of Ki67, Granzyme B, NKG2C, and CD57 in natural killer cells due to the adaptive response in controlling viral replication.


claim_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca:claim:f1856474aee6a42131b5
claim_id: claim:f1856474aee6a42131b5
paper_key: biorxiv:278ac735-6c7d-1014-a21b-fd84484249ca
span_literal:
A study by Ishiyama et al.68 showed that CMV-infected patients exhibit increased expression of proliferation and cytotoxicity markers, such as Ki67, Granzyme B, NKG2C, and CD57, largely due to the adaptive response of natural killer (NK) cells and CD8+ T cells in controlling viral replication.

summary:
In Homo sapiens, CMV-infected patients exhibit increased expression of Ki67, Granzyme B, NKG2C, and CD57 in CD8-positive T cells due to the adaptive response in controlling viral replication.


claim_key: biorxiv:2991147a-6cb7-1014-9cbe-8ba81ca3274c:claim:4b4e21fe294e1e9ed828
claim_id: claim:4b4e21fe294e1e9ed828
paper_key: biorxiv:2991147a-6cb7-1014-9cbe-8ba81ca3274c
span_literal:
Immunofluorescence of the cells showed that undifferentiated progenitors expressed PAX6 and SOX2 (90-95%), consistent with a homogenous culture of radial glia 29, 30 (Figure 1B).

summary:
In Homo sapiens, radial glia express PAX6 and SOX2, as shown by immunofluorescence of undifferentiated progenitors.


claim_key: biorxiv:2991147a-6cb7-1014-9cbe-8ba81ca3274c:claim:1df3ad0650dbcd515ea8
claim_id: claim:1df3ad0650dbcd515ea8
paper_key: biorxiv:2991147a-6cb7-1014-9cbe-8ba81ca3274c
span_literal:
Immunofluorescence of the cells showed that undifferentiated progenitors expressed SOX2 (in red) and PAX6 (in green), and expression of EGFP (in green) in 8-week differentiated neurons labelled with AAV2-hSyn1-EGFP (scale bar is 100 μm, DAPI in blue).

summary:
In Homo sapiens, undifferentiated neural progenitors expressed SOX2 and PAX6, while differentiated neurons were labelled by EGFP driven by the SYN1 promoter.


claim_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e:claim:cd27d955b8f9424e0a4c
claim_id: claim:cd27d955b8f9424e0a4c
paper_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e
span_literal:
a fraction of plaque smooth muscle cells showed to lack detectable expression of some canonical SMC genes, but express mesenchymal (Sca1, CD105), as well as myofibroblast (αSMA, PDGFRB) markers (7)

summary:
In Homo sapiens, a fraction of plaque smooth muscle cells express mesenchymal markers Sca1 and CD105, as well as myofibroblast markers alpha-smooth muscle actin and PDGFRB.


claim_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e:claim:71ffafb08ca0985043e8
claim_id: claim:71ffafb08ca0985043e8
paper_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e
span_literal:
express extracellular matrix proteins (FN1, COL1A1, DCN) and smooth muscle cell markers (ACTA2, MYH11, CNN1)

summary:
In Homo sapiens, cultured plaque cells express extracellular matrix proteins FN1, COL1A1, and DCN, and smooth muscle cell markers ACTA2, MYH11, and CNN1.


claim_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e:claim:1272c3aa069ae106ec91
claim_id: claim:1272c3aa069ae106ec91
paper_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e
span_literal:
They express ACTA2, TAGLN, CNN1, MYH11, TPM2 and IL6, FBLN1, DCN, which are accepted as SMC and fibroblast markers, respectively (16).

summary:
In Homo sapiens, plaque cells express ACTA2, TAGLN, CNN1, MYH11, and TPM2, which are accepted as smooth muscle cell markers, and IL6, FBLN1, and DCN, which are accepted as fibroblast markers.


claim_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e:claim:0681df454e9c3fcd89b8
claim_id: claim:0681df454e9c3fcd89b8
paper_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e
span_literal:
They express ACTA2, TAGLN, CNN1, MYH11, TPM2 and IL6, FBLN1, DCN, which are accepted as SMC and fibroblast markers, respectively (16).

summary:
In Homo sapiens, plaque cells express IL6, FBLN1, and DCN, which are accepted as fibroblast markers.


claim_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e:claim:106ec70c3dbffbd9f7c9
claim_id: claim:106ec70c3dbffbd9f7c9
paper_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e
span_literal:
The downregulation or absence of MYOCD is considered as the marker that indicates the switch of medial VSMCs toward this more plastic phenotype (21).

summary:
In Homo sapiens, the downregulation or absence of MYOCD is considered a marker indicating the switch of medial vascular smooth muscle cells toward a more plastic phenotype such as the myofibroblast.


claim_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e:claim:745164d4aca181a8d763
claim_id: claim:745164d4aca181a8d763
paper_key: biorxiv:29ae8fb9-6d50-1014-8923-847f08fdc25e
span_literal:
The expression of canonical SMC and fibroblast markers (ACTA2, MYH11, CNN1, FN1, COL1A1, DCN) (16) was consistent from passage (p) 2 to 5, indicating transcriptome stability (Fig. 3 B).

summary:
In Homo sapiens, plaque cells stably express canonical smooth muscle cell and fibroblast markers ACTA2, MYH11, CNN1, FN1, COL1A1, and DCN across passages.


claim_key: biorxiv:29d2ed63-7041-1014-8745-c8282d7b1eac:claim:ad4fc6c373cb68408321
claim_id: claim:ad4fc6c373cb68408321
paper_key: biorxiv:29d2ed63-7041-1014-8745-c8282d7b1eac
span_literal:
snRNA-seq UMAP analysis results showed that TRPV1 is highly expressed in nociceptors, mechanoreceptors, and trigeminal neurons.

summary:
In Homo sapiens iPSC-derived sensory neurons, TRPV1 is highly expressed in nociceptors, mechanoreceptors, and trigeminal neurons.


claim_key: biorxiv:29d2ed63-7041-1014-8745-c8282d7b1eac:claim:38b401ccc45daf4c93fd
claim_id: claim:38b401ccc45daf4c93fd
paper_key: biorxiv:29d2ed63-7041-1014-8745-c8282d7b1eac
span_literal:
The sensory neurons were immunoassayed to examine their expression of peripherin, a marker for peripheral neurons, and ACE2, the receptor for SARS-CoV-2.

summary:
In Homo sapiens, peripherin is a marker for peripheral neurons, and angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2.


claim_key: biorxiv:29d2ed63-7041-1014-8745-c8282d7b1eac:claim:d3e68c53f744555a822e
claim_id: claim:d3e68c53f744555a822e
paper_key: biorxiv:29d2ed63-7041-1014-8745-c8282d7b1eac
summary: In Homo sapiens iPSC-derived cultures, olfactory neurons expressed TRPV1.
span_literal:
The results demonstrated that olfactory neurons expressed TRPV1 and are susceptible to direct infection by the virus.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:a36c33b4537b54c24dac
claim_id: claim:a36c33b4537b54c24dac
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
Multinucleated cells digesting cartilage in RA, OA and the primary bone tumour giant cell tumour of bone (GCTB) express an osteoclast phenotype (CD14−, HLA-DR−, CD45+, CD68+ CD51+, TRAP+, cathepsin K+ and MMP9+)

summary:
In Homo sapiens, multinucleated osteoclasts digesting cartilage in rheumatoid arthritis, osteoarthritis, and giant cell tumour of bone express CD45, CD68, CD51, tartrate-resistant acid phosphatase, cathepsin K, and MMP9 positively, while being negative for CD14 and HLA-DR.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:16aa26c04119a3d5dfe7
claim_id: claim:16aa26c04119a3d5dfe7
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
CD14+ monocytes differentiated on healthy human articular cartilage express immunophenotypic markers characteristic of osteoclasts (CD68+, CD14− and CD51+) and degrade cartilage via release of glycosaminoglycans (GAG).

summary:
In Homo sapiens, osteoclasts differentiated from CD14-positive monocytes on healthy human articular cartilage express CD68 and CD51 positively and are negative for CD14.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:3e5189ecf19c8c6fab1e
claim_id: claim:3e5189ecf19c8c6fab1e
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
osteoclasts differentiated on acellular human cartilage formed multinucleated cells expressing characteristic osteoclast marker genes (e.g. CTSK, MMP9) and proteins (TRAP, VNR) that visibly damaged the cartilage surface by SEM, but without the formation of resorption pits.

summary:
In Homo sapiens, osteoclasts differentiated on acellular human cartilage express the marker genes CTSK and MMP9 and the marker proteins TRAP and VNR (vitronectin receptor).


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:06d23fb19a13193c6fd7
claim_id: claim:06d23fb19a13193c6fd7
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
No difference in the expression of classical osteoclast marker genes (ACP5 (TRAP), ATP6V1A 21S, CA2, CLCN7, CSTK, MMP9) was evident between osteoclasts formed on dentine or on cartilage (Figure 1d).

summary:
In Homo sapiens, osteoclasts express the classical marker genes ACP5 (TRAP), ATP6V1A, CA2, CLCN7, CTSK, and MMP9 on both dentine and cartilage substrates.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:8d6c29012826029894da
claim_id: claim:8d6c29012826029894da
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
Osteoclasts differentiated on cartilage explants formed large multi-nucleated cells with the equivalent immunophenotypic characteristics (TRAP+, VNR+) and gene expression profile (CTSK, MMP9, ATP6V1A 21S, CAII, CLCN7, STAT3) of osteoclasts on dentine.

summary:
In Homo sapiens, osteoclasts differentiated on cartilage explants express TRAP, VNR (vitronectin receptor), CTSK, MMP9, ATP6V1A, CAII, CLCN7, and STAT3, equivalent to osteoclasts on dentine.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:6260f46b6294fa8138d5
claim_id: claim:6260f46b6294fa8138d5
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
MMP8 showed the greatest fold upregulation in osteoclasts on cartilage versus dentine (8.89-fold, p = 0.0133)

summary:
In Homo sapiens, MMP8 is upregulated in osteoclasts on cartilage compared to osteoclasts on dentine.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:2e5c121652a867c59ed6
claim_id: claim:2e5c121652a867c59ed6
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
RNA sequencing and RT-qPCR analysis identified MMP8 as overexpressed in osteoclasts differentiated on cartilage versus dentine, while MMP9 was the most highly expressed MMP on both substrates.

summary:
In Homo sapiens, MMP8 is overexpressed in osteoclasts differentiated on cartilage versus dentine, while MMP9 is the most highly expressed matrix metalloproteinase in osteoclasts on both substrates.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:3e57a56621ffefad3083
claim_id: claim:3e57a56621ffefad3083
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
Multinucleated cells form within the inflammatory synovium in RA but only express the calcitonin receptor, a marker of fully differentiated osteoclasts, when they come into direct contact with calcified cartilage or subchondral bone, suggesting that contact with either form of mineralised tissue can direct the final stages of differentiation

summary:
In Homo sapiens, fully differentiated osteoclasts express the calcitonin receptor as a marker when in direct contact with calcified cartilage or subchondral bone.


claim_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6:claim:7a342524c2b65a3cfd2b
claim_id: claim:7a342524c2b65a3cfd2b
paper_key: biorxiv:29dae57b-6d36-1014-8489-e77255373be6
span_literal:
They are formed by the fusion of CD14+ monocytes and regulate skeletal development and maintenance via homeostatic interactions with bone-forming osteoblasts.

summary:
In Homo sapiens, osteoclasts are formed by the fusion of CD14-positive monocytes, indicating that CD14 is a positive marker of the monocyte precursors.


claim_key: biorxiv:2c125abd-6c2b-1014-ae79-dfd1c32485ea:claim:6e97c4f1933c51132cb1
claim_id: claim:6e97c4f1933c51132cb1
paper_key: biorxiv:2c125abd-6c2b-1014-ae79-dfd1c32485ea
span_literal:
Hence, we have shown the expression of pluripotent markers OCT4, SOX2, SSEA4 and TRA-1-60 by immunostaining after single-cell cloning and expansion (Figure 5B).

summary:
In Homo sapiens, induced pluripotent stem cells express the pluripotency markers OCT4, SOX2, SSEA4, and TRA-1-60 as shown by immunostaining after single-cell cloning and expansion.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:f26873110603ae536430
claim_id: claim:f26873110603ae536430
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
sertoli cells, in addition to specifically expressing classical markers AMH and SOX9 (Fröjdman, Harley, Pelliniemi, & biology, 2000; Lasala et al., 2011), also exhibited strong expression of APOA1 (Figure 1F).

summary:
In Homo sapiens, Sertoli cells specifically express the classical markers AMH and SOX9, and also exhibit strong expression of APOA1.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:3962e8ea80360a8c9c62
claim_id: claim:3962e8ea80360a8c9c62
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
we identified that the PMCs not only expressed the classical marker MYH11 (Lottrup et al., 2014), which is concurrently highly expressed in smooth muscle cells, displaying limited specificity, but also demonstrated higher specificity in the expression of DPEP1, suggesting its potential as a specific marker for PMCs.

summary:
In Homo sapiens, peritubular myoid cells express the classical marker MYH11 and demonstrate higher specificity in the expression of DPEP1, suggesting its potential as a specific marker for peritubular myoid cells.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:0aad9c3650f6fbae1de5
claim_id: claim:0aad9c3650f6fbae1de5
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
C19orf84, PIWIL4, ST3GAL4, UTF1, ID4, and A2M were expressed on SSC0 and SSC1 subtypes, ITGB1 and L1TD1 were expressed SSC0, SSC1, SSC2 (Figure S1B).

summary:
In Homo sapiens, C19orf84, PIWIL4, ST3GAL4, UTF1, ID4, and A2M are expressed in spermatogonial stem cell 0 and spermatogonial stem cell 1 subtypes. In Homo sapiens, ITGB1 and L1TD1 are expressed in spermatogonial stem cell 0, spermatogonial stem cell 1, and spermatogonial stem cell 2.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:dac418775e5cb12edc29
claim_id: claim:dac418775e5cb12edc29
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
C19orf84, PIWIL4, ST3GAL4, UTF1, ID4, and A2M were expressed on SSC0 and SSC1 subtypes, ITGB1 and L1TD1 were expressed SSC0, SSC1, SSC2 (Figure S1B).

summary:
In Homo sapiens, C19orf84, PIWIL4, ST3GAL4, UTF1, ID4, and A2M are expressed in spermatogonial stem cell 1 subtypes. In Homo sapiens, ITGB1 and L1TD1 are expressed in spermatogonial stem cell 1.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:8825eca3f800ba349fab
claim_id: claim:8825eca3f800ba349fab
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal: PIWIL4, C19orf84 and ST3GAL4 were specifically expressed in SSC0 (belong to cluster 2).
summary:
In Homo sapiens, PIWIL4, C19orf84, and ST3GAL4 are specifically expressed in spermatogonial stem cell 0.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:907838dfb2c11b6f50d4
claim_id: claim:907838dfb2c11b6f50d4
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal: DMRT1, ASB9 and NANOS3 were the main specifically expressed genes in SSC2 (belong to cluster 3).
summary:
In Homo sapiens, DMRT1, ASB9, and NANOS3 are the main specifically expressed genes in spermatogonial stem cell 2.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:1a06b6e95f6b2b6adf6d
claim_id: claim:1a06b6e95f6b2b6adf6d
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal: DYNLL1, APRT and MKI67 were specifically expressed in Diffing-SPG (belong to cluster 1/2/3).
summary:
In Homo sapiens, DYNLL1, APRT, and MKI67 are specifically expressed in differentiating spermatogonia.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:5af7440d1aee04a41a62
claim_id: claim:5af7440d1aee04a41a62
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal: CTCFL, TEX19 and SMC1B were specifically expressed in Diffed-SPG (belong to cluster 1).
summary:
In Homo sapiens, CTCFL, TEX19, and SMC1B are specifically expressed in differentiated spermatogonia.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:6836ae4d238e79e45f26
claim_id: claim:6836ae4d238e79e45f26
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
no cluster-specific distinctive features were identified in SC1, as the marker genes (TF, SLC16A1 and CCNL1) of SC1 were also highly expressed in other Sertoli cells subclusters (Figure 4C).

summary:
In Homo sapiens, the marker genes TF, SLC16A1, and CCNL1 are expressed in Sertoli cell subtype 1, though they are also highly expressed in other Sertoli cell subclusters.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:a6abcbd5ddb4232dd4ba
claim_id: claim:a6abcbd5ddb4232dd4ba
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal: SPATS1, LINC01120 and LINC01206 were specifically expressed in SC3.
summary:
In Homo sapiens, SPATS1, LINC01120, and LINC01206 are specifically expressed in Sertoli cell subtype 3.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:017370c09a094c79245d
claim_id: claim:017370c09a094c79245d
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
we identified three novel Sertoli cell subtypes (namely SC4/7/8) and their specific markers, and defined SC4 (PRAP1) as immature, SC7 (BST2) as mature, and SC8 (CCDC62) as further mature (Figure 5D).

summary:
In Homo sapiens, PRAP1 is a specific marker of immature Sertoli cell subtype 4, BST2 is a specific marker of mature Sertoli cell subtype 7, and CCDC62 is a specific marker of further mature Sertoli cell subtype 8.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:e8094f88b89e531b0b04
claim_id: claim:e8094f88b89e531b0b04
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
We found that UTF1 and ID4 were specifically expressed in SSC1, and DMRT1 was specifically expressed in Diffing SPG.

summary:
In Homo sapiens, UTF1 and ID4 are specifically expressed in spermatogonial stem cell 1, and DMRT1 is specifically expressed in differentiating spermatogonia.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:fdd98c808b270dc6ef2e
claim_id: claim:fdd98c808b270dc6ef2e
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
In this study, UTF1 was specifically expressed in SSC1, and DMRT1 and NANOS3 were the main specifically expressed genes in SSC2.

summary:
In Homo sapiens, UTF1 is specifically expressed in spermatogonial stem cell 1, and DMRT1 and NANOS3 are the main specifically expressed genes in spermatogonial stem cell 2.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:e16f6b6d93aab02f2a31
claim_id: claim:e16f6b6d93aab02f2a31
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
span_literal:
In this study, UTF1 was specifically expressed in SSC1, and DMRT1 and NANOS3 were the main specifically expressed genes in SSC2.

summary:
In Homo sapiens, DMRT1 and NANOS3 are the main specifically expressed genes in spermatogonial stem cell 2.


claim_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90:claim:d33588ca8cd5b2933850
claim_id: claim:d33588ca8cd5b2933850
paper_key: biorxiv:2db922a0-7010-1014-aa5e-9a5620278c90
summary: In Homo sapiens, Sertoli cell subtype 3 is marked by SPATS1.
span_literal:
We determined the process of spermatogenesis and found that SC3 subtypes (marked by SPATS1) of Sertoli cell played an important role in this process.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:ffcb75338f6757e2a454
claim_id: claim:ffcb75338f6757e2a454
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
the Neural G0 cluster showed most significant enrichment for genes defining quiescent neural stem cells and oligodendrocyte progenitor cells (Figs. 2A-D). These genes include, among others: CLU, HOPX, ID3, OLIG2, PTN, SYT11, S100B, SOX9, PTPRZ1, and TTYH1 (Fig. 2B).

summary:
In Homo sapiens, the Neural G0 cluster of neural stem cells is enriched for quiescent neural stem cell and oligodendrocyte progenitor cell genes including CLU, HOPX, ID3, OLIG2, PTN, SYT11, S100B, SOX9, PTPRZ1, and TTYH1.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:912e4ea224111ee6dba1
claim_id: claim:912e4ea224111ee6dba1
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
the Neural G0 cluster showed most significant enrichment for genes defining quiescent neural stem cells and oligodendrocyte progenitor cells (Figs. 2A-D). These genes include, among others: CLU, HOPX, ID3, OLIG2, PTN, SYT11, S100B, SOX9, PTPRZ1, and TTYH1 (Fig. 2B).

summary:
In Homo sapiens, the Neural G0 cluster of neural stem cells is enriched for oligodendrocyte progenitor cell genes including CLU, HOPX, ID3, OLIG2, PTN, SYT11, S100B, SOX9, PTPRZ1, and TTYH1.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:452cc08684f492b3015a
claim_id: claim:452cc08684f492b3015a
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
The Neural G0 cluster also showed significant repression of 246 genes peaking in other phases of cell cycle, including suppression of CCND1 expression, which is an indicator of cell cycle exit (Sherr, 1995) and other cell cycle regulated genes such as AURKB, CCNB1/2, CDC20, CDK1, and MKI67 (Figs. 1E & S1C).

summary:
In Homo sapiens, the Neural G0 cluster of neural stem cells shows suppression of CCND1, AURKB, CCNB1/2, CDC20, CDK1, and MKI67, indicating cell cycle exit.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:9f57dd2c87a3cb301266
claim_id: claim:9f57dd2c87a3cb301266
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
the 158 up regulated genes defining this cluster were key genes with roles in neural development, including glial cell differentiation, neurogenesis, neuron differentiation, and oligodendrocyte differentiation (Figs. 1E, S1C, & S2; Supplementary Table SS). These genes included transcription factors with known roles in balancing stem cell identity and differentiation, including BEX1, HEY1, HOPX, OLIG2, SOX2, SOX4, and SOX9 (Bergsland et al, 2006; Sakamoto et al, 2003; Scott et al, 2010) (Figs. 1E & S2).

summary:
In Homo sapiens, the Neural G0 cluster of neural stem cells is defined by upregulated genes including BEX1, HEY1, HOPX, OLIG2, SOX2, SOX4, and SOX9, which have roles in balancing stem cell identity and differentiation.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:0d21b4f31b27fa846135
claim_id: claim:0d21b4f31b27fa846135
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal: IGFBP3 and IGFBP5
summary:
In Homo sapiens, the G1 cluster of neural stem cells is enriched for insulin-like growth factor receptor 1 signaling genes including IGFBP3 and IGFBP5.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:b213659315988e2c414e
claim_id: claim:b213659315988e2c414e
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
The Late G1 cluster was defined by genes important in G1 cell cycle progression, including CCND1 and MYC, and enriched for cholesterol biosynthesis, cell adhesion genes, and the subset of YAP target genes, such as CTGF and SERPINE1 (Figs. 1E, S1B, S1C, & S2).

summary:
In Homo sapiens, the Late G1 cluster of neural stem cells is defined by CCND1, MYC, CTGF, and SERPINE1.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:bba99a799f94432f1fd0
claim_id: claim:bba99a799f94432f1fd0
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
Cyclin expression patterns are consistent with prior knowledge where CCND1 is a marker gene for the Late G1 and S phase clusters, CCNE2 is a marker gene for S phase cluster only, CCNA2 is a marker for the S/G2 and G2/M phase clusters, CCNA1 and CCNB1 for G2/M phase cluster only, and CCNB2 for G2/M and M/Early G1 phase clusters.

summary:
In Homo sapiens neural stem cells, CCND1 is a marker gene for the Late G1 and S phase clusters, CCNE2 is a marker gene for the S phase cluster, CCNA2 is a marker for the S/G2 and G2/M phase clusters, CCNA1 and CCNB1 for the G2/M phase cluster, and CCNB2 for the G2/M and M/Early G1 phase clusters.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:ca13a84fc3bf843117dc
claim_id: claim:ca13a84fc3bf843117dc
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
summary:
In Homo sapiens neural stem cells, CCNA2, CCNA1, CCNB1, and CCNB2 are marker genes for the G2/M phase cluster.


claim_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191:claim:853a4959e063df4144f5
claim_id: claim:853a4959e063df4144f5
paper_key: biorxiv:2e0cb1c8-7146-1014-adb8-b57e9dddb191
span_literal:
12 genes, in particular, showed the strongest intersection between data sets (Suppl. Table S4; Suppl. Fig S5), including included EDNRB, FABP7, GPM6A, GMP6B, HEY1, PRDX1, PTPRZ1, SCD5, and TTYH1.

summary:
In Homo sapiens glioma, Neural G0 cells are enriched for EDNRB, FABP7, GPM6A, GPM6B, HEY1, PRDX1, PTPRZ1, SCD5, and TTYH1.


claim_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d:claim:13aac3ad6000de27a7da
claim_id: claim:13aac3ad6000de27a7da
paper_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d
span_literal:
In HAstV1-infected organoids, viral RNA was strongly co-localized with the expression of MKI67 (Fig.3D), a marker of proliferation which in our organoid system is expressed predominantly in cycling transit-amplifying cells (Fig.3B).

summary:
In Homo sapiens intestinal organoids, MKI67 is a marker of proliferation expressed predominantly in cycling transit-amplifying cells.


claim_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d:claim:7d783538f9932789f54e
claim_id: claim:7d783538f9932789f54e
paper_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d
summary: In Homo sapiens intestinal organoids, OLFM4 is a marker of stem-like cells.
span_literal:
Viral RNA was also detected, although to lesser extent, in stem-like cells (marker OLFM4) (Fig.3F), enteroendocrine cells (marker CHGB) (Fig.3G), as well as goblet cells (marker FCGBP) (Fig.3H).


claim_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d:claim:bf0993b4f036454c4a83
claim_id: claim:bf0993b4f036454c4a83
paper_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d
summary: In Homo sapiens intestinal organoids upon viral infection, APOA1 is upregulated in enterocytes.
span_literal:
This response includes canonical marker genes for the detected cell types e.g. upregulation of APOA1 in enterocytes, downregulation of OLFM4 in stem cells and TA cells, and upregulation of CHGA in enteroendocrine cells (Fig.4E).


claim_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d:claim:9e2fc7f8006d89902aa5
claim_id: claim:9e2fc7f8006d89902aa5
paper_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d
span_literal:
This response includes canonical marker genes for the detected cell types e.g. upregulation of APOA1 in enterocytes, downregulation of OLFM4 in stem cells and TA cells, and upregulation of CHGA in enteroendocrine cells (Fig.4E).

summary:
In Homo sapiens intestinal organoids upon viral infection, OLFM4 is downregulated in transit-amplifying cells.


claim_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d:claim:0504b3cab48d7c40a3be
claim_id: claim:0504b3cab48d7c40a3be
paper_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d
summary:
In Homo sapiens intestinal organoids upon viral infection, CHGA is upregulated in enteroendocrine cells.


claim_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d:claim:7d2c9f33b90680032910
claim_id: claim:7d2c9f33b90680032910
paper_key: biorxiv:30133163-6da7-1014-b9ea-c64da98c767d
span_literal:
The probes directed against SMOC2, MKI67, CHGB, FCGBP, OLFM4, FABP6 and LYZ showed discrete staining overlapping within cell borders suggesting cell type specificity.

summary:
In Homo sapiens intestinal organoids, probes for SMOC2, MKI67, CHGB, FCGBP, OLFM4, FABP6, and LYZ showed cell type-specific staining patterns.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:b8926f2c1a125893dea7
claim_id: claim:b8926f2c1a125893dea7
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
clusters 15 to 20 show a consistently higher expression of the T-cell marker genes CD3D, CD3E, and CD3G relative to all other clusters

summary:
In Homo sapiens, T cells are marked by positive expression of CD3D, CD3E, and CD3G in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:7a9dee9abc7dfb365109
claim_id: claim:7a9dee9abc7dfb365109
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal: Clusters 17, 18, and 19 show consistent expression of CD8A and CD8B, while the others do not
summary:
In Homo sapiens, CD8-positive T cells are marked by positive expression of CD8A and CD8B in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:083e74715c69b45059ef
claim_id: claim:083e74715c69b45059ef
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
cluster 17 has high expression of naive T cell marker CCR7, whereas cluster 18 has a consistent expression of NK cell marker GNLY, KLRG1, and granzyme genes GZMA and GZMH, so we labeled them naive cytotoxic T cells and NK T cells

summary:
In Homo sapiens, naive cytotoxic T cells are marked by positive expression of CCR7 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:1325a0818cc5a2a4238e
claim_id: claim:1325a0818cc5a2a4238e
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
cluster 17 has high expression of naive T cell marker CCR7, whereas cluster 18 has a consistent expression of NK cell marker GNLY, KLRG1, and granzyme genes GZMA and GZMH, so we labeled them naive cytotoxic T cells and NK T cells

summary:
In Homo sapiens, natural killer T cells are marked by positive expression of GNLY, KLRG1, GZMA, and GZMH in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:d72c64f6974d0147f8fb
claim_id: claim:d72c64f6974d0147f8fb
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
Scaled normalized expressions of representative gene markers show clustering of cell subpopulations including T-cells (CD3D), B-cells (CD19), natural killer cells (KLRD1), FCGR3A+ monocytes (FCGR3A), CD14+ monocytes (CD14), dendritic cells (FCER1A), plasmacytoid dendritic cells (CLEC4C), megakaryocytes (ITGA2B), and CD34+ progenitor cells (CD34).

summary:
In Homo sapiens, T cells are marked by positive expression of CD3D in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:4bcceefd8b71a22a2078
claim_id: claim:4bcceefd8b71a22a2078
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
Scaled normalized expressions of representative gene markers show clustering of cell subpopulations including T-cells (CD3D), B-cells (CD19), natural killer cells (KLRD1), FCGR3A+ monocytes (FCGR3A), CD14+ monocytes (CD14), dendritic cells (FCER1A), plasmacytoid dendritic cells (CLEC4C), megakaryocytes (ITGA2B), and CD34+ progenitor cells (CD34).

summary:
In Homo sapiens, B cells are marked by positive expression of CD19 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:5eb4c004928a83177aa1
claim_id: claim:5eb4c004928a83177aa1
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
Scaled normalized expressions of representative gene markers show clustering of cell subpopulations including T-cells (CD3D), B-cells (CD19), natural killer cells (KLRD1), FCGR3A+ monocytes (FCGR3A), CD14+ monocytes (CD14), dendritic cells (FCER1A), plasmacytoid dendritic cells (CLEC4C), megakaryocytes (ITGA2B), and CD34+ progenitor cells (CD34).

summary:
In Homo sapiens, natural killer cells are marked by positive expression of KLRD1 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:69d7ee9b9c240bfa22af
claim_id: claim:69d7ee9b9c240bfa22af
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
summary:
In Homo sapiens, FCGR3A-positive monocytes are marked by positive expression of FCGR3A in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:c5cfe6746cc8fefcd013
claim_id: claim:c5cfe6746cc8fefcd013
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
summary:
In Homo sapiens, CD14-positive monocytes are marked by positive expression of CD14 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:c1416d0c99877348774c
claim_id: claim:c1416d0c99877348774c
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
summary:
In Homo sapiens, dendritic cells are marked by positive expression of FCER1A in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:3442da24fc00a59921a1
claim_id: claim:3442da24fc00a59921a1
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
summary:
In Homo sapiens, plasmacytoid dendritic cells are marked by positive expression of CLEC4C in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:8970ea3d1242a8e70602
claim_id: claim:8970ea3d1242a8e70602
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
summary:
In Homo sapiens, megakaryocytes are marked by positive expression of ITGA2B in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:2681e065c22378161e19
claim_id: claim:2681e065c22378161e19
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
summary:
In Homo sapiens, CD34-positive progenitor cells are marked by positive expression of CD34 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:32cb8194fef67da100e9
claim_id: claim:32cb8194fef67da100e9
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
Given that B lymphocyte antigen receptor genes CD79A, CD79B, and B lymphocyte cell surface antigens MS4A1, CD19 are grouped in module 10, we can infer that the cells in cell cluster 2, 3, and 4 are B cells

summary:
In Homo sapiens, B cells are marked by positive expression of CD79A, CD79B, MS4A1, and CD19 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:935913ecd15c1f299c8c
claim_id: claim:935913ecd15c1f299c8c
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
We found that plasmacytoid dendritic cell (pDC) marker genes ITM2C, IRF7, LILRA4, and CLEC4C are highly expressed in module 21, indicating that cells in cell cluster 7 are pDCs

summary:
In Homo sapiens, plasmacytoid dendritic cells are marked by positive expression of ITM2C, IRF7, LILRA4, and CLEC4C in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:e7af6f6efef6f6fac074
claim_id: claim:e7af6f6efef6f6fac074
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
Natural killer (NK) cell markers NKG7, GZMA, CST7, KLRD1, and GZMH are categorized in module 40, suggesting that cells in cell cluster 9 are NK cells

summary:
In Homo sapiens, natural killer cells are marked by positive expression of NKG7, GZMA, CST7, KLRD1, and GZMH in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:20146dd50c866971d9b1
claim_id: claim:20146dd50c866971d9b1
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
Module 74 contains T cell receptor genes including TRAC, CD3D, TRBC1, and CD3G, which indicates cells from cell clusters 15 to 20 are T cells

summary:
In Homo sapiens, T cells are marked by positive expression of TRAC, CD3D, TRBC1, and CD3G in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:47d3c40ae39ec04f3cce
claim_id: claim:47d3c40ae39ec04f3cce
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal: the top 5 genes in module 43 are monocyte genes S100A9, S100A8, S100A12, VCAN, and CD14
summary:
In Homo sapiens, monocytes are marked by positive expression of S100A9, S100A8, S100A12, VCAN, and CD14 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:a4ed84b1b0d13a52f71e
claim_id: claim:a4ed84b1b0d13a52f71e
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal: T cell markers CD3D, TRAC and NK cell markers CST7, NKG7 are both positively correlated with PC 2
summary:
In Homo sapiens, T cells are marked by positive expression of CD3D and TRAC, while natural killer cells are marked by positive expression of CST7 and NKG7 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:27c2a27154c4c5472cc3
claim_id: claim:27c2a27154c4c5472cc3
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal: T cell markers CD3D, TRAC and NK cell markers CST7, NKG7 are both positively correlated with PC 2
summary:
In Homo sapiens, natural killer cells are marked by positive expression of CST7 and NKG7 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:0b14bad55a1fb4f42c5a
claim_id: claim:0b14bad55a1fb4f42c5a
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
FCGR3A (FCGR3A+ monocyte marker) and LILRA4 (plasmacytoid dendritic cell marker) are both negatively correlated with PC 7.

summary:
In Homo sapiens, FCGR3A-positive monocytes are marked by positive expression of FCGR3A, and plasmacytoid dendritic cells are marked by positive expression of LILRA4 in peripheral blood mononuclear cells.


claim_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3:claim:4c617b494cc54c41df78
claim_id: claim:4c617b494cc54c41df78
paper_key: biorxiv:307b2bd7-6cb9-1014-a6b4-a58a7220bba3
span_literal:
FCGR3A (FCGR3A+ monocyte marker) and LILRA4 (plasmacytoid dendritic cell marker) are both negatively correlated with PC 7.

summary:
In Homo sapiens, plasmacytoid dendritic cells are marked by positive expression of LILRA4 in peripheral blood mononuclear cells.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:b84a95c865449bc6844b
claim_id: claim:b84a95c865449bc6844b
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
As well as the more traditional markers of activated fibroblasts, COL1A1 and ACTA2, (7, 8) novel markers of high collagen expressing fibroblast populations in IPF include CTHRC1, HAS1 and PLIN2.

summary:
In Homo sapiens, COL1A1 and ACTA2 are traditional markers of activated fibroblasts, while CTHRC1, HAS1, and PLIN2 are novel markers of high collagen expressing fibroblast populations in idiopathic pulmonary fibrosis.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:7e29717fe590ced545da
claim_id: claim:7e29717fe590ced545da
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
As well as the more traditional markers of activated fibroblasts, COL1A1 and ACTA2, (7, 8) novel markers of high collagen expressing fibroblast populations in IPF include CTHRC1, HAS1 and PLIN2.

summary:
In Homo sapiens, CTHRC1, HAS1, and PLIN2 are novel markers of high collagen expressing fibroblast populations in idiopathic pulmonary fibrosis.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:122f4374df8340ef5cb9
claim_id: claim:122f4374df8340ef5cb9
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
In contrast CTHRC1 was identified as a more specific marker of the small subset of fibroblasts that produce the highest levels of ECM proteins in pulmonary fibrosis and other fibrotic diseases (8).

summary:
In Homo sapiens, collagen triple helix repeat containing 1 (CTHRC1) was identified as a more specific marker of the small subset of fibroblasts that produce the highest levels of extracellular matrix proteins in pulmonary fibrosis.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:e2a458f8ba293e8f7acd
claim_id: claim:e2a458f8ba293e8f7acd
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
summary: In Homo sapiens idiopathic pulmonary fibrosis lung, ACTA2 is a positive marker of myofibroblasts.
span_literal:
These include alveolar fibroblasts, ACTA2-positive myofibroblasts, HAS1-high fibroblasts, PLIN2-positive fibroblasts and CTHRC1-expressing fibroblasts (7, 8).


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:2a03da7360afc8264d99
claim_id: claim:2a03da7360afc8264d99
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
These include alveolar fibroblasts, ACTA2-positive myofibroblasts, HAS1-high fibroblasts, PLIN2-positive fibroblasts and CTHRC1-expressing fibroblasts (7, 8).

summary:
In Homo sapiens idiopathic pulmonary fibrosis lung, HAS1 is a positive marker of HAS1-high fibroblasts.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:5e2e3ef8395bdd5e0d7f
claim_id: claim:5e2e3ef8395bdd5e0d7f
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
These include alveolar fibroblasts, ACTA2-positive myofibroblasts, HAS1-high fibroblasts, PLIN2-positive fibroblasts and CTHRC1-expressing fibroblasts (7, 8).

summary:
In Homo sapiens idiopathic pulmonary fibrosis lung, PLIN2 is a positive marker of PLIN2-positive fibroblasts.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:44be4e4db4057f971e4a
claim_id: claim:44be4e4db4057f971e4a
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
summary:
In Homo sapiens idiopathic pulmonary fibrosis lung, CTHRC1 is a positive marker of CTHRC1-expressing fibroblasts.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:b5b561a82bff87f4cf46
claim_id: claim:b5b561a82bff87f4cf46
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
We identified 6 genes with the highest positive fold changes that define the transcriptional identity of the CTHRC1+ fibroblast population including CTHRC1 and COL1A1, as expected (individual expression levels shown in Figure 4c), as well as ASPN, POSTN, ADAM12 and TGFBI (individual expression levels shown in Figure 4d).

summary:
In Homo sapiens, six genes with the highest positive fold changes define the transcriptional identity of the CTHRC1+ fibroblast population: CTHRC1, COL1A1, ASPN, POSTN, ADAM12, and TGFBI.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:45f6391d060a8026bd3e
claim_id: claim:45f6391d060a8026bd3e
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
COL1A1 is unsurprisingly one of the most positively regulated genes within this population but to the best of our knowledge ASPN, ADAM12 and TGFBI have not been previously reported to be highly expressed by the pathologic CTHRC1+ fibroblast population.

summary:
In Homo sapiens, COL1A1 is one of the most positively regulated genes in the pathologic CTHRC1+ fibroblast population, and ASPN, ADAM12, and TGFBI are also highly expressed by this population.


claim_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748:claim:5824b00e392f117edb20
claim_id: claim:5824b00e392f117edb20
paper_key: biorxiv:30a348aa-6c75-1014-b586-8a08f0d76748
span_literal:
ASPN encodes the proteoglycan asporin which has also been reported to be highly upregulated in the lungs of IPF patients (36) and has been found to be localised to ACTA2-positive myofibroblasts (37).

summary:
In Homo sapiens, ASPN (encoding asporin) has been found to be localised to ACTA2-positive myofibroblasts in idiopathic pulmonary fibrosis lungs.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:abc4159d0457e1eb6299
claim_id: claim:abc4159d0457e1eb6299
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Our analysis highlights NKG7 expression as a strong marker of cytotoxicity, exhibiting a strong correlation with overall cytotoxic activity (r = 0.97) and surpassing traditional markers such as Granzyme B and Perforin in reliability.

summary:
In Homo sapiens, Natural Killer Cell Granule Protein 7 (NKG7) is a strong positive marker of cytotoxic cells, exhibiting a strong correlation with overall cytotoxic activity and surpassing Granzyme B (GZMB) and Perforin (PRF1) in reliability.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:1971253cdd19c55adbdf
claim_id: claim:1971253cdd19c55adbdf
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: Of note, pDCs displayed high expression of GZMB but no other cytotoxic molecule.
summary:
In Homo sapiens, plasmacytoid dendritic cells display high expression of GZMB but no other cytotoxic molecule.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:7677dad2f4c61bced2db
claim_id: claim:7677dad2f4c61bced2db
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
The analysis revealed that NKG7 expression had the strongest correlation (r = 0.97) with cytotoxicity score (Figure 2A).

summary:
In Homo sapiens, NKG7 expression had the strongest correlation with cytotoxicity score across peripheral blood mononuclear cell subsets, marking cytotoxic cells.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:c8a6bb95c5134578b557
claim_id: claim:c8a6bb95c5134578b557
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
This verified NK cells as potent expressers of NKG7 with both CD56Bright and CD56Dim populations expressing NKG7.

summary:
In Homo sapiens, natural killer cells are potent expressers of NKG7, with both CD56Bright and CD56Dim populations expressing NKG7.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:a8238734c9db0931ef15
claim_id: claim:a8238734c9db0931ef15
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Indeed, we found that NKG7 positive CD4 T-cells were enriched for cytotoxic molecules such as GZMA, GZMB, and PRF (Figure 2E).

summary:
In Homo sapiens, NKG7-positive CD4 T cells were enriched for cytotoxic molecules such as GZMA, GZMB, and PRF1.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:399018374eadbe74c38b
claim_id: claim:399018374eadbe74c38b
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: Therefore, NKG7 may serve as a valuable phenotypic marker to capture CD4-CTLs.
summary:
In Homo sapiens, NKG7 may serve as a valuable phenotypic marker to capture CD4 cytotoxic T lymphocytes.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:e350dd71a9e2b92bd92f
claim_id: claim:e350dd71a9e2b92bd92f
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
This revealed that NKG7 is consistently expressed across NK cells from various tissue locations (Figure 3A).

summary:
In Homo sapiens, NKG7 is consistently expressed across natural killer cells from various tissue locations.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:2f2973ab60914778c3a8
claim_id: claim:2f2973ab60914778c3a8
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Across both NK and CD8+ T-cells, GZMA, GZMM, PRF1, and NKG7 were consistently expressed and detected regardless of tissue.

summary:
In Homo sapiens, GZMA, GZMM, PRF1, and NKG7 were consistently expressed in natural killer cells regardless of tissue.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:4fe33f45436a5549cb88
claim_id: claim:4fe33f45436a5549cb88
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Across both NK and CD8+ T-cells, GZMA, GZMM, PRF1, and NKG7 were consistently expressed and detected regardless of tissue.

summary:
In Homo sapiens, GZMA, GZMM, PRF1, and NKG7 were consistently expressed in CD8-positive T cells regardless of tissue.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:d02bc76855f0fa4301bb
claim_id: claim:d02bc76855f0fa4301bb
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Importantly, GZMB had variable expression within CD8+ T-cells and was minimally detected in lymph node, salivary gland, and thymic tissues.

summary:
In Homo sapiens, GZMB had variable expression within CD8-positive T cells and was minimally detected in lymph node, salivary gland, and thymus tissues.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:0ff13c26dc3c8194b197
claim_id: claim:0ff13c26dc3c8194b197
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Interestingly, the gdT-V9D2 population could be distinguished from remaining gdT cells by the expression of GZMK.

summary:
In Homo sapiens, the Vγ9Vδ2 gamma delta T cell population could be distinguished from remaining gamma delta T cells by the expression of GZMK.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:cebff9a8cdfc5e32a4e6
claim_id: claim:cebff9a8cdfc5e32a4e6
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Meanwhile, MAIT cells expressed high levels of expression of all cytotoxic molecules except GZMB and GZMH.

summary:
In Homo sapiens, mucosal-associated invariant T cells expressed high levels of all cytotoxic molecules except GZMB and GZMH.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:1b32ebe95773d2ef30a4
claim_id: claim:1b32ebe95773d2ef30a4
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Conversely, NK-Bright cells, which are typically described as pro-inflammatory or regulatory in nature, expressed high levels of all markers except GZMH.

summary:
In Homo sapiens, CD56BrightCD16-negative natural killer cells expressed high levels of all cytotoxic markers except GZMH.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:a03f20800ec44522a704
claim_id: claim:a03f20800ec44522a704
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
This revealed GZMK as poorly and inversely correlated with the expression of other cytotoxic genes in both CD8 and NK subsets (Supplementary Figure 1A).

summary:
In Homo sapiens, GZMK was poorly and inversely correlated with the expression of other cytotoxic genes in CD8 T cell subsets.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:b95c96e98a9069271f01
claim_id: claim:b95c96e98a9069271f01
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
This revealed GZMK as poorly and inversely correlated with the expression of other cytotoxic genes in both CD8 and NK subsets (Supplementary Figure 1A).

summary:
In Homo sapiens, GZMK was poorly and inversely correlated with the expression of other cytotoxic genes in natural killer cell subsets.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:caf765c1141cd0ec7069
claim_id: claim:caf765c1141cd0ec7069
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
NKG7 also functioned to demarcate CD4-CTLs, a subset with emerging relevance in anti-tumor responses.

summary:
In Homo sapiens, NKG7 functioned to demarcate CD4 cytotoxic T lymphocytes, a subset with emerging relevance in anti-tumor responses.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:7b222adfe07dafad428a
claim_id: claim:7b222adfe07dafad428a
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
it was observed that a considerable proportion (∼27%) of pro-inflammatory NK-Bright cells co-expressed GZMA, GZMK, GNLY, PRF1, and NKG7 (Figure 4A).

summary:
In Homo sapiens, a considerable proportion of CD56BrightCD16-negative natural killer cells co-expressed GZMA, GZMK, GNLY, PRF1, and NKG7.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:89f56731e1168cffe49a
claim_id: claim:89f56731e1168cffe49a
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
In contrast, the cytotoxic NK-Dim subset consistently co-expressed GZMA, GZMB, GNLY, PRF1, and NKG7, with polyfunctional populations of NK-Dim cells differing in their co-expression of GZMH and GZMM.

summary:
In Homo sapiens, the CD56DimCD16-positive natural killer cell subset consistently co-expressed GZMA, GZMB, GNLY, PRF1, and NKG7, with polyfunctional populations differing in their co-expression of GZMH and GZMM.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:b4696f2bc28437248faf
claim_id: claim:b4696f2bc28437248faf
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Interestingly, circa 20% of dnT cells were observed to exhibit solitary expression of GZMK, while a small subset of dnT cells co-expressed GZMK with either GZMA, GZMM, or both.

summary:
In Homo sapiens, approximately 20% of double-negative T cells exhibited solitary expression of GZMK, while a small subset co-expressed GZMK with either GZMA, GZMM, or both.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:fe63c316ab3ee953583d
claim_id: claim:fe63c316ab3ee953583d
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
For example, while the top five most abundant co-expression patterns for CD8-EM and CD4-CTLs consistently contained GZMA and NKG7, there was variable usage of other cytotoxic molecules.

summary:
In Homo sapiens, the top co-expression patterns for CD8 effector memory T cells consistently contained GZMA and NKG7.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:70d1dd387cd44afe29a2
claim_id: claim:70d1dd387cd44afe29a2
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
For example, while the top five most abundant co-expression patterns for CD8-EM and CD4-CTLs consistently contained GZMA and NKG7, there was variable usage of other cytotoxic molecules.

summary:
In Homo sapiens, the top co-expression patterns for CD4 cytotoxic T lymphocytes consistently contained GZMA and NKG7.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:22f4fb83c43e1e473b8b
claim_id: claim:22f4fb83c43e1e473b8b
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: While GZMK was absent from the top five most abundant CD4-CTL cell patterns.
summary:
In Homo sapiens, GZMK was absent from the top co-expression patterns of CD4 cytotoxic T lymphocytes.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:86489d14136da2d8a04f
claim_id: claim:86489d14136da2d8a04f
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: Notably, three of the top five most abundant CD8-EM and CD4-CTL patterns did not contain PRF1.
summary:
In Homo sapiens, three of the top five most abundant CD8 effector memory T cell co-expression patterns did not contain PRF1.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:d52b8a74725c8c881775
claim_id: claim:d52b8a74725c8c881775
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: Notably, three of the top five most abundant CD8-EM and CD4-CTL patterns did not contain PRF1.
summary:
In Homo sapiens, three of the top five most abundant CD4 cytotoxic T lymphocyte co-expression patterns did not contain PRF1.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:9fe690ef46ea3f92d20e
claim_id: claim:9fe690ef46ea3f92d20e
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: Indeed, NKG7 is the strongest correlate of cytotoxicity across tumor-infiltrating immune cells.
summary:
In Homo sapiens, NKG7 is the strongest correlate of cytotoxicity across tumor-infiltrating immune cells.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:2a5b605a56c0e2994853
claim_id: claim:2a5b605a56c0e2994853
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal: Within these tumor-infiltrating NK subsets, NKG7 was consistently expressed (Figure 5E).
summary:
In Homo sapiens, NKG7 was consistently expressed within tumor-infiltrating natural killer cell subsets.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:47506d94cb4e7e60a2e8
claim_id: claim:47506d94cb4e7e60a2e8
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
For instance, pro-inflammatory (NK-Bright) and cytotoxic (NK-Dim) cells exhibit distinct usage of GZMK and GZMH, reflecting functional specialization within cytotoxic programs (Jiang et al., 2011).

summary:
In Homo sapiens, CD56BrightCD16-negative natural killer cells and CD56DimCD16-positive natural killer cells exhibit distinct usage of GZMK and GZMH, reflecting functional specialization.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:f7a484e01358a3ec162f
claim_id: claim:f7a484e01358a3ec162f
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
For instance, pro-inflammatory (NK-Bright) and cytotoxic (NK-Dim) cells exhibit distinct usage of GZMK and GZMH, reflecting functional specialization within cytotoxic programs (Jiang et al., 2011).

summary:
In Homo sapiens, CD56DimCD16-positive natural killer cells and CD56BrightCD16-negative natural killer cells exhibit distinct usage of GZMK and GZMH, reflecting functional specialization.


claim_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d:claim:b57ca99843cc152081fd
claim_id: claim:b57ca99843cc152081fd
paper_key: biorxiv:315fa881-726d-1014-9d3d-bbe9b5731a1d
span_literal:
Indeed, NKG7 is frequently observed in gene signatures of CD4-CTLs across numerous disease contexts (Cachot et al., 2021; Maehara et al., 2020; Oh et al., 2020; Preglej & Ellmeier, 2022; Zhang et al., 2020; Zheng et al., 2017).

summary:
In Homo sapiens, NKG7 is frequently observed in gene signatures of CD4 cytotoxic T lymphocytes across numerous disease contexts.


claim_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c:claim:da4f0401fd4081b4cf1d
claim_id: claim:da4f0401fd4081b4cf1d
paper_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c
summary: In Homo sapiens pancreatic islets, INS is a marker gene for beta cells.
span_literal:
Genes such as INS (beta), GCG (alpha), SST (delta), PPY (PP/gamma), PRSS1 (acinar), the extracellular matrix protein gene COL1A1 (stellate) and the structural keratin gene KRT19 (ductal) were identified as marker genes to their respective cell-types by MICTI.


claim_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c:claim:116b8c75e55c953cbf6a
claim_id: claim:116b8c75e55c953cbf6a
paper_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c
span_literal:
The gene set enrichment analysis for marker genes of Acinar pancreatic islet (REG1A, PRSS1, CTRB1, REG1B, CELA3A, CPA1, CTRB2, REG3A, CLPS, PLA2G1B, SYCN, SPINK1) shows that they are enriched for the KEGG pathway of Pancreatic secretion (KEGG:04972).

summary:
In Homo sapiens pancreatic islets, REG1A, PRSS1, CTRB1, REG1B, CELA3A, CPA1, CTRB2, REG3A, CLPS, PLA2G1B, SYCN, and SPINK1 are marker genes for acinar cells.


claim_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c:claim:667084193ddf32f44a1d
claim_id: claim:667084193ddf32f44a1d
paper_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c
span_literal:
Alpha pancreatic islet marker genes, for example, CHGB, PAPPA2, SCG2, SERPINA1, were enriched for the Reactome pathway term of regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (REAC:R-HSA-381426).

summary:
In Homo sapiens pancreatic islets, CHGB, PAPPA2, SCG2, and SERPINA1 are marker genes for alpha cells.


claim_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c:claim:7257cbe182aefe93543d
claim_id: claim:7257cbe182aefe93543d
paper_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c
span_literal:
The regulation of insulin secretion (GO:0050796) was also an enriched GO term for the beta-pancreatic islet cell’s marker genes (ABCC8, CASR, PFKFB2, RBP4, HADH, G6PC2, SLC30A8, EFNA5).

summary:
In Homo sapiens pancreatic islets, ABCC8, CASR, PFKFB2, RBP4, HADH, G6PC2, SLC30A8, and EFNA5 are marker genes for beta cells.


claim_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c:claim:7c036ed1f377d2191844
claim_id: claim:7c036ed1f377d2191844
paper_key: biorxiv:3491a20c-6c0b-1014-8496-82b032785c2c
span_literal:
Insulin processing (REAC:R-HSA-264876) and Insulin secretion (KEGG:04911) were the Reactome and KEEG pathways enriched for the MICTI identified markers for beta-pancreatic islet cells (SLC30A8, PCSK1, ABCC8, ADCYAP1, INS) respectively.

summary:
In Homo sapiens pancreatic islets, SLC30A8, PCSK1, ABCC8, ADCYAP1, and INS are marker genes for beta cells.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:7974d5d330b6ca4fdac1
claim_id: claim:7974d5d330b6ca4fdac1
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
summary: In Homo sapiens, early myeloid progenitors are marked by CD123 and CLEC12A.
span_literal:
four terminal states were identified, which we named based on known cell surface proteins 52–55: 1) CD123+CLEC12A+ early myeloid progenitors (Myelo), 2) CD49f+CD41+ megakaryocyte progenitors (Mega), 3) CD44+FCER1A+CLEC12A+ basophil progenitors (Baso) and 4) CD36+CD71+CD235ab+ differentiated erythroid cells (Ery)


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:12c6c28b6d1283971461
claim_id: claim:12c6c28b6d1283971461
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
we identified hematopoietic stem cells (HSCs; CD34⁺CD38⁻CD90⁺), which expressed MECOM, PRDM16, HLF, and ERG and were non-proliferating

summary:
In Homo sapiens, hematopoietic stem cells are positive for CD34, CD90, MECOM, PRDM16, HLF, and ERG, and negative for CD38.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:5f8315a119ecdecf3ca2
claim_id: claim:5f8315a119ecdecf3ca2
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
We also found erythroid progenitors (CFU-es; CD34⁻CD36⁺CD71⁺CD235ab⁻) characterized by MYC and E2F1 expression and high proliferative activity

summary:
In Homo sapiens, erythroid progenitors (colony-forming unit-erythroid) are positive for CD36, CD71, MYC, and E2F1, and negative for CD34 and CD235ab.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:0c225d78771f6b1cdf43
claim_id: claim:0c225d78771f6b1cdf43
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
terminally differentiated erythroid cells (Poly-OrthoEBs; CD36lowCD71⁺CD235ab⁺) expressing NFE2, TAL1, GATA1, and HBB with low proliferation

summary:
In Homo sapiens, terminally differentiated erythroid cells (Poly-OrthoEBs) are positive for CD71, CD235ab, NFE2, TAL1, GATA1, and HBB.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:3028a5fe99b0b17288e8
claim_id: claim:3028a5fe99b0b17288e8
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
we identified megakaryocyte progenitors (MegaP; CD34⁻CD36⁺CD41⁺CD49f⁺) expressing FLI1, MEF2C, and MEIS1

summary:
In Homo sapiens, megakaryocyte progenitors are positive for CD36, CD41, CD49f, FLI1, MEF2C, and MEIS1, and negative for CD34.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:b12d20de05dfaf4d4c44
claim_id: claim:b12d20de05dfaf4d4c44
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal: basophil progenitors (BasoP; CD34⁻CLEC12A⁺FCER1A⁺CD44⁺) expressing GATA2
summary:
In Homo sapiens, basophil progenitors are positive for CLEC12A, FCER1A, CD44, and GATA2, and negative for CD34.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:ac1c79537f7d8f6befee
claim_id: claim:ac1c79537f7d8f6befee
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
based on surface marker expression (CD34⁺ CD38⁺ CD36⁻ CD71⁺ CD123⁻) and transcript levels (GATA1, TAL1, MEIS1, KLF1, FLI1, MYB), four clusters were identified as megakaryocyte-erythroid progenitors (MEPs)

summary:
In Homo sapiens, megakaryocyte-erythroid progenitors are positive for CD34, CD38, CD71, GATA1, TAL1, MEIS1, KLF1, FLI1, and MYB, and negative for CD36 and CD123.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:d4654ce129a6e66c7d38
claim_id: claim:d4654ce129a6e66c7d38
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
the eMEP population expressing higher levels of CD38 (Fig. 2C), consistent with previously validated erythroid-biased MEPs 59, whereas the mMEP population expresses higher levels of CD41 and MEF2C (Fig. 2C), consistent with previously validated megakaryocyte-biased MEPs

summary:
In Homo sapiens, erythroid-biased megakaryocyte-erythroid progenitors express higher levels of CD38, whereas megakaryocyte-biased megakaryocyte-erythroid progenitors express higher levels of CD41 and MEF2C.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:708f45821e703eb5372f
claim_id: claim:708f45821e703eb5372f
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
the eMEP population expressing higher levels of CD38 (Fig. 2C), consistent with previously validated erythroid-biased MEPs 59, whereas the mMEP population expresses higher levels of CD41 and MEF2C (Fig. 2C), consistent with previously validated megakaryocyte-biased MEPs

summary:
In Homo sapiens, megakaryocyte-biased megakaryocyte-erythroid progenitors express higher levels of CD41 and MEF2C compared to erythroid-biased megakaryocyte-erythroid progenitors.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:88de0b571bfa402fe9a1
claim_id: claim:88de0b571bfa402fe9a1
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
surface protein profiling along these trajectories not only confirmed gradual phenotypic transitions but also revealed candidate markers, such as GPR56 in HSCs (Fig. 2D; Fig. S3B), which is linked to the maintenance of stemness

summary:
In Homo sapiens, GPR56 is a candidate marker of hematopoietic stem cells linked to the maintenance of stemness.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:cb45e62ef8258f16f338
claim_id: claim:cb45e62ef8258f16f338
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
Central to this HSPC-specific network are many well-established master regulators of stemness, including ERG 81–83, MEIS1 84, ZEB1 85, PRDM16 86, HES1 87, RUNX1 88, ETV6 89, and ELF1 90, among others

summary:
In Homo sapiens, hematopoietic stem and progenitor cells are characterized by the master regulators ERG, MEIS1, ZEB1, PRDM16, HES1, RUNX1, ETV6, and ELF1.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:129c961f429b132965e5
claim_id: claim:129c961f429b132965e5
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
The highly proliferative colony-forming erythroid (CFU-e) population was characterized by an eGRN centered on pro-proliferative TFs such as MYC

summary:
In Homo sapiens, the colony-forming unit-erythroid population is characterized by the pro-proliferative transcription factor MYC.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:be646c896dc2fbcfb7aa
claim_id: claim:be646c896dc2fbcfb7aa
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
the pro-erythroblast (proEB) population displayed an eGRN dominated by cell cycle regulators including E2F8, E2F7, E2F1 and their obligate partner TFDP1

summary:
In Homo sapiens, the pro-erythroblast population is characterized by cell cycle regulators E2F8, E2F7, E2F1, and TFDP1.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:62fb6857606532054eb8
claim_id: claim:62fb6857606532054eb8
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
eGRNs were centered on canonical master regulators of erythropoiesis, including GATA1, KLF1 and FOXO3 (most active in BasoEBs) as well as TAL1 and NFE2 (most active in Poly-OrthoEBs)

summary:
In Homo sapiens, basophilic erythroblasts are characterized by the master regulators GATA1, KLF1, and FOXO3.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:11ba58e3bba78f9a773d
claim_id: claim:11ba58e3bba78f9a773d
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
eGRNs were centered on canonical master regulators of erythropoiesis, including GATA1, KLF1 and FOXO3 (most active in BasoEBs) as well as TAL1 and NFE2 (most active in Poly-OrthoEBs)

summary:
In Homo sapiens, polychromatic-orthochromatic erythroblasts (Poly-OrthoEBs) are characterized by the master regulators TAL1 and NFE2.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:b707d4509de98b028a69
claim_id: claim:b707d4509de98b028a69
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
span_literal:
we also identified an eGRN specific to megakaryocyte progenitors, centered on master regulators of megakaryopoiesis, including FLI1, ETS2, and MEF2C

summary:
In Homo sapiens, megakaryocyte progenitors are characterized by the master regulators of megakaryopoiesis FLI1, ETS2, and MEF2C.


claim_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096:claim:dacbf3da4c635d9c8eaa
claim_id: claim:dacbf3da4c635d9c8eaa
paper_key: biorxiv:35208be1-70ce-1014-9f75-f7d24dac9096
summary: In Homo sapiens, early basophil progenitors are characterized by the known regulator GATA2.
span_literal:
we were nevertheless able to identify a cell-specific eGRN for early progenitors, which included the known regulator GATA2


claim_key: biorxiv:36b52534-7118-1014-9621-c8d35d0ed1df:claim:92c47428ec9b7a276901
claim_id: claim:92c47428ec9b7a276901
paper_key: biorxiv:36b52534-7118-1014-9621-c8d35d0ed1df
span_literal:
CHIT1), lysozyme (Lyz1), lipase (LIPF), legumain (LGMN), Nlrp3, alpha-N-acetylgalactosaminidase (NAGA), zinc finger E-box-binding homeobox 1(zfh1), caspase1 (Casp1) and NPC intracellular cholesterol transporter 2 (NPC2) were also specifically expressed in human macrophage (Figure 3A; figures supplement 2B and 4)(Karlsson et al., 2021), which strongly suggest that MH2 was probably the invertebrate homolog of human macrophage

summary:
In Homo sapiens, chitotriosidase (CHIT1), lysozyme (Lyz1), lipase (LIPF), legumain (LGMN), NOD-like receptor protein 3 (NLRP3), alpha-N-acetylgalactosaminidase (NAGA), zinc finger E-box-binding homeobox 1 (ZFH1), caspase 1 (CASP1), and NPC intracellular cholesterol transporter 2 (NPC2) are specifically expressed in macrophage.


claim_key: biorxiv:36b52534-7118-1014-9621-c8d35d0ed1df:claim:35af983d13b199a92ba2
claim_id: claim:35af983d13b199a92ba2
paper_key: biorxiv:36b52534-7118-1014-9621-c8d35d0ed1df
span_literal:
NOD-like receptor protein 3 (Nlrp3) is the key component for inflammasome and is highly expressed in monocyte/macrophage for processing of IL1ß

summary:
In Homo sapiens, NOD-like receptor protein 3 (NLRP3) is highly expressed in monocyte/macrophage for processing of interleukin 1 beta.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:7a2c61f14c8038da488c
claim_id: claim:7a2c61f14c8038da488c
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
iAstrocytes in cluster 1 expressed markers related to the acute phase response such as C3, IL6, and IL1B, whereas iAstrocytes in cluster 2 expressed markers related to interferon signaling such as VCAM1, CXCL10, and LTB56

summary:
In Homo sapiens, inflammatory reactive astrocyte state 1 (IRAS1) expresses C3, IL6, and IL1B as markers related to the acute phase response in iPSC-derived astrocytes.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:2035dec4cfba4e66d46d
claim_id: claim:2035dec4cfba4e66d46d
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
iAstrocytes in cluster 1 expressed markers related to the acute phase response such as C3, IL6, and IL1B, whereas iAstrocytes in cluster 2 expressed markers related to interferon signaling such as VCAM1, CXCL10, and LTB56

summary:
In Homo sapiens, inflammatory reactive astrocyte state 2 (IRAS2) expresses VCAM1 and CXCL10 as markers related to interferon signaling in iPSC-derived astrocytes.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:34171432cb7c3ee2422d
claim_id: claim:34171432cb7c3ee2422d
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
We found a dramatic increase in the transcript levels of VCAM1 (Fig. 1j), which encodes a cell-adhesion sialoglycoprotein known to facilitate the infiltration of peripheral immune cells into the central nervous system (CNS) during neuroinflammation27, 28.

summary:
In Homo sapiens, VCAM1 transcript levels are dramatically increased in inflammatory reactive astrocytes upon treatment with IL-1α+TNF+C1q.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:3c2161f8a15df69ab5ab
claim_id: claim:3c2161f8a15df69ab5ab
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
Enrichment analysis of cluster 2 markers confirmed a strong, specific enrichment (i.e. unique to cluster 2 markers) for interferon-related pathways (e.g. “Interferon Gamma Response”, “Interferon Alpha Response”) and transcription factor regulons (e.g. STAT1, IRF1)

summary:
In Homo sapiens, inflammatory reactive astrocyte state 2 (IRAS2) markers are enriched for STAT1 and IRF1 transcription factor regulons.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:c0a47fa1996f0c2d7d70
claim_id: claim:c0a47fa1996f0c2d7d70
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
While Barbar et al. astrocytes co-clustering with IRAS1 iAstrocytes expressed IRAS1 markers such as IL6, CXCL2, and CXCL5, those co-clustering with IRAS2 iAstrocytes expressed IRAS2 markers such as CXCL10, IFIT3, and ISG15

summary:
In Homo sapiens, inflammatory reactive astrocyte state 1 (IRAS1) expresses IL6, CXCL2, and CXCL5 as markers, while inflammatory reactive astrocyte state 2 (IRAS2) expresses CXCL10, IFIT3, and ISG15 as markers.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:f2cb143eff2d32fb9f02
claim_id: claim:f2cb143eff2d32fb9f02
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
While Barbar et al. astrocytes co-clustering with IRAS1 iAstrocytes expressed IRAS1 markers such as IL6, CXCL2, and CXCL5, those co-clustering with IRAS2 iAstrocytes expressed IRAS2 markers such as CXCL10, IFIT3, and ISG15

summary:
In Homo sapiens, inflammatory reactive astrocyte state 2 (IRAS2) expresses CXCL10, IFIT3, and ISG15 as markers.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:5ebe22a8b38a7f5eedf3
claim_id: claim:5ebe22a8b38a7f5eedf3
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
We performed immunostaining of C3 and VCAM1, markers of IRAS1 and IRAS2 respectively, in post-mortem brain tissue derived from AD cases vs. age-matched controls

summary:
In Homo sapiens, C3 is a marker of inflammatory reactive astrocyte state 1 (IRAS1) and VCAM1 is a marker of inflammatory reactive astrocyte state 2 (IRAS2) in post-mortem brain tissue from Alzheimer's disease cases.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:2f17f97d0ec68532cbcd
claim_id: claim:2f17f97d0ec68532cbcd
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
We performed immunostaining of C3 and VCAM1, markers of IRAS1 and IRAS2 respectively, in post-mortem brain tissue derived from AD cases vs. age-matched controls

summary:
In Homo sapiens, VCAM1 is a marker of inflammatory reactive astrocyte state 2 (IRAS2) in post-mortem brain tissue from Alzheimer's disease cases.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:50a357ab0217a5be5214
claim_id: claim:50a357ab0217a5be5214
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
Lastly, using C3 and VCAM1 as markers of IRAS1 and IRAS2, respectively, we validated the above finding with flow cytometry in an independent experiment (Fig. 4f).

summary:
In Homo sapiens, C3 is used as a marker of inflammatory reactive astrocyte state 1 (IRAS1) and VCAM1 is used as a marker of inflammatory reactive astrocyte state 2 (IRAS2) in iPSC-derived astrocytes.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:5dfc1b6ce50e89e1468d
claim_id: claim:5dfc1b6ce50e89e1468d
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
Lastly, using C3 and VCAM1 as markers of IRAS1 and IRAS2, respectively, we validated the above finding with flow cytometry in an independent experiment (Fig. 4f).

summary:
In Homo sapiens, VCAM1 is used as a marker of inflammatory reactive astrocyte state 2 (IRAS2) in iPSC-derived astrocytes.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:43002abbd61471c46bb5
claim_id: claim:43002abbd61471c46bb5
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
M4 genes contained and had similar enrichments as IRAS1 markers (e.g. IL6; see Supplementary Table 7) and displayed reduced induction upon knockdown of G2 regulators, whereas M3 and M9 genes contained and had similar enrichments as IRAS2 markers (e.g. VCAM1; see Supplementary Table 7)

summary:
In Homo sapiens, IL6 is a marker of inflammatory reactive astrocyte state 1 (IRAS1) and VCAM1 is a marker of inflammatory reactive astrocyte state 2 (IRAS2) in iPSC-derived astrocytes.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:142c8e8cb1be2ad79f8f
claim_id: claim:142c8e8cb1be2ad79f8f
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal:
M4 genes contained and had similar enrichments as IRAS1 markers (e.g. IL6; see Supplementary Table 7) and displayed reduced induction upon knockdown of G2 regulators, whereas M3 and M9 genes contained and had similar enrichments as IRAS2 markers (e.g. VCAM1; see Supplementary Table 7)

summary:
In Homo sapiens, VCAM1 is a marker of inflammatory reactive astrocyte state 2 (IRAS2) in iPSC-derived astrocytes.


claim_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2:claim:1839e29c903529b687a2
claim_id: claim:1839e29c903529b687a2
paper_key: biorxiv:37132c64-6c91-1014-a7ae-a25544128cc2
span_literal: Transcript levels of CSF2 and GM-CSF overlaid onto the UMAP embedding from Fig. 3a.
summary:
In Homo sapiens, CSF2 (encoding granulocyte-macrophage colony-stimulating factor) is expressed in inflammatory reactive astrocyte state 1 (IRAS1) iPSC-derived astrocytes.


claim_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d:claim:c0c47690c564ef1aac2a
claim_id: claim:c0c47690c564ef1aac2a
paper_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d
span_literal:
we confirmed that β cells are not only enriched in key identity markers, such as INS, IAPP, PDX1, and NKX6-1, compared to other cell types but also that β cells have increased ITGA1 (CD49a) expression

summary:
In Homo sapiens stem cell-derived islets, beta cells are enriched in INS, IAPP, PDX1, NKX6-1, and ITGA1 compared to other cell types.


claim_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d:claim:450b19f3d7461d14526d
claim_id: claim:450b19f3d7461d14526d
paper_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d
summary: In Homo sapiens stem cell-derived islets, alpha cells express GCG and ARX.
span_literal:
other major cell types expressed expected cell markers, such as GCG and ARX for α cells, SST and HHEX for δ cells, and TPH1 and SLC18A1 for enterochromaffin cells


claim_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d:claim:9aede94bd55c5da43fa1
claim_id: claim:9aede94bd55c5da43fa1
paper_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d
summary: In Homo sapiens stem cell-derived islets, endocrine cells express high levels of CHGA.
span_literal:
We observed all cell populations expressing high levels of CHGA, consistent with prior observations that in vitro differentiation produces cellular populations that are of high endocrine cell purity.


claim_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d:claim:c9758bc8125cfeb8dfd3
claim_id: claim:c9758bc8125cfeb8dfd3
paper_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d
span_literal:
Interestingly, CD49a (Integrin alpha-1, ITGA1) is an integrin involved in adhesion with the extracellular matrix and has been identified to be enriched in SC-β cells within SC-islets

summary:
In Homo sapiens stem cell-derived islets, ITGA1 (also known as CD49a or integrin alpha-1) is enriched in stem cell-derived beta cells.


claim_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d:claim:da68458d515c35c37f00
claim_id: claim:da68458d515c35c37f00
paper_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d
span_literal:
Quantification of the fraction of cells expressing markers of β cells (C-peptide), α cells (GCG), δ cells (SST), and enterochromaffin cells (SLC18A1)

summary:
In Homo sapiens stem cell-derived islets, C-peptide marks beta cells, GCG marks alpha cells, SST marks delta cells, and SLC18A1 marks enterochromaffin cells.


claim_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d:claim:5ab60f46cbb395b7f7d6
claim_id: claim:5ab60f46cbb395b7f7d6
paper_key: biorxiv:37af1a73-74bd-1014-bb95-96ab82111b0d
span_literal: high ITGA1 transcript was observed specifically in the β cell population
summary:
In Homo sapiens stem cell-derived islets, high ITGA1 transcript is observed specifically in the beta cell population.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:ee48323f4dc0e1da2bce
claim_id: claim:ee48323f4dc0e1da2bce
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
We applied bulk and single gene expression profiling of human CD4+ memory T cells and identified surface markers, KLRB1, KLRG1, GPR56 and KLRF1, allowing classification into “low”, “high” or “exhausted” cytokine producers.

summary:
In Homo sapiens, KLRB1, KLRG1, GPR56, and KLRF1 are surface markers of CD4+ memory T cells that allow classification into low, high, or exhausted cytokine producers.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:64edb0e1085b57b97859
claim_id: claim:64edb0e1085b57b97859
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal: highest production of multiple cytokines was observed in KLRB1+KLRG1+GPR56+ T cells.
summary:
In Homo sapiens, KLRB1+KLRG1+GPR56+ T cells show the highest production of multiple cytokines, marking them as high cytokine-producing CD4+ T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:8884291c412b5076d0f7
claim_id: claim:8884291c412b5076d0f7
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal: Only additional KLRF1 expression was associated with a decline in cytokine production.
summary:
In Homo sapiens, additional KLRF1 expression on CD4+ memory T cells is associated with a decline in cytokine production, marking exhausted cytokine producers.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:7195306e72e0bc568ef0
claim_id: claim:7195306e72e0bc568ef0
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
Based on the expression patterns of lymph node homing receptors (CD62L or CCR7) and CD45 splice variants, CD8+ and CD4+ T cells were classified into CD45RA+CCR7+ naïve (TN), CD45RA-CCR7+ central memory (TCM), CD45RA- CCR7- effector memory (TEM) and CD45RA+CCR7- terminally differentiated effector memory (TEMRA) cells (14-16).

summary:
In Homo sapiens, CD45RA and CCR7 expression patterns classify T cells into naïve T cells (CD45RA+CCR7+), central memory T cells (CD45RA-CCR7+), effector memory T cells (CD45RA-CCR7-), and terminally differentiated effector memory T cells (CD45RA+CCR7-).


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:9951859d164c06d58241
claim_id: claim:9951859d164c06d58241
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
Based on the expression patterns of lymph node homing receptors (CD62L or CCR7) and CD45 splice variants, CD8+ and CD4+ T cells were classified into CD45RA+CCR7+ naïve (TN), CD45RA-CCR7+ central memory (TCM), CD45RA- CCR7- effector memory (TEM) and CD45RA+CCR7- terminally differentiated effector memory (TEMRA) cells (14-16).

summary:
In Homo sapiens, central memory T cells are defined by CD45RA-negative and CCR7-positive expression.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:5f5f0599052c098e4856
claim_id: claim:5f5f0599052c098e4856
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
Based on the expression patterns of lymph node homing receptors (CD62L or CCR7) and CD45 splice variants, CD8+ and CD4+ T cells were classified into CD45RA+CCR7+ naïve (TN), CD45RA-CCR7+ central memory (TCM), CD45RA- CCR7- effector memory (TEM) and CD45RA+CCR7- terminally differentiated effector memory (TEMRA) cells (14-16).

summary:
In Homo sapiens, effector memory T cells are defined by CD45RA-negative and CCR7-negative expression.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:30e5cf1f70eb5e1a2cd8
claim_id: claim:30e5cf1f70eb5e1a2cd8
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
summary:
In Homo sapiens, terminally differentiated effector memory T cells are defined by CD45RA-positive and CCR7-negative expression.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:4ac13fd793e277c6a11e
claim_id: claim:4ac13fd793e277c6a11e
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal: they do acquire KLRG1 and CD57 but loose CD28 and CD27 expression (21).
summary:
In Homo sapiens, terminally differentiated effector memory T cells acquire KLRG1 and CD57 but lose CD28 and CD27 expression.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:46446573f11c6fe9f90f
claim_id: claim:46446573f11c6fe9f90f
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
Among the top-ranked genes up-regulated in both CD4+ TEM and TEMRA cells were genes previously shown to be highly expressed in more differentiated T cells such as FASLG or LAG3, genes encoding various toll-like receptors or HLA-DR beta chains but especially genes associated with NK cells such as members of the killer-like receptor family, KLRG1 and KLRF1, or NKG7, CD300A and CD300C.

summary:
In Homo sapiens, FASLG, LAG3, KLRG1, KLRF1, NKG7, CD300A, and CD300C are among the top-ranked genes up-regulated in both CD4+ effector memory T cells and terminally differentiated effector memory T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:3d464a8069fddce80922
claim_id: claim:3d464a8069fddce80922
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
Among the top-ranked genes up-regulated in both CD4+ TEM and TEMRA cells were genes previously shown to be highly expressed in more differentiated T cells such as FASLG or LAG3, genes encoding various toll-like receptors or HLA-DR beta chains but especially genes associated with NK cells such as members of the killer-like receptor family, KLRG1 and KLRF1, or NKG7, CD300A and CD300C.

summary:
In Homo sapiens, FASLG, LAG3, KLRG1, KLRF1, NKG7, CD300A, and CD300C are among the top-ranked genes up-regulated in both CD4+ effector memory T cells and CD4+ terminally differentiated effector memory T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:90d027d19f8ef9770851
claim_id: claim:90d027d19f8ef9770851
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
In addition, genes encoding proteins regulating cell migration and adhesion such as S1PR5, CXC3CR1 and ADGRG1 (also known as GPR56) were highly up-regulated.

summary:
In Homo sapiens, S1PR5, CX3CR1, and ADGRG1 (also known as GPR56) are highly up-regulated in CD4+ effector memory T cells and terminally differentiated effector memory T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:9b5e72d19ee108b70578
claim_id: claim:9b5e72d19ee108b70578
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
The microarray analysis also identified genes, whose expression was specifically increased in TEM cells such as genes encoding c-Kit or the killer-like receptor KLRB1 (see also supplementary table 1 – last 6 genes).

summary:
In Homo sapiens, c-Kit and KLRB1 expression is specifically increased in CD4+ effector memory T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:0cd337ef81251562b306
claim_id: claim:0cd337ef81251562b306
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
only a few CD4+ TEM- & TEMRA-specific genes such as NKG7, GPR56 or KLRG1 were expressed by nearly all TEM and TEMRA cells (figure 1b, c).

summary:
In Homo sapiens, NKG7, GPR56, and KLRG1 are expressed by nearly all CD4+ effector memory T cells and terminally differentiated effector memory T cells at the single cell level.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:f0f5e5696169d6f249d3
claim_id: claim:f0f5e5696169d6f249d3
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
only a few CD4+ TEM- & TEMRA-specific genes such as NKG7, GPR56 or KLRG1 were expressed by nearly all TEM and TEMRA cells (figure 1b, c).

summary:
In Homo sapiens, NKG7, GPR56, and KLRG1 are expressed by nearly all CD4+ terminally differentiated effector memory T cells at the single cell level.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:416e4a8379d6f9f2e75b
claim_id: claim:416e4a8379d6f9f2e75b
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
CD4+ TEMRA cells contained the highest frequencies of KLRG1 and GPR56 as well as KLRF1 and KLRB1 double expressing cells, whereas CD4+ TEM cells were characterised by double but also KLRB1, KLRG1 and GPR56 single expressing cells (figure 2a).

summary:
In Homo sapiens, CD4+ terminally differentiated effector memory T cells contain the highest frequencies of KLRG1, GPR56, KLRF1, and KLRB1 co-expressing cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:06b8a0614d8f6032e00b
claim_id: claim:06b8a0614d8f6032e00b
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
CD4+ TEMRA cells contained the highest frequencies of KLRG1 and GPR56 as well as KLRF1 and KLRB1 double expressing cells, whereas CD4+ TEM cells were characterised by double but also KLRB1, KLRG1 and GPR56 single expressing cells (figure 2a).

summary:
In Homo sapiens, CD4+ effector memory T cells are characterised by KLRB1, KLRG1, and GPR56 expression.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:cec4cf3797d6b83b6b9f
claim_id: claim:cec4cf3797d6b83b6b9f
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
summary: In Homo sapiens, KLRB1 is the first marker acquired during CD4+ memory T cell differentiation.
span_literal:
According to this analysis, KLRB1 expression was the first marker to be acquired during CD4+ memory T cell differentiation, a result which is nicely confirmed by our bulk and single cell-based gene expression analyses (figures 1 and 2).


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:9eb1997d492ed7b7b62c
claim_id: claim:9eb1997d492ed7b7b62c
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
summary: In Homo sapiens, KLRB1 (also known as CD161) is expressed by CD4+ T cells.
span_literal:
The C-type lectin KLRB1 also known as CD161 has been shown to be expressed by CD4+ and CD8+ T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:f0afa64dd0d2e8d250ba
claim_id: claim:f0afa64dd0d2e8d250ba
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
summary: In Homo sapiens, killer cell lectin-like G1 (KLRG1) is a marker for senescent T cells.
span_literal:
The killer cell lectin-like G1 (KLRG1) is a marker for T cell senescence as expressing cells have limited proliferative capacity (19, 21).


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:96ff6dd5d56ad6600b3d
claim_id: claim:96ff6dd5d56ad6600b3d
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
GPR56 was shown to be expressed by cytotoxic NK and T lymphocytes including CD8+, CD4+ and γd+ T cells (41).

summary:
In Homo sapiens, GPR56 is expressed by cytotoxic natural killer cells and T lymphocytes including CD8+ T cells, CD4+ T cells, and gamma-delta T cells.


claim_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e:claim:e4c2b21d673661e6f2ee
claim_id: claim:e4c2b21d673661e6f2ee
paper_key: biorxiv:380e1251-6c2c-1014-8b2d-a217f3491f5e
span_literal:
Co-expression of KLRB1 with either KLRG1 or GPR56 or co-expression of all three markers was associated with high TNF-α/IFN-γ co-expression potential while additional acquisition of KLRF1 expression during terminal differentiation resulted in a reduction of the cytokine production capacity.

summary:
In Homo sapiens, co-expression of KLRB1 with KLRG1 or GPR56 on CD4+ memory T cells is associated with high TNF-alpha/IFN-gamma co-expression potential, while additional KLRF1 expression results in reduced cytokine production capacity.


claim_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53:claim:bca00829ce15e0d5c886
claim_id: claim:bca00829ce15e0d5c886
paper_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53
span_literal: PTN is mainly expressed in macrophages
summary:
In Homo sapiens, pleiotrophin (PTN) is mainly expressed in macrophages in the testicular microenvironment.


claim_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53:claim:40211fb19239b2d4c810
claim_id: claim:40211fb19239b2d4c810
paper_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53
span_literal: In AZFa_Del patients, about 75% of monocytes/macrophages highly expressed DCN and APOE
summary:
In Homo sapiens AZFa_Del patients, about 75% of monocytes/macrophages highly expressed decorin (DCN) and apolipoprotein E (APOE).


claim_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53:claim:e29858673a671155fa1d
claim_id: claim:e29858673a671155fa1d
paper_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53
span_literal:
In KS patients, about 75% of monocytes/macrophages and CD4+T cells expressed DCN, APOE, TIMP3, and about 75% of CD4+T cells highly expressed IGF1

summary:
In Homo sapiens Klinefelter syndrome patients, about 75% of monocytes/macrophages expressed decorin (DCN), apolipoprotein E (APOE), and tissue inhibitor of metalloproteinases 3 (TIMP3).


claim_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53:claim:9fadc2b5dd969dd9b11f
claim_id: claim:9fadc2b5dd969dd9b11f
paper_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53
span_literal:
In KS patients, about 75% of monocytes/macrophages and CD4+T cells expressed DCN, APOE, TIMP3, and about 75% of CD4+T cells highly expressed IGF1

summary:
In Homo sapiens Klinefelter syndrome patients, about 75% of CD4+ T cells expressed decorin (DCN), apolipoprotein E (APOE), tissue inhibitor of metalloproteinases 3 (TIMP3), and highly expressed insulin-like growth factor 1 (IGF1).


claim_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53:claim:3a6ed26c4b18091f3afc
claim_id: claim:3a6ed26c4b18091f3afc
paper_key: biorxiv:38f92858-6c77-1014-a70a-b9d4e7b85d53
span_literal: It has been proved that LRP1 is highly expressed in macrophages
summary:
Low-density lipoprotein receptor-related protein 1 (LRP1) is highly expressed in macrophages in Homo sapiens.


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:a4e28216e324541bf6e5
claim_id: claim:a4e28216e324541bf6e5
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, CD19 is a positive marker of B cells and CD3E is a positive marker of T cells.
span_literal:
an immunologist may know based on their literature expertise and firsthand experience that CD19 and CD3E are specific markers of B cells and T cells, respectively


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:6be4dcc97b2fc71bd9cb
claim_id: claim:6be4dcc97b2fc71bd9cb
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, T cells are strongly associated with CD3E.
span_literal:
T cells, B cells, pancreatic beta cells, hepatocytes, and trophoblasts are strongly associated with genes including CD3E, CD20, insulin, albumin, and HLA-G, respectively


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:9ef522e7ddc16e19e92a
claim_id: claim:9ef522e7ddc16e19e92a
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, CLIC6 is a poorly characterized marker of retinal pigment epithelial cells.
span_literal:
contextualization of differential expression analyses with these GCAs highlights poorly characterized markers of established cell types, such as CLIC6 and DNASE1L3 in retinal pigment epithelial cells and endothelial cells, respectively


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:c5083bf669591d5e90ee
claim_id: claim:c5083bf669591d5e90ee
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, RPE65 and BEST1 are established markers of retinal pigment epithelium cells.
span_literal:
Several of these genes were established RPE markers such as RPE65 and BEST1, mutations in both of which can cause retinitis pigmentosa and other retinopathies


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:c4e4ad05b5186a8f22f2
claim_id: claim:c4e4ad05b5186a8f22f2
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
span_literal:
Other markers showing moderate to strong literature associations with the RPE included genes involved in vitamin A metabolism (e.g., TTR, RLBP1, RBP1, LRAT).

summary:
In Homo sapiens, TTR, RLBP1, RBP1, and LRAT are markers of retinal pigment epithelium cells showing moderate to strong literature associations.


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:1697a6afd46ad8f7bbd5
claim_id: claim:1697a6afd46ad8f7bbd5
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
span_literal:
However, we also identified several CDGs with little or no literature association to RPE cells, including genes encoding ion transporters (SLC6A13, CLIC6) and proteins that modulate Wnt signaling (FRZB, SFRP5).

summary:
In Homo sapiens, SLC6A13, CLIC6, FRZB, and SFRP5 are cluster defining genes of retinal pigment epithelium cells with little or no prior literature association.


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:e97a255e4ab9d7f4463b
claim_id: claim:e97a255e4ab9d7f4463b
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, PECAM1, VWF, and ICAM1 are strongly associated markers of endothelial cells.
span_literal:
While 24 of the top 50 genes were strongly associated with ECs (e.g., PECAM1, VWF, ICAM1), several other genes were poorly characterized or previously uncharacterized endothelial markers (Figure 7B).


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:8f981b9b330c605e3178
claim_id: claim:8f981b9b330c605e3178
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
span_literal:
For example, DNASE1L3 was identified as an EC marker whereas it is canonically reported to be expressed by macrophages and dendritic cells

summary:
In Homo sapiens, DNASE1L3 was identified as an endothelial cell marker, whereas it is canonically reported to be expressed by macrophages and dendritic cells.


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:56a15ce7031443bd434a
claim_id: claim:56a15ce7031443bd434a
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, CD31 (PECAM1), AQP1, VWF, PLVAP, and ESAM are canonical endothelial cell markers.
span_literal:
To verify the given annotation of one or more clusters in each dataset as endothelial cells, we computed an endothelial signature score for each individual cell, defined as the geometric mean of CP10K values for a selected set of canonical endothelial markers; that is, Endothelial Signature = (CP10KGene 1 x CP10KGene 2 x … CP10KGene N)1/n. The five endothelial markers considered were CD31 (PECAM1), AQP1, VWF, PLVAP, and ESAM.


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:7cf3a97f899078daa011
claim_id: claim:7cf3a97f899078daa011
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
summary: In Homo sapiens, CLEC4G and CLEC4M are markers of liver sinusoidal endothelial cells.
span_literal:
For liver sinusoidal endothelial cells, which are known to display a distinct expression profile compared to other endothelial cells, we considered CLEC4G and CLEC4M as markers rather than the previously listed set.


claim_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f:claim:695b75e278be89697539
claim_id: claim:695b75e278be89697539
paper_key: biorxiv:3912ca11-6e98-1014-9c67-9a3ee3e3b07f
span_literal:
DNASE1L3 is an extracellular DNase which is historically reported to be released specifically by macrophages and dendritic cells

summary:
In Homo sapiens, DNASE1L3 is historically reported to be released specifically by macrophages and dendritic cells.


claim_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0:claim:01f9b175774b506e6596
claim_id: claim:01f9b175774b506e6596
paper_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0
span_literal:
Feature plots of the expression of the most protective genes show that SEMA4A, IL17RA, CTSD, CD68 and GAA were mainly expressed in monocytes.

summary:
In Homo sapiens, SEMA4A, IL17RA, CTSD, CD68, and GAA are primarily expressed in monocytes, as shown by single cell CITE-seq feature plots from vaccinated participants.


claim_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0:claim:ad96f780a41f19d34df4
claim_id: claim:ad96f780a41f19d34df4
paper_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0
span_literal:
CD14 monocytes also had the greatest number of differentially expressed genes that were associated with ADCP (Fig. 5E).

summary:
In Homo sapiens, CD14-positive monocytes had the greatest number of differentially expressed genes associated with antibody-dependent cellular phagocytosis, indicating CD14 as a marker of this monocyte subset.


claim_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0:claim:bbd09d73e0f4ebcfa305
claim_id: claim:bbd09d73e0f4ebcfa305
paper_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0
span_literal:
RNA was extracted from sorted B cells (Aqua live/dead−CD20+CD3−) and monocytes (Aqua live/dead−CD20−CD3−CD56−HLA-DR+CD14+ from PBMC of HVTN 505 vaccinees using RNAzolRT (MRC Inc.) as per recommendations from the manufacturer.

summary:
In Homo sapiens, B cells were sorted as CD20-positive and CD3-negative from peripheral blood mononuclear cells of HVTN 505 vaccinees.


claim_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0:claim:c1e0132467532e837e5b
claim_id: claim:c1e0132467532e837e5b
paper_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0
span_literal:
RNA was extracted from sorted B cells (Aqua live/dead−CD20+CD3−) and monocytes (Aqua live/dead−CD20−CD3−CD56−HLA-DR+CD14+ from PBMC of HVTN 505 vaccinees using RNAzolRT (MRC Inc.) as per recommendations from the manufacturer.

summary:
In Homo sapiens, monocytes were sorted as CD20-negative, CD3-negative, CD56-negative, HLA-DR-positive, and CD14-positive from peripheral blood mononuclear cells of HVTN 505 vaccinees.


claim_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0:claim:28cb51596256398abf83
claim_id: claim:28cb51596256398abf83
paper_key: biorxiv:39510275-6e7f-1014-81d5-da3b7edd0de0
span_literal:
A stepwise logistic regression analysis identified specific genes (SEMA4A, SLC36A1, SERINC5, IL17RA, CTSD, CD68, GAA) to have independent associations with reduced risk of acquisition and were mainly expressed in the monocyte compartment (Fig. 5D).

summary:
In Homo sapiens, SEMA4A, SLC36A1, SERINC5, IL17RA, CTSD, CD68, and GAA were mainly expressed in the monocyte compartment and independently associated with reduced risk of HIV-1 acquisition.


claim_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca:claim:2f1e4bd82de598b48f1f
claim_id: claim:2f1e4bd82de598b48f1f
paper_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca
span_literal:
basal interfollicular epidermis (IFE) expressing KRT15 and COL17A1 but lacking DIO2 and TCEAL2 expression

summary:
In Homo sapiens, basal interfollicular epidermis cells express KRT15 and COL17A1 but lack DIO2 and TCEAL2 expression.


claim_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca:claim:6e0e66d609ca29dadbde
claim_id: claim:6e0e66d609ca29dadbde
paper_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca
span_literal:
HF-SCs expressed a core set of stemness-associated genes, including key transcription factors such as SOX9, LHX2, and RUNX1, which help maintain stem cell quiescence and an undifferentiated state.

summary:
In Homo sapiens, hair follicle stem cells express stemness-associated transcription factors SOX9, LHX2, and RUNX1.


claim_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca:claim:7bda57bf818c2e6aac8a
claim_id: claim:7bda57bf818c2e6aac8a
paper_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca
span_literal: IFE basal cells maintained SOX9, RUNX1, and COL17A1, while ORS cells retained SOX9, LHX2, and FGF18
summary:
In Homo sapiens, basal interfollicular epidermis cells maintain expression of SOX9, RUNX1, and COL17A1.


claim_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca:claim:697cab2fbe80933d488a
claim_id: claim:697cab2fbe80933d488a
paper_key: biorxiv:39623bbc-6d42-1014-9e37-a92d75e9c8ca
span_literal:
CD4+ T cells exhibited a cytotoxic phenotype, characterized by elevated expression of GZMA and KLRB1, which was confirmed by immunofluorescence

summary:
In Homo sapiens, CD4-positive T cells exhibit a cytotoxic phenotype characterized by elevated expression of GZMA and KLRB1.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:95dd872e38f5d245a356
claim_id: claim:95dd872e38f5d245a356
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal: CD4-C5-CCR7-expressing cells are naïve cells, and CD4-C0-AQP3-expressing cells are memory cells.
summary:
In Homo sapiens, naïve CD4+ T cells express CCR7, while memory CD4+ T cells express AQP3 in peripheral blood mononuclear cells.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:540f7a2fe02b34b56195
claim_id: claim:540f7a2fe02b34b56195
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal: CD4-C5-CCR7-expressing cells are naïve cells, and CD4-C0-AQP3-expressing cells are memory cells.
summary:
In Homo sapiens, memory CD4+ T cells express AQP3, while naïve CD4+ T cells express CCR7 in peripheral blood mononuclear cells.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:6b5f0e7be51b66eac7de
claim_id: claim:6b5f0e7be51b66eac7de
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal:
CD4+ cells expressed markedly higher levels of CD4, CCR7, SELL, LEF1, TSHZ2, MAL, TCF and AQP3 than did CD8+ cells, while CD8+ cells expressed greater amounts of GZMK, GNLY, and NKG7 than did CD4+ cells.

summary:
In Homo sapiens, CD4+ T cells expressed markedly higher levels of CD4, CCR7, SELL, LEF1, TSHZ2, MAL, TCF, and AQP3 compared to CD8+ T cells.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:49199d2f06a19c0f41bd
claim_id: claim:49199d2f06a19c0f41bd
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal:
CD4+ cells expressed markedly higher levels of CD4, CCR7, SELL, LEF1, TSHZ2, MAL, TCF and AQP3 than did CD8+ cells, while CD8+ cells expressed greater amounts of GZMK, GNLY, and NKG7 than did CD4+ cells.

summary:
In Homo sapiens, CD8+ T cells expressed greater amounts of GZMK, GNLY, and NKG7 compared to CD4+ T cells.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:2cd70176d40718e14039
claim_id: claim:2cd70176d40718e14039
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal:
FCGR3A+ monocytes expressed markedly higher levels of FCGR3A, CDKN1C, RHOC, HES4, TCF7L2 and INSR than did CD14+ monocytes and macrophages, while CD14+ monocytes and macrophages expressed higher amounts of S100A8, S100A9, VCAN, CD14, MS4A6A, LGALS2, and CD163 than did FCGR3A+ monocytes.

summary:
In Homo sapiens, FCGR3A+ monocytes expressed markedly higher levels of FCGR3A, CDKN1C, RHOC, HES4, TCF7L2, and INSR compared to CD14+ monocytes and macrophages.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:acd5a76fc62b5ce0c450
claim_id: claim:acd5a76fc62b5ce0c450
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal:
FCGR3A+ monocytes expressed markedly higher levels of FCGR3A, CDKN1C, RHOC, HES4, TCF7L2 and INSR than did CD14+ monocytes and macrophages, while CD14+ monocytes and macrophages expressed higher amounts of S100A8, S100A9, VCAN, CD14, MS4A6A, LGALS2, and CD163 than did FCGR3A+ monocytes.

summary:
In Homo sapiens, CD14+ monocytes and macrophages expressed higher amounts of S100A8, S100A9, VCAN, CD14, MS4A6A, LGALS2, and CD163 compared to FCGR3A+ monocytes.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:a0a7ad7fa962deb7362b
claim_id: claim:a0a7ad7fa962deb7362b
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal:
The results suggest that the CD14+ monocytes in our T2DM cohort were in the classic monocyte state, while the FCGR3A+ monocytes were in the nonclassical monocyte state

summary:
In Homo sapiens, CD14+ monocytes are classical monocytes marked by CD14, while FCGR3A+ monocytes are nonclassical monocytes marked by FCGR3A.


claim_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81:claim:9c3d9d09461b24f2dd20
claim_id: claim:9c3d9d09461b24f2dd20
paper_key: biorxiv:396ad855-6e2e-1014-85f5-9bd33dea0f81
span_literal:
We constructed quasitime differentiation and developmental trajectories of monocytes/macrophages. According to the biological background analysis combined with this trajectory, there was partial differentiation from CD14+ monocytes and FCGR3A+ monocytes to IFI44L+ macrophages.

summary:
In Homo sapiens, macrophages are marked by IFI44L expression, differentiating from CD14+ monocytes and FCGR3A+ monocytes.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:c04858ad3d274e568777
claim_id: claim:c04858ad3d274e568777
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal:
Protoplasmic astrocytes (GFAPLow)24, homeostatic microglia (P2RY12High, absence of activation markers), and OPALIN+ oligodendrocytes made up the majority of human brain glial cells.

summary:
In Homo sapiens brain, protoplasmic astrocytes are marked by low GFAP expression, homeostatic microglia are marked by high P2RY12 expression, and oligodendrocytes are marked by OPALIN expression.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:436d64656d89d7a0ddaf
claim_id: claim:436d64656d89d7a0ddaf
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
summary: In Homo sapiens, fibrous astrocytes are marked by high GFAP expression.
span_literal:
This was followed by fibrous (GFAPHigh) astrocytes, an intermediate DAM-like microglial subtype (Micro_DAM_Int1: APOEHigh/SPP1Low/GPNMBLow), and RBFOX1+/RASGRF1+ oligodendrocyte populations for each respective glial type.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:3d08b44f3ace3f73593f
claim_id: claim:3d08b44f3ace3f73593f
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal:
This was followed by fibrous (GFAPHigh) astrocytes, an intermediate DAM-like microglial subtype (Micro_DAM_Int1: APOEHigh/SPP1Low/GPNMBLow), and RBFOX1+/RASGRF1+ oligodendrocyte populations for each respective glial type.

summary:
In Homo sapiens, intermediate disease-associated microglia subtype 1 is marked by high APOE, low SPP1, and low GPNMB expression.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:db5905dc0b11eccea5b0
claim_id: claim:db5905dc0b11eccea5b0
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal:
Compared to previously published human16,28,29 and mouse30,31 DAM signatures from AD and Aβ mouse models, the hnDAM signature shares key marker genes such as GPNMB, SPP1, MYO1E (Fig. 3E).

summary:
In Homo sapiens, the human neurodegenerative disease-associated microglia signature shares key marker genes GPNMB, SPP1, and MYO1E with previously published disease-associated microglia signatures.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:fce5e26e094919fdff58
claim_id: claim:fce5e26e094919fdff58
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal:
The hnDAM signature (Table S7) includes key hub genes that either modify the function of microglia in models of disease (e.g., LGALS3, SPP1)32,33 or carry genetic risk for one or more NDD (ABCA1, ADARB1, DMXL2, DSCAM, FMN1, FNIP2, GPNMB, IQGAP2, LGALS3, MYO1D, NHSL1, PRKCE, RASGRP3, SAMD4A, SCARB2, SOCS6, SULT1C2, TANC2, UGCG)34–36.

summary:
In Homo sapiens, the human neurodegenerative disease-associated microglia signature includes key hub genes LGALS3, SPP1, ABCA1, ADARB1, DMXL2, DSCAM, FMN1, FNIP2, GPNMB, IQGAP2, MYO1D, NHSL1, PRKCE, RASGRP3, SAMD4A, SCARB2, SOCS6, SULT1C2, TANC2, and UGCG.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:545dc44bd558ebebac8e
claim_id: claim:545dc44bd558ebebac8e
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal: The hnDAM signature contains four transcription factors: ARID5B, MAFB, MITF, and PPARG.
summary:
In Homo sapiens, the human neurodegenerative disease-associated microglia signature contains the transcription factors ARID5B, MAFB, MITF, and PPARG.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:c8271ca6ca0c313d3ed9
claim_id: claim:c8271ca6ca0c313d3ed9
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
summary: In Homo sapiens, microglia were identified based on expression of the canonical marker gene CSF1R.
span_literal:
microglia, astrocytes, and oligodendrocytes were identified based on expression of canonical marker genes (CSF1R, AQP4/GFAP, and MOG, respectively)


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:eeaf303b8006699c64e1
claim_id: claim:eeaf303b8006699c64e1
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal:
microglia, astrocytes, and oligodendrocytes were identified based on expression of canonical marker genes (CSF1R, AQP4/GFAP, and MOG, respectively)

summary:
In Homo sapiens, astrocytes were identified based on expression of the canonical marker genes AQP4 and GFAP.


claim_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558:claim:702e7ff90b1fc076eea3
claim_id: claim:702e7ff90b1fc076eea3
paper_key: biorxiv:3ae0337b-6d88-1014-9c93-86c75bb9b558
span_literal:
microglia, astrocytes, and oligodendrocytes were identified based on expression of canonical marker genes (CSF1R, AQP4/GFAP, and MOG, respectively)

summary:
In Homo sapiens, oligodendrocytes were identified based on expression of the canonical marker gene MOG.


claim_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3:claim:97106a58d9d194ca94ad
claim_id: claim:97106a58d9d194ca94ad
paper_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3
span_literal:
In human cells, only two genes were present in >25% of the human senescence signatures (Fig 4E): Myosin light chain 9 (MYL9) and matrix metallopeptidase 9 (MMP9).

summary:
In Homo sapiens, senescent cells are marked by myosin light chain 9 (MYL9) and matrix metallopeptidase 9 (MMP9), which were the most prevalent genes across human cell-type-specific senescence signatures.


claim_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3:claim:d5a1e0524de6a6a7b11b
claim_id: claim:d5a1e0524de6a6a7b11b
paper_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3
span_literal:
The marker found to increase dynamically with age in the largest number of human cell types was CCL4, but this marker was only dynamic in 21 of 50 (42%) cell populations.

summary:
In Homo sapiens, CCL4 was the senescence marker found to increase dynamically with age in the largest number of human cell types, though it was only dynamic in 42% of cell populations.


claim_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3:claim:2f2cec7760e563134a97
claim_id: claim:2f2cec7760e563134a97
paper_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3
span_literal:
CDKN2A was one of the most enriched markers of senescence in both humans and mice, but it was only dynamic in 26% of human and 32% of mouse cell types.

summary:
In Homo sapiens, CDKN2A is an enriched marker of senescent cells, but it was only dynamic in 26% of human cell types.


claim_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3:claim:de36ace80d12d06c1446
claim_id: claim:de36ace80d12d06c1446
paper_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3
span_literal:
CDKN2A, CXCR2, and CCL3 were the only common genes that were previously established senescence markers.

summary:
In Homo sapiens, CDKN2A, CXCR2, and CCL3 are previously established markers of senescent cells that were common across both mouse and human cell-type-specific senescence signatures.


claim_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3:claim:5cba1c81f96172de58fc
claim_id: claim:5cba1c81f96172de58fc
paper_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3
span_literal: MMP9 is a known SASP component and is present in our curated set of senescence markers.
summary:
In Homo sapiens, matrix metallopeptidase 9 (MMP9) is a known senescence-associated secretory phenotype component and a marker of senescent cells.


claim_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3:claim:1d8e405c96b376fd5c38
claim_id: claim:1d8e405c96b376fd5c38
paper_key: biorxiv:3b950402-6cf0-1014-89b7-e9ca05b505d3
span_literal:
In comparison, CDKN2A was only present in 8 of 51 signatures but still higher than what would be expected by random chance (p = 0.01).

summary:
In Homo sapiens, CDKN2A was present in 8 of 51 human senescent cell signatures, which was higher than expected by random chance.


claim_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9:claim:88bed628380a2e01ffd9
claim_id: claim:88bed628380a2e01ffd9
paper_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9
summary: In Homo sapiens, smooth muscle cells in the lymph node medulla express MYH11 and CALD1.
span_literal:
Myh11 and Cald1 expressed in cluster 3 are associated with smooth muscle actin and anatomically represent the medulla of this lymph node sample


claim_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9:claim:d51a94daa99cad508837
claim_id: claim:d51a94daa99cad508837
paper_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9
span_literal:
Cluster 4 which is in close proximity to cluster 3, showed differential expression of MARCO (a macrophage receptor) expressed by macrophages lining the medullary cords

summary:
In Homo sapiens, macrophages lining the medullary cords of the lymph node express MARCO (macrophage receptor with collagenous structure).


claim_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9:claim:a914cfdbceefea36fa10
claim_id: claim:a914cfdbceefea36fa10
paper_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9
span_literal:
CD20+ B cells and CD21+ follicular dendritic cells in defined follicles, and CD3ɛ+ T cells mainly in interfollicular areas alongside SMA+ smooth muscle cells

summary:
In Homo sapiens lymph node, B cells are positive for CD20, follicular dendritic cells are positive for CD21, T cells are positive for CD3ɛ, and smooth muscle cells are positive for SMA.


claim_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9:claim:1023c91161ddbd7ae86d
claim_id: claim:1023c91161ddbd7ae86d
paper_key: biorxiv:3b9c75ca-6d7b-1014-829f-f049f95ac2b9
span_literal:
we observed the diffuse arrangement of B cells marked by CD20 expression as well as patches of CD4 T helper cells

summary:
In Homo sapiens diffuse large B cell lymphoma tissue, B cells are marked by CD20 expression and T helper cells are marked by CD4 expression.


claim_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3:claim:e9503257186dbb21ddf3
claim_id: claim:e9503257186dbb21ddf3
paper_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3
span_literal:
Each combination probed a TREG with a panel of cell type marker genes including SLC17A7, GAD1, and MBP (labeling excitatory neurons, inhibitory neurons, and oligodendrocytes, respectively).

summary:
In Homo sapiens, SLC17A7 is a marker gene labeling excitatory neurons in the dorsolateral prefrontal cortex.


claim_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3:claim:35b71a8ebe54abfc2a35
claim_id: claim:35b71a8ebe54abfc2a35
paper_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3
span_literal:
Each combination probed a TREG with a panel of cell type marker genes including SLC17A7, GAD1, and MBP (labeling excitatory neurons, inhibitory neurons, and oligodendrocytes, respectively).

summary:
In Homo sapiens, GAD1 is a marker gene labeling inhibitory neurons in the dorsolateral prefrontal cortex.


claim_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3:claim:2a240a6fd953d2d005c7
claim_id: claim:2a240a6fd953d2d005c7
paper_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3
span_literal:
Each combination probed a TREG with a panel of cell type marker genes including SLC17A7, GAD1, and MBP (labeling excitatory neurons, inhibitory neurons, and oligodendrocytes, respectively).

summary:
In Homo sapiens, MBP is a marker gene labeling oligodendrocytes in the dorsolateral prefrontal cortex.


claim_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3:claim:0c6ffe879bb685bdd9e9
claim_id: claim:0c6ffe879bb685bdd9e9
paper_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3
span_literal:
Nuclei with only MBP expression were classified as oligodendrocytes (Oligo), with only SLC17A7 expression as excitatory neurons (Excit), and with only GAD1 expression as inhibitory neurons (Inhib).

summary:
In Homo sapiens, nuclei with only MBP expression were classified as oligodendrocytes in the dorsolateral prefrontal cortex.


claim_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3:claim:45738a7ff8bba832cf02
claim_id: claim:45738a7ff8bba832cf02
paper_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3
span_literal:
Nuclei with only MBP expression were classified as oligodendrocytes (Oligo), with only SLC17A7 expression as excitatory neurons (Excit), and with only GAD1 expression as inhibitory neurons (Inhib).

summary:
In Homo sapiens, nuclei with only SLC17A7 expression were classified as excitatory neurons in the dorsolateral prefrontal cortex.


claim_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3:claim:d5037ecacf2aadc8b7eb
claim_id: claim:d5037ecacf2aadc8b7eb
paper_key: biorxiv:3e5ca4f3-6c81-1014-b4d3-c820f430adb3
span_literal:
Nuclei with only MBP expression were classified as oligodendrocytes (Oligo), with only SLC17A7 expression as excitatory neurons (Excit), and with only GAD1 expression as inhibitory neurons (Inhib).

summary:
In Homo sapiens, nuclei with only GAD1 expression were classified as inhibitory neurons in the dorsolateral prefrontal cortex.


claim_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12:claim:d99b0ecb3c8a10f95b37
claim_id: claim:d99b0ecb3c8a10f95b37
paper_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12
span_literal:
ScRAT also identified CD14_mono as critical cell types. The data in (Stephenson et al., 2021) implies that CD14+ monocytes preferentially replenish the bronchoalveolar macrophages in health, while a much smaller and specific subset of monocytes, namely the C1QA/B/C+/CD16+ monocytes, replenish the bronchoalveolar macrophages of the COVID-19 patients.

summary:
In Homo sapiens, CD14-positive monocytes express CD14, and a specific subset of monocytes that replenishes bronchoalveolar macrophages in COVID-19 patients expresses C1QA, C1QB, C1QC, and CD16.


claim_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12:claim:514f9519763bddbc3154
claim_id: claim:514f9519763bddbc3154
paper_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12
span_literal:
ScRAT also identified CD14_mono as critical cell types. The data in (Stephenson et al., 2021) implies that CD14+ monocytes preferentially replenish the bronchoalveolar macrophages in health, while a much smaller and specific subset of monocytes, namely the C1QA/B/C+/CD16+ monocytes, replenish the bronchoalveolar macrophages of the COVID-19 patients.

summary:
In Homo sapiens, C1QA/C1QB/C1QC-positive CD16-positive monocytes express C1QA, C1QB, C1QC, and CD16, and replenish bronchoalveolar macrophages in COVID-19 patients.


claim_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12:claim:29a4e18f75e71a4e2aa9
claim_id: claim:29a4e18f75e71a4e2aa9
paper_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12
span_literal:
There are recent reports about their association with COVID, including an increased of CD163+ CD14+ cells within the DC3 cell type in COVID patients with severe symptoms (Winheim et al., 2021).

summary:
In Homo sapiens, dendritic cell type 3 includes a subset of CD163-positive CD14-positive cells that are increased in COVID patients with severe symptoms.


claim_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12:claim:32e824b2001f5e82e412
claim_id: claim:32e824b2001f5e82e412
paper_key: biorxiv:3f635787-6d46-1014-b395-8d9063a7ab12
span_literal: HSC_CD38pos are early hematopoietic progenitors and are rarely observed in PBMC samples.
summary:
In Homo sapiens, CD38-positive hematopoietic stem cells are early hematopoietic progenitors that express CD38 and are rarely observed in peripheral blood mononuclear cell samples.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:6a40f7c6c302acc26084
claim_id: claim:6a40f7c6c302acc26084
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
One example is kinase insert domain receptor (KDR; Figure 2C, left), which functions as the VEGF receptor, causing endothelial proliferation, survival, migration, tubular morphogenesis and sprouting (16).

summary:
In Homo sapiens, kinase insert domain receptor (KDR) is a marker of endothelial cells, functioning as the vascular endothelial growth factor receptor.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:e2b5aeca81cee8dfa31b
claim_id: claim:e2b5aeca81cee8dfa31b
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
summary: In Homo sapiens, intercellular adhesion molecule 2 (ICAM2) is a marker of endothelial cells.
span_literal:
Another example is intercellular adhesion molecule 2 (ICAM2, Figure 2C, right), which is an endothelial marker and is involved in the binding to white blood cells that occurs during the antigen-specific immune response (17).


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:a1e690325dcee2395fae
claim_id: claim:a1e690325dcee2395fae
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
For example, heart and neural crest derivatives expressed 2 (HAND2) and GATA binding protein 4 (GATA4) were expressed in HAoECs, HENDCs and HPAECs (cluster 3).

summary:
In Homo sapiens, heart and neural crest derivatives expressed 2 (HAND2) is expressed in human aortic endothelial cells. In Homo sapiens, GATA binding protein 4 (GATA4) is expressed in human aortic endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:a18a016e43313ec9a973
claim_id: claim:a18a016e43313ec9a973
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
For example, heart and neural crest derivatives expressed 2 (HAND2) and GATA binding protein 4 (GATA4) were expressed in HAoECs, HENDCs and HPAECs (cluster 3).

summary:
In Homo sapiens, heart and neural crest derivatives expressed 2 (HAND2) is expressed in human endocardial cells. In Homo sapiens, GATA binding protein 4 (GATA4) is expressed in human endocardial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:8b75900cda415f57ed5d
claim_id: claim:8b75900cda415f57ed5d
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
For example, heart and neural crest derivatives expressed 2 (HAND2) and GATA binding protein 4 (GATA4) were expressed in HAoECs, HENDCs and HPAECs (cluster 3).

summary:
In Homo sapiens, heart and neural crest derivatives expressed 2 (HAND2) is expressed in human pulmonary artery endothelial cells. In Homo sapiens, GATA binding protein 4 (GATA4) is expressed in human pulmonary artery endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:1e62444171d954a6b9db
claim_id: claim:1e62444171d954a6b9db
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
Another example is hes related family bHLH transcription factor with YRPW motif 2 (HEY2, also called Hrt2), a positive marker for arterial EC specification (26), which was grouped to cluster 5 and was expressed specifically in aorta-derived ECs but not in vein-derived ECs (HUVECs and HGSVECs).

summary:
In Homo sapiens, hes related family bHLH transcription factor with YRPW motif 2 (HEY2) is a positive marker for arterial endothelial cell specification, expressed in aorta-derived endothelial cells but not in vein-derived endothelial cells such as human umbilical vein endothelial cells and human great saphenous vein endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:a7005fdf8ec1d6ab1881
claim_id: claim:a7005fdf8ec1d6ab1881
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
summary: In Homo sapiens, cadherin 4 (CDH4) is uniquely upregulated in human renal artery endothelial cells.
span_literal:
HRAECs showed uniquely upregulated genes, including cadherin 4 (CDH4); the protein product of this gene mediates cell-cell adhesion, and mutation of this gene is significantly associated with chronic kidney disease in the Japanese population (27).


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:f262034dd8ed9f9d8dcc
claim_id: claim:f262034dd8ed9f9d8dcc
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
Whereas CLDN5 has been reported as a major constituent of the brain EC tight junctions that make up the blood-brain barrier (29), we found that seven other genes belonging to the claudin family (CLDN1, 7, 10, 11, 12, 14 and 15) were expressed in ECs, and their expression pattern varied across EC types (Supplementary Figure S11).

summary:
In Homo sapiens, CLDN5 is a major constituent of brain endothelial cell tight junctions that make up the blood-brain barrier.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:492cedbd18227a12d67b
claim_id: claim:492cedbd18227a12d67b
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
For example, in HUVECs, CLDN11 was highly expressed but CLDN14 was not, although the two claudins share a similar function for cation permeability (30).

summary:
In Homo sapiens, CLDN11 is highly expressed in human umbilical vein endothelial cells. In Homo sapiens, CLDN14 is not expressed in human umbilical vein endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:d690d563e614bb44abde
claim_id: claim:d690d563e614bb44abde
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
summary: In Homo sapiens, HOXD10 is highly expressed in human great saphenous vein endothelial cells.
span_literal:
Figure 5A shows that HOXD10 was highly expressed in HGSVECs, which evokes the inhibition of the angiogenic phenotype as regulated by HOXD10 in this cell type.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:a516852c3afcbd83cd73
claim_id: claim:a516852c3afcbd83cd73
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
In addition to HOX genes, multiple non-HOX homeobox genes were also differentially regulated across ECs. For example, cluster 3 in the DEGs contained NK2 homeobox 5 (Nkx-2.5), which is essential for maintenance of ventricular identity (36); paired like homeodomain 2 (PITX2) and paired related homeobox 1 (PRRX1), which are both associated with the atrial fibrillation and cardioembolic ischemic stroke variants loci (37–39); and Meis homeobox 1 (MEIS1), which is required for heart development in mice (40).

summary:
In Homo sapiens, NK2 homeobox 5 (NKX2-5), paired like homeodomain 2 (PITX2), paired related homeobox 1 (PRRX1), and Meis homeobox 1 (MEIS1) are differentially expressed in endothelial cells from the heart region (cluster 3), including human aortic endothelial cells, human endocardial cells, and human pulmonary artery endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:21f597eb63df003eb288
claim_id: claim:21f597eb63df003eb288
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
Another example is Mesenchyme Homeobox 2 (MEOX2, also known as Gax; cluster 4), which regulates senescence and proliferation in HUVECs (41) and was also expressed in HUAECs and HGSVECs but not in other cell types.

summary:
In Homo sapiens, Mesenchyme Homeobox 2 (MEOX2) is expressed in human umbilical vein endothelial cells, human umbilical artery endothelial cells, and human great saphenous vein endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:beb08e07112dc9e96164
claim_id: claim:beb08e07112dc9e96164
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
Another example is Mesenchyme Homeobox 2 (MEOX2, also known as Gax; cluster 4), which regulates senescence and proliferation in HUVECs (41) and was also expressed in HUAECs and HGSVECs but not in other cell types.

summary:
In Homo sapiens, Mesenchyme Homeobox 2 (MEOX2) is expressed in human umbilical artery endothelial cells.


claim_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574:claim:87046bc742ec6c78cc31
claim_id: claim:87046bc742ec6c78cc31
paper_key: biorxiv:40f54d15-6bfe-1014-9477-a1fa2d43a574
span_literal:
Another example is Mesenchyme Homeobox 2 (MEOX2, also known as Gax; cluster 4), which regulates senescence and proliferation in HUVECs (41) and was also expressed in HUAECs and HGSVECs but not in other cell types.

summary:
In Homo sapiens, Mesenchyme Homeobox 2 (MEOX2) is expressed in human great saphenous vein endothelial cells.


claim_key: biorxiv:414330fe-6dc1-1014-9272-db67323171ad:claim:2cc1d93c69c150c50ad9
claim_id: claim:2cc1d93c69c150c50ad9
paper_key: biorxiv:414330fe-6dc1-1014-9272-db67323171ad
span_literal:
LRP2 (proximal tubule [PT] marker, green), AQP2 (collecting duct [CD] principal-cell marker, red), and ILF2 (cyan).

summary:
In Homo sapiens kidney, LRP2 is a marker of proximal tubule cells and AQP2 is a marker of collecting duct principal cells.


claim_key: biorxiv:414330fe-6dc1-1014-9272-db67323171ad:claim:5eeab0079cb1cd8f8647
claim_id: claim:5eeab0079cb1cd8f8647
paper_key: biorxiv:414330fe-6dc1-1014-9272-db67323171ad
summary: In Homo sapiens kidney, LRP2 marks proximal tubule cells and AQP2 marks collecting duct cells.
span_literal:
Quantification was performed on nuclei detected within LRP2⁺ (PT) or AQP2⁺ (CD) regions using QuPath software.


claim_key: biorxiv:414330fe-6dc1-1014-9272-db67323171ad:claim:5de68e5eb00d9e343031
claim_id: claim:5de68e5eb00d9e343031
paper_key: biorxiv:414330fe-6dc1-1014-9272-db67323171ad
summary: In Homo sapiens kidney, LRP2 is used as a marker for proximal tubule cells.
span_literal:
in human kidney sections, an anti-Lrp2 antibody (BiCell, #31012; 1:200) with its corresponding secondary antibody (1:1000) was applied for proximal tubule staining.


claim_key: biorxiv:416666f2-6cf5-1014-99b7-f739c447cf39:claim:0d133e5cd69d5e08cb3a
claim_id: claim:0d133e5cd69d5e08cb3a
paper_key: biorxiv:416666f2-6cf5-1014-99b7-f739c447cf39
span_literal:
These included KLF2 and KLF4 (general markers of endothelial function(12)), ASS1 (involved in NO metabolism (12)), and CYP1B1 (indicative of stress protection (11)).

summary:
In Homo sapiens, Krüppel-like factor 2 and Krüppel-like factor 4 are general markers of endothelial cell function. In Homo sapiens, argininosuccinate synthetase 1 is involved in nitric oxide metabolism in endothelial cells. In Homo sapiens, cytochrome P450 1B1 is a marker indicative of stress protection in endothelial cells.


claim_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5:claim:cf30ee322479ba076561
claim_id: claim:cf30ee322479ba076561
paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
span_literal:
Strikingly, progenitor-exhausted–like (Tpex-like) cells among CD4⁺ and CD8⁺ populations (TCF7high CCR7high TOX2high KLF2low) were markedly enriched in MGA271 and Hu8H9 CAR-T cells compared with B7H3.BC CAR-T cells

summary:
In Homo sapiens, progenitor-exhausted-like T cells are characterized by high expression of TCF7, CCR7, and TOX2, and low expression of KLF2.


claim_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5:claim:2913fb7241e8dbb3ab39
claim_id: claim:2913fb7241e8dbb3ab39
paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
span_literal:
Transcriptome analysis of T cell functional states indicated that B7H3.BC CAR-T cells also exhibited reduced expression of exhaustion- and effector-associated genes and elevated expression of stemness markers such as KLF2, SELL (which encodes CD62L), and MYC compared to MGA271 and Hu8H9 CAR-T cells

summary:
In Homo sapiens, CAR-T cells with subdued tonic signaling exhibit elevated expression of stemness markers KLF2, SELL, and MYC, indicating a stem-like T cell phenotype.


claim_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5:claim:d9ef98e1bbec82b51402
claim_id: claim:d9ef98e1bbec82b51402
paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
span_literal:
Surface expression of CD62L and CD45RO was used to distinguish naïve T cells/stem cell memory T cells (TN/TSCM, CD62L⁺CD45RO⁻), central memory T cells (TCM, CD62L⁺CD45RO⁺), effector memory T cells (TEM, CD62L⁻CD45RO⁺), and effector T cells (TEFF, CD62L⁻CD45RO⁻)

summary:
In Homo sapiens, naïve T cells/stem cell memory T cells are identified as CD62L-positive and CD45RO-negative, central memory T cells as CD62L-positive and CD45RO-positive, effector memory T cells as CD62L-negative and CD45RO-positive, and effector T cells as CD62L-negative and CD45RO-negative.


claim_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5:claim:980ab7a51d310449f16c
claim_id: claim:980ab7a51d310449f16c
paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
span_literal:
Flow cytometry analysis of CD62L, CCR7, and CD45RA, which are stem-like markers, and CD45RO, a T cell memory marker

summary:
In Homo sapiens, CD62L, CCR7, and CD45RA are stem-like markers of T cells, while CD45RO is a T cell memory marker.


claim_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5:claim:0b97873285d8dd088bb0
claim_id: claim:0b97873285d8dd088bb0
paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
summary: In Homo sapiens, PD-1, TIM3, and LAG3 are exhaustion markers of T cells.
span_literal:
Flow cytometry analysis showed that B7H3.BC CAR-T cells had lower levels of surface expression of exhaustion markers (PD-1, TIM3, and LAG3)


claim_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5:claim:7d17a74bb0cf5d6a205a
claim_id: claim:7d17a74bb0cf5d6a205a
paper_key: biorxiv:41a5df78-7c74-1014-a3a2-9b6aef50b1e5
summary: In Homo sapiens, CD25 and CD69 are T cell activation markers.
span_literal:
Flow cytometry analysis showed that B7H3.BC CAR-T cells had lower levels of surface expression of exhaustion markers (PD-1, TIM3, and LAG3) 30 and T cell activation markers (CD25 and CD69) than did MGA271 and Hu8H9 CAR-T cells


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:cf0385aec37aef8753aa
claim_id: claim:cf0385aec37aef8753aa
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal: 39,169 epithelial cells (characterized by KRT19, TFF1, and PGA4)
summary:
In Homo sapiens gastric tissue, epithelial cells are characterized by expression of KRT19, TFF1, and PGA4.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:8e12c1580a2d2466878c
claim_id: claim:8e12c1580a2d2466878c
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal: 71,360 B and plasma cells (B cells: MS4A1; plasma cells: IGHG1, IGHA1, IGKC, and IGHG4)
summary:
In Homo sapiens gastric tissue, plasma cells are characterized by expression of IGHG1, IGHA1, IGKC, and IGHG4.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:d18aed01cc483f25b3d8
claim_id: claim:d18aed01cc483f25b3d8
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
We subclustered 39,169 epithelial cells into 11 clusters comprising foveolar subtypes (characterized by MUC5AC, GKN1, GKN2, TFF1, TFF2, and ADH1C), PG/neck cells (MUC6, PGC, and TFF2), chief cells (PGA4, PGC, and LIPF), parietal cells (ATP4A, ATP4B, and CKB), enterocytes (FABP1, FABP2, and CDH17), goblet cells (MUC2, TFF3, and SPINK4), neuroendocrine (NE) cells (GAST, SST, GHRL, CHGA, MAOB, and CHGB), and proliferating cells (MKI67, HMGB2, and STMN1)

summary:
In Homo sapiens gastric tissue, foveolar cells are characterized by MUC5AC, GKN1, GKN2, TFF1, TFF2, and ADH1C expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:d784d9d733c5a4b88af8
claim_id: claim:d784d9d733c5a4b88af8
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
We subclustered 39,169 epithelial cells into 11 clusters comprising foveolar subtypes (characterized by MUC5AC, GKN1, GKN2, TFF1, TFF2, and ADH1C), PG/neck cells (MUC6, PGC, and TFF2), chief cells (PGA4, PGC, and LIPF), parietal cells (ATP4A, ATP4B, and CKB), enterocytes (FABP1, FABP2, and CDH17), goblet cells (MUC2, TFF3, and SPINK4), neuroendocrine (NE) cells (GAST, SST, GHRL, CHGA, MAOB, and CHGB), and proliferating cells (MKI67, HMGB2, and STMN1)

summary:
In Homo sapiens gastric tissue, pyloric gland/neck cells are characterized by MUC6, PGC, and TFF2 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:81262d3ee5c9516dbeb0
claim_id: claim:81262d3ee5c9516dbeb0
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, parietal cells are characterized by ATP4A, ATP4B, and CKB expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:bf0eecbd6dad76d31b7b
claim_id: claim:bf0eecbd6dad76d31b7b
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, enterocytes are characterized by FABP1, FABP2, and CDH17 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:f5208b52a33181ee6ae7
claim_id: claim:f5208b52a33181ee6ae7
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, goblet cells are characterized by MUC2, TFF3, and SPINK4 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:9559632a14f7051101e2
claim_id: claim:9559632a14f7051101e2
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, neuroendocrine cells are characterized by GAST, SST, GHRL, CHGA, MAOB, and CHGB expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:d3b26edf0a8e62ec19b7
claim_id: claim:d3b26edf0a8e62ec19b7
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, proliferating cells are characterized by MKI67, HMGB2, and STMN1 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:ee0ffe2106497b5ede17
claim_id: claim:ee0ffe2106497b5ede17
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary: In Homo sapiens gastric tissue, D cells are marked by SST expression.
span_literal:
NE cells commonly expressed CHGA and CHGB and were clustered into at least five populations, including G cells and D cells, based on the expression of hormones or enzymes, such as SST (D cell marker), GHRL (X/A-like cell marker), GAST (G cell marker), and MAOB (enterochromaffin cell marker; Figures S1B and S1C; Busslinger et al. (2021)).


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:9946c70730f048ec4ff7
claim_id: claim:9946c70730f048ec4ff7
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
Among PG/Neck2 cells, the candidates of specific markers for “linking” cells were LEFTY1, OLFM4, and CLDN4 in differentially expressed genes (Figure 2F).

summary:
In Homo sapiens gastric tissue, linking cells (a potential stem cell population within pyloric gland/neck 2 cells) are marked by LEFTY1, OLFM4, and CLDN4 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:d90393698b9515ef8279
claim_id: claim:d90393698b9515ef8279
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
Whereas OLFM4 and CLDN4 were expressed not only in linking cells, but in the enterocytes and goblet cells (Figures S2A and S2B), LEFTY1 was highly enriched in the “linking” cells (Figure 2G).

summary:
In Homo sapiens gastric tissue, LEFTY1 is highly enriched in linking cells, distinguishing them as a potential stem cell population.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:583795ec93c8aa6c6aec
claim_id: claim:583795ec93c8aa6c6aec
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
These cells also expressed AQP5, ODAM, and PRR4 as differentially expressed markers, all of which are known salivary gland markers (Hosoi, 2016; Huang et al., 2021), although the underlying physiological basis of the similarity between the stomach and saliva is unclear.

summary:
In Homo sapiens gastric tissue, pyloric gland/neck 2 cells express AQP5, ODAM, and PRR4 as differentially expressed markers.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:afe43690902aca36f217
claim_id: claim:afe43690902aca36f217
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
We identified LEFTY1+ as a potential stem cell marker in both gastric and intestinal metaplastic glands.

summary:
In Homo sapiens, LEFTY1 is identified as a potential stem cell marker in both gastric and intestinal metaplastic glands.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:f6c132ce30038e12b718
claim_id: claim:f6c132ce30038e12b718
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
We also revealed skewed distribution patterns for PDGFRA+BMP4+WNT5A+ fibroblasts that play pivotal roles in, or even precede, the phenotypic changes from gastric to metaplastic mucosa.

summary:
In Homo sapiens gastric tissue, fibroblasts involved in metaplastic transformation are marked by PDGFRA, BMP4, and WNT5A expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:bace9bed24d727288535
claim_id: claim:bace9bed24d727288535
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
KLF+ cells (characteristic expression of KLF4, SFRP1, SFRP2, and PI16), CCL11+ cells (CCL11, ABCA8, APOE, and ADAM28), PDGFR+ cells (PLAT, POSTN, PDGFRA, BMP4, and WNT5A), FibSmo (Fibroblasts which express both fibroblastic and smooth muscle markers; He et al., 2020) (HHIP, MYLK, and ACTG2), smooth muscle cells (RERGL, ADIRF, MYH11, and TAGLN), and myofibroblasts (RGS5 and CD36)

summary:
In Homo sapiens gastric tissue, KLF+ fibroblasts are characterized by KLF4, SFRP1, SFRP2, and PI16 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:cc34567bdb07893f0a22
claim_id: claim:cc34567bdb07893f0a22
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
KLF+ cells (characteristic expression of KLF4, SFRP1, SFRP2, and PI16), CCL11+ cells (CCL11, ABCA8, APOE, and ADAM28), PDGFR+ cells (PLAT, POSTN, PDGFRA, BMP4, and WNT5A), FibSmo (Fibroblasts which express both fibroblastic and smooth muscle markers; He et al., 2020) (HHIP, MYLK, and ACTG2), smooth muscle cells (RERGL, ADIRF, MYH11, and TAGLN), and myofibroblasts (RGS5 and CD36)

summary:
In Homo sapiens gastric tissue, CCL11+ fibroblasts are characterized by CCL11, ABCA8, APOE, and ADAM28 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:d07250804ecdfb8f7455
claim_id: claim:d07250804ecdfb8f7455
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
KLF+ cells (characteristic expression of KLF4, SFRP1, SFRP2, and PI16), CCL11+ cells (CCL11, ABCA8, APOE, and ADAM28), PDGFR+ cells (PLAT, POSTN, PDGFRA, BMP4, and WNT5A), FibSmo (Fibroblasts which express both fibroblastic and smooth muscle markers; He et al., 2020) (HHIP, MYLK, and ACTG2), smooth muscle cells (RERGL, ADIRF, MYH11, and TAGLN), and myofibroblasts (RGS5 and CD36)

summary:
In Homo sapiens gastric tissue, PDGFR+ fibroblasts are characterized by PLAT, POSTN, PDGFRA, BMP4, and WNT5A expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:bacd82253aae80e35b2b
claim_id: claim:bacd82253aae80e35b2b
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, FibSmo cells (fibroblasts expressing both fibroblastic and smooth muscle markers) are characterized by HHIP, MYLK, and ACTG2 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:546eec7c158ff963857c
claim_id: claim:546eec7c158ff963857c
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, smooth muscle cells are characterized by RERGL, ADIRF, MYH11, and TAGLN expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:20b80b9c27a9ce834b49
claim_id: claim:20b80b9c27a9ce834b49
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal: KLF+ fibroblasts (Figure 5A) characteristically expressed SFRP1, SFRP2, PI16, and CD34
summary:
In Homo sapiens gastric tissue, KLF+ fibroblasts characteristically express SFRP1, SFRP2, PI16, and CD34.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:cb48dd7185f70aadc17c
claim_id: claim:cb48dd7185f70aadc17c
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
FibSmo cells specifically express high levels of HHIP (hedgehog interaction protein; Figure 5B; Figure S4A), which functions as a regulatory component of the Hedgehog signaling pathway, a pathway required in the development of the normal stomach in both mice and human (El-Zaatari et al., 2009; Katoh and Katoh, 2006).

summary:
In Homo sapiens gastric tissue, FibSmo cells specifically express high levels of HHIP (hedgehog interacting protein).


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:ff889753d9ea9384f804
claim_id: claim:ff889753d9ea9384f804
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
We also found that expression of BARX1, which encodes a stomach fibroblast-specific transcription factor, was highest in FibSmo cells (Figure 5B; Figure S4A).

summary:
In Homo sapiens gastric tissue, BARX1 expression is highest in FibSmo cells among fibroblast subtypes.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:3e405d7c6be7599cb66e
claim_id: claim:3e405d7c6be7599cb66e
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary: In Homo sapiens gastric tissue, B cells are characterized by MS4A1 and HLA-DRA expression.
span_literal:
41,544 plasma cells (with characteristic expression of immunoglobulins, such as IGHG1, IGHA1, and IGKC), 29,816 B cells (MS4A1 and HLA-DRA)


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:03111ec3d10ce3c20744
claim_id: claim:03111ec3d10ce3c20744
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary: In Homo sapiens gastric tissue, CD8 T cells are characterized by CD8A and CD8B expression.
span_literal:
CD8 T cells (CD8A and CD8B; including the GZMK+ CD8 subtype), CD4+CTLA4+T cells (CD4, PDCD1, CTLA4, and FOXP3), CD4+CD40LG+T cells (CD4 and CD40LG), and γδ T cells (TRDC and TRGC1)


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:abac9d393ca2e76cca36
claim_id: claim:abac9d393ca2e76cca36
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
CD8 T cells (CD8A and CD8B; including the GZMK+ CD8 subtype), CD4+CTLA4+T cells (CD4, PDCD1, CTLA4, and FOXP3), CD4+CD40LG+T cells (CD4 and CD40LG), and γδ T cells (TRDC and TRGC1)

summary:
In Homo sapiens gastric tissue, CD4+CTLA4+ T cells are characterized by CD4, PDCD1, CTLA4, and FOXP3 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:e32cece0a6fd12dfe87e
claim_id: claim:e32cece0a6fd12dfe87e
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary: In Homo sapiens gastric tissue, PLVAP+ endothelial cells are characterized by PLVAP expression.
span_literal:
1,950 PLVAP+ endothelial cells, 748 ACKR1+ cells, 243 FN1+ cells (characteristic for DEPP1, FN1, and CXCL2), and 130 lymphatic endothelial cells (CCL21 and LYVE1)


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:c0105615a95bd75cac5a
claim_id: claim:c0105615a95bd75cac5a
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
span_literal:
1,950 PLVAP+ endothelial cells, 748 ACKR1+ cells, 243 FN1+ cells (characteristic for DEPP1, FN1, and CXCL2), and 130 lymphatic endothelial cells (CCL21 and LYVE1)

summary:
In Homo sapiens gastric tissue, FN1+ endothelial cells are characterized by DEPP1, FN1, and CXCL2 expression.


claim_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315:claim:e4ea02f8cbafdb83738c
claim_id: claim:e4ea02f8cbafdb83738c
paper_key: biorxiv:446f40c7-6f7f-1014-8708-b70b3848c315
summary:
In Homo sapiens gastric tissue, lymphatic endothelial cells are characterized by CCL21 and LYVE1 expression.


claim_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072:claim:12548bb7af04b3d0606a
claim_id: claim:12548bb7af04b3d0606a
paper_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072
summary: In Homo sapiens, MUC5AC is a canonical marker of mucus producing secretory goblet cells.
span_literal:
Interestingly, the smoking cluster includes MUC5AC gene, consistent with the previous report that cigarette smoking increases MUC5AC expression [38, 39]. MUC5AC is a canonical marker of mucus producing secretory goblet cells, which suggests the relation between smoking and goblet cells population as we confirm in Section 2.4.


claim_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072:claim:70fc64e1425add4f6c1a
claim_id: claim:70fc64e1425add4f6c1a
paper_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072
summary: In Homo sapiens, MRC1 and CD14 are markers of macrophages, which are myeloid leukocytes.
span_literal:
Next, we observe that the innate immune cluster includes markers of myeloid leukocytes such as MRC1, CD14 (macrophages), S100A9 (neutrophils).


claim_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072:claim:e36977a745b5049a0c17
claim_id: claim:e36977a745b5049a0c17
paper_key: biorxiv:45bdaf04-6c56-1014-8dc5-bc370e8f2072
summary: In Homo sapiens, TMPRSS4 is expressed in secretory cells of lung epithelium.
span_literal:
The cluster also includes TMPRSS4, an alternative protease promoting the entry of virus, which was found expressed in secretory cells of lung epithelium in previous studies [41, 42], supporting the expansion of secretory goblet cells caused by smoking.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:14547a5a782d442fe364
claim_id: claim:14547a5a782d442fe364
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Regional identity of the cells was confirmed by strong expression of LGE genes including those that mark striatal progenitors (DLX2, GSX2) and MSNs (ASCL1, FOXP1, FOXP2, BCL11B and DARPP32)

summary:
In Homo sapiens iPSC-derived cells, DLX2 and GSX2 are markers of striatal progenitors, while ASCL1, FOXP1, FOXP2, BCL11B, and DARPP32 are markers of medium spiny neurons in the lateral ganglionic eminence.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:c0f78bbee1d2a1d48642
claim_id: claim:c0f78bbee1d2a1d48642
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Regional identity of the cells was confirmed by strong expression of LGE genes including those that mark striatal progenitors (DLX2, GSX2) and MSNs (ASCL1, FOXP1, FOXP2, BCL11B and DARPP32)

summary:
In Homo sapiens iPSC-derived cells, ASCL1, FOXP1, FOXP2, BCL11B, and DARPP32 are markers of medium spiny neurons.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:6dcc1f0256c45053a486
claim_id: claim:6dcc1f0256c45053a486
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
an integrated transcriptomic analysis of iPSC-derived MSNs and foetal striatal neurons identified conserved markers across LGE progenitors (GSX2, ASCL1) and nascent MSNs (MEIS2, BCL11B, FOXP1/2)

summary:
In Homo sapiens, GSX2 and ASCL1 are conserved markers of lateral ganglionic eminence progenitors, identified through integrated transcriptomic analysis of iPSC-derived and foetal striatal neurons.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:6a81733d069220a94e7e
claim_id: claim:6a81733d069220a94e7e
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
an integrated transcriptomic analysis of iPSC-derived MSNs and foetal striatal neurons identified conserved markers across LGE progenitors (GSX2, ASCL1) and nascent MSNs (MEIS2, BCL11B, FOXP1/2)

summary:
In Homo sapiens, MEIS2, BCL11B, FOXP1, and FOXP2 are conserved markers of nascent medium spiny neurons, identified through integrated transcriptomic analysis of iPSC-derived and foetal striatal neurons.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:aae8d6f0604bd4c8d2f7
claim_id: claim:aae8d6f0604bd4c8d2f7
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Importantly, known dMSN genes (EBF1, TAC1, ZFHX3, GAP43) and iMSN markers (SIX3, ZFHX4) were similarly conserved across in vitro and in vivo

summary:
In Homo sapiens, EBF1, TAC1, ZFHX3, and GAP43 are known markers of direct pathway medium spiny neurons, conserved across in vitro and in vivo striatal data.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:1b7c381d7362acd7993f
claim_id: claim:1b7c381d7362acd7993f
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Importantly, known dMSN genes (EBF1, TAC1, ZFHX3, GAP43) and iMSN markers (SIX3, ZFHX4) were similarly conserved across in vitro and in vivo

summary:
In Homo sapiens, SIX3 and ZFHX4 are known markers of indirect pathway medium spiny neurons, conserved across in vitro and in vivo striatal data.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:dee557692e1365f86867
claim_id: claim:dee557692e1365f86867
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Results confirmed known LGE progenitor markers (FABP7, VIM, SALL3, ASCL1), nascent MSN genes (BCL11B, SP8/9, GAD1/2), and mature subtype markers (ARPP21, SIX3, ZFHX3/4, GAP43), as well as identified NRGN (Neurogranin) and SYNPR (Synaptoporin) as candidate new markers for MSN subtype precursors, and NRN1 (Neuritin 1) for dMSNs

summary:
In Homo sapiens, FABP7, VIM, SALL3, and ASCL1 are confirmed markers of lateral ganglionic eminence progenitors in iPSC-derived striatal cultures.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:5a8bc3a9a40060833598
claim_id: claim:5a8bc3a9a40060833598
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Results confirmed known LGE progenitor markers (FABP7, VIM, SALL3, ASCL1), nascent MSN genes (BCL11B, SP8/9, GAD1/2), and mature subtype markers (ARPP21, SIX3, ZFHX3/4, GAP43), as well as identified NRGN (Neurogranin) and SYNPR (Synaptoporin) as candidate new markers for MSN subtype precursors, and NRN1 (Neuritin 1) for dMSNs

summary:
In Homo sapiens, BCL11B, SP8, SP9, GAD1, and GAD2 are confirmed markers of nascent medium spiny neurons in iPSC-derived striatal cultures.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:37efc0efd121841007dd
claim_id: claim:37efc0efd121841007dd
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
Results confirmed known LGE progenitor markers (FABP7, VIM, SALL3, ASCL1), nascent MSN genes (BCL11B, SP8/9, GAD1/2), and mature subtype markers (ARPP21, SIX3, ZFHX3/4, GAP43), as well as identified NRGN (Neurogranin) and SYNPR (Synaptoporin) as candidate new markers for MSN subtype precursors, and NRN1 (Neuritin 1) for dMSNs

summary:
In Homo sapiens, NRGN (Neurogranin) and SYNPR (Synaptoporin) are identified as candidate new markers for medium spiny neuron subtype precursors in iPSC-derived striatal cultures.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:4881f71db5924abe71eb
claim_id: claim:4881f71db5924abe71eb
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
summary:
In Homo sapiens, NRN1 (Neuritin 1) is identified as a candidate new marker for direct pathway medium spiny neurons in iPSC-derived striatal cultures.


claim_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7:claim:1a08ae7de2296516b77c
claim_id: claim:1a08ae7de2296516b77c
paper_key: biorxiv:46ff2083-6fc4-1014-a2bb-cccc45a311c7
span_literal:
For instance, known dMSN marker GAP43 showed earlier, more pronounced expression in both genotypes, while the novel direct-pathway candidate gene NRN1 was markedly higher in 16p11.2del MSN subtype precursors (28.5% vs. 5.5% cells in controls) and dMSNs (39.0% vs. 31.2%)

summary:
In Homo sapiens, GAP43 is a known marker of direct pathway medium spiny neurons, and NRN1 is a novel direct-pathway candidate gene showing elevated expression in direct pathway medium spiny neurons.


claim_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f:claim:ef7986693b983b1c504d
claim_id: claim:ef7986693b983b1c504d
paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
span_literal:
The iMSCs displayed a fibroblast-like morphology and expressed bone marrow mesenchymal stromal cell (BM-MSC) markers CD44, CD73, CD90 and CD105

summary:
In Homo sapiens, induced mesenchymal stem cells express bone marrow mesenchymal stromal cell markers CD44, CD73, CD90, and CD105.


claim_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f:claim:a9c7f47bb04873607cd4
claim_id: claim:a9c7f47bb04873607cd4
paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
span_literal:
MAN13-iMSCs underwent osteogenic differentiation in monolayer culture, forming a mineralised matrix by day 28 (Alizarin Red staining) and expressing osteogenic markers RUNX2, ALPL (Alkaline Phosphatase), BGLAP (Osteocalcin), SP7 (Osterix) and SPP7 (Osteopontin)

summary:
In Homo sapiens, osteogenically differentiated induced mesenchymal stem cells express osteogenic markers RUNX2, ALPL (alkaline phosphatase), BGLAP (osteocalcin), SP7 (osterix), and SPP1 (osteopontin).


claim_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f:claim:aef9e34bff887fef1071
claim_id: claim:aef9e34bff887fef1071
paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
span_literal:
The changes in gene expression are consistent with a loss of pluripotency (e.g. decreased POU5F1, NANOG, SOX2) and a gain of mesenchymal (e.g. increased CD44, NT5E, ENG and ALCAM) phenotype

summary:
In Homo sapiens, induced mesenchymal stem cells show decreased expression of pluripotency markers POU5F1, NANOG, and SOX2, and increased expression of mesenchymal markers CD44, NT5E, ENG, and ALCAM compared to pluripotent stem cells.


claim_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f:claim:5ba232f301ccbc75ef74
claim_id: claim:5ba232f301ccbc75ef74
paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
span_literal:
The changes in gene expression are consistent with a loss of pluripotency (e.g. decreased POU5F1, NANOG, SOX2) and a gain of mesenchymal (e.g. increased CD44, NT5E, ENG and ALCAM) phenotype

summary:
In Homo sapiens, pluripotent stem cells express POU5F1, NANOG, and SOX2, which are lost upon differentiation to induced mesenchymal stem cells.


claim_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f:claim:1f3f7f2ab7cdacb8216d
claim_id: claim:1f3f7f2ab7cdacb8216d
paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
span_literal:
Transcripts significantly upregulated from iMSC stage to D21 cartilage pellet included SOX9, COL2A1 and ACAN which are associated with chondrogenesis in addition to PTH1R, IHH and COL10A1 which are associated with pre-hypertrophic/hypertrophic differentiation and the MED causal gene MATN3

summary:
In Homo sapiens, human pluripotent stem cell-derived chondrocytes in cartilage pellets upregulate SOX9, COL2A1, and ACAN (associated with chondrogenesis) as well as PTH1R, IHH, COL10A1 (associated with pre-hypertrophic/hypertrophic differentiation), and MATN3 compared to induced mesenchymal stem cells.


claim_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f:claim:1b349ac7945726ba0e14
claim_id: claim:1b349ac7945726ba0e14
paper_key: biorxiv:48122146-7aab-1014-a240-edfb3f67c90f
span_literal:
The pellets expressed transcripts characteristic of chondrocytes e.g. SOX9, COL2A1, ACAN and MATN3 as well as growth plate chondrocyte-specific markers including PTH1R, IHH and COL10A1 by day 21 of the protocol.

summary:
In Homo sapiens, chondrocytes express SOX9, COL2A1, ACAN, and MATN3, while growth plate chondrocytes specifically express PTH1R, IHH, and COL10A1.


claim_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1:claim:c6dff55f213f54899f11
claim_id: claim:c6dff55f213f54899f11
paper_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1
span_literal: WGAHigh Tm cells express more CD4 and CCR5 than WGALow Tm cells do.
summary:
In Homo sapiens, WGA-high memory CD4+ T cells express higher levels of CD4 and CCR5 than WGA-low memory CD4+ T cells.


claim_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1:claim:1f1a50a6565dfde612e4
claim_id: claim:1f1a50a6565dfde612e4
paper_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1
span_literal:
we also compared expression levels of activation markers on the WGALow and WGAHigh cells, and found that six markers of T cell activation (HLADR, CD69, CD38, CD25, CD28, and ICOS) were all elevated on the latter population

summary:
In Homo sapiens, WGA-high memory CD4+ T cells express elevated levels of the activation markers HLADR, CD69, CD38, CD25, CD28, and ICOS compared to WGA-low memory CD4+ T cells.


claim_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1:claim:f772026ac3062732a2d9
claim_id: claim:f772026ac3062732a2d9
paper_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1
span_literal:
WGAHigh Tm cells express higher levels of the pro-survival factors CD127, BIRC5, and Ox40 than WGALow Tm cells do.

summary:
In Homo sapiens, WGA-high memory CD4+ T cells express higher levels of the pro-survival factors CD127, BIRC5, and OX40 than WGA-low memory CD4+ T cells.


claim_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1:claim:cc75e3e2b7643b52e5d8
claim_id: claim:cc75e3e2b7643b52e5d8
paper_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1
span_literal:
The CD127, CCR7 and CD62L receptors are expressed at lower levels in WGAHigh relative to WGALow Tm cells.

summary:
In Homo sapiens, WGA-low memory CD4+ T cells express higher levels of CD127, CCR7, and CD62L compared to WGA-high memory CD4+ T cells.


claim_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1:claim:91088d6e9d605ecb46ef
claim_id: claim:91088d6e9d605ecb46ef
paper_key: biorxiv:4c4207c3-7213-1014-8a55-9b25fcf723e1
span_literal:
markers preferentially expressed on the WGALow cells were those of central memory T cells, including CD27, CCR7, and CD62L

summary:
In Homo sapiens, WGA-low memory CD4+ T cells preferentially express central memory T cell markers CD27, CCR7, and CD62L.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:993b6d6c9e6530d1b8a4
claim_id: claim:993b6d6c9e6530d1b8a4
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
summary: In Homo sapiens, glucagon (GCG) is a well-established protein marker for pancreatic alpha cells.
span_literal:
This includes several of the well-established markers for pancreatic endocrine cells, such as GCG for alpha cells, INS beta cells, and SST for delta cells.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:a03227d43b8f5b74ae68
claim_id: claim:a03227d43b8f5b74ae68
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
span_literal:
This includes several of the well-established markers for pancreatic endocrine cells, such as GCG for alpha cells, INS beta cells, and SST for delta cells.

summary:
In Homo sapiens, somatostatin (SST) is a well-established protein marker for pancreatic delta cells.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:ed5be97416d2278af9bf
claim_id: claim:ed5be97416d2278af9bf
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
span_literal:
Importantly, we also identified several marker proteins that, to the best of our knowledge, have only been established at the mRNA level in single-cells (ALDH1A1, SLC7A2, TMEM176B, and GLS for alpha cells; HADH, ERO1B, and ADCYAP1 for beta cells; RBP4 and PCSK1 for delta cells)38,39, as well as proteins that have not been identified as markers in large scale sequencing datasets (ERP29 and ELAPOR1 in alpha cells, ACP3 in beta cells).

summary:
In Homo sapiens, ALDH1A1, SLC7A2, TMEM176B, and GLS are marker proteins for pancreatic alpha cells, confirmed at the protein level. In Homo sapiens, ERP29 and ELAPOR1 are novel protein markers for pancreatic alpha cells not previously identified in large-scale sequencing datasets.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:44476c27472689d9b9e3
claim_id: claim:44476c27472689d9b9e3
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
span_literal:
Importantly, we also identified several marker proteins that, to the best of our knowledge, have only been established at the mRNA level in single-cells (ALDH1A1, SLC7A2, TMEM176B, and GLS for alpha cells; HADH, ERO1B, and ADCYAP1 for beta cells; RBP4 and PCSK1 for delta cells)38,39, as well as proteins that have not been identified as markers in large scale sequencing datasets (ERP29 and ELAPOR1 in alpha cells, ACP3 in beta cells).

summary:
In Homo sapiens, HADH, ERO1B, and ADCYAP1 are marker proteins for pancreatic beta cells, confirmed at the protein level. In Homo sapiens, ACP3 is a novel protein marker for pancreatic beta cells not previously identified in large-scale sequencing datasets.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:690c8b68000e578caed5
claim_id: claim:690c8b68000e578caed5
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
span_literal:
Importantly, we also identified several marker proteins that, to the best of our knowledge, have only been established at the mRNA level in single-cells (ALDH1A1, SLC7A2, TMEM176B, and GLS for alpha cells; HADH, ERO1B, and ADCYAP1 for beta cells; RBP4 and PCSK1 for delta cells)38,39, as well as proteins that have not been identified as markers in large scale sequencing datasets (ERP29 and ELAPOR1 in alpha cells, ACP3 in beta cells).

summary:
In Homo sapiens, RBP4 and PCSK1 are marker proteins for pancreatic delta cells, confirmed at the protein level.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:f2cd8510cad9efafa2d6
claim_id: claim:f2cd8510cad9efafa2d6
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
span_literal:
Like the pancreatic endocrine cells, established mRNA markers were observed (ACP5, HLA-DRB3, ALOX5AP, and LSP1) as well as proteins with more limited mRNA expression (FERMT3 and CYBB)27.

summary:
In Homo sapiens, ACP5, HLA-DRB3, ALOX5AP, LSP1, FERMT3, and CYBB are markers for pancreatic immune cells.


claim_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef:claim:ff9b76b136137c5e21e0
claim_id: claim:ff9b76b136137c5e21e0
paper_key: biorxiv:4c59ca94-6c5e-1014-84d0-e9a5aa46ffef
summary: In Homo sapiens, NPTX2 has been identified as a beta cell marker at the mRNA level.
span_literal:
NPTX2 has only recently been identified as a beta cell marker at the mRNA level, and ERO1B is an oxidoreductase necessary for proper folding of proinsulin38,44.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:e529babdc1f350b72596
claim_id: claim:e529babdc1f350b72596
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
germinal center (GC) B cell profile including MME (CD10)91, BCL692,93, BCL11A94, POU2F2 (OCT2)95, and AICDA (AID)

summary:
In Homo sapiens, germinal center B cells exhibit a profile including MME (CD10), BCL6, BCL11A, POU2F2 (OCT2), and AICDA (AID).


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:129ddb9a8dd59cc1ea7a
claim_id: claim:129ddb9a8dd59cc1ea7a
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal: Lytic cells expressed known host biomarkers of reactivation (SGK1, NHLH1, PRDM1
summary:
In Homo sapiens, lytic cells express known host biomarkers of reactivation including SGK1, NHLH1, and PRDM1.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:1478c84954dc0a8b6bae
claim_id: claim:1478c84954dc0a8b6bae
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal: downregulation of genes targeted by virus-induced host shutoff (HLA-A, ACTB, B2M)
summary:
In Homo sapiens, lytic cells show downregulation of HLA-A, ACTB, and B2M due to virus-induced host shutoff.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:ba91cc4adecd0769c4f7
claim_id: claim:ba91cc4adecd0769c4f7
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
expression of genes that escape host shutoff (e.g., GADD45B, IL6, CCND1, JAG1, SERPINB2, FOXC1, ATF3)

summary:
In Homo sapiens, lytic cells express genes that escape host shutoff including GADD45B, IL6, CCND1, JAG1, SERPINB2, FOXC1, and ATF3.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:bdff24911c22de1d6d34
claim_id: claim:bdff24911c22de1d6d34
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
Cluster C, which was comprised of 4HT-treated samples, displayed antiviral restriction (APOBEC3G, PPP1R15A, TRIM14, FURIN), inflammatory (CCL4L2, CCL3L1, NKG7), and NF-κB signaling (NFKBIA, ICAM1, CD83, BCL2, BCL2A1) signatures.

summary:
In Homo sapiens, abortive lytic cells display antiviral restriction genes APOBEC3G, PPP1R15A, TRIM14, FURIN, inflammatory genes CCL4L2, CCL3L1, NKG7, and NF-κB signaling genes NFKBIA, ICAM1, CD83, BCL2, and BCL2A1.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:a86a6e0ebec15a6d2579
claim_id: claim:a86a6e0ebec15a6d2579
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
Using markers identified in Fig. 2D we were able to clearly distinguish unstimulated, abortive lytic, and lytic cells using CD38, BCL2A1, and BLLF1 expression, respectively

summary:
In Homo sapiens, unstimulated cells are marked by CD38 expression, distinguishing them from abortive lytic and lytic cells.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:5dcc6831db1b2869478d
claim_id: claim:5dcc6831db1b2869478d
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
Using markers identified in Fig. 2D we were able to clearly distinguish unstimulated, abortive lytic, and lytic cells using CD38, BCL2A1, and BLLF1 expression, respectively

summary:
In Homo sapiens, abortive lytic cells are marked by BCL2A1 expression, distinguishing them from unstimulated and lytic cells.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:530a006d6f9f4d13ef1d
claim_id: claim:530a006d6f9f4d13ef1d
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
Although MYC was downregulated, the master pluripotency regulators POU5F1 (OCT4), SOX2, KLF4, NANOG, and LIN28A were expressed in E2 and E3

summary:
In Homo sapiens, lytic subcluster E2 and E3 cells express the master pluripotency regulators POU5F1 (OCT4), SOX2, KLF4, NANOG, and LIN28A while MYC is downregulated.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:01bc06c0da2f9ed1a545
claim_id: claim:01bc06c0da2f9ed1a545
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
Expression of ALDH1A1, ALPL, ITGA6, CD44, PROM1 (CD133), LGR5, and YAP1 upregulated in the E2 and E3 phenotypes was consistent with cancer hallmarks including cell plasticity, self-renewal, and drug-tolerant persistence

summary:
In Homo sapiens, lytic subcluster E2 and E3 cells upregulate ALDH1A1, ALPL, ITGA6, CD44, PROM1 (CD133), LGR5, and YAP1, consistent with cancer stemness and self-renewal.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:6d40a3117678d34c3a93
claim_id: claim:6d40a3117678d34c3a93
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
We also used flow cytometry to validate increased expression of the CSC biomarkers CD44, CD133 (PROM1), and CD166 (ALCAM) at the protein level in gp350+ cells (late lytic) relative to gp350- subsets across treatment conditions

summary:
In Homo sapiens, late lytic cells (gp350-positive) show increased expression of the cancer stem cell biomarkers CD44, PROM1 (CD133), and ALCAM (CD166) relative to gp350-negative cells.


claim_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050:claim:b8ea9af7710368c4e209
claim_id: claim:b8ea9af7710368c4e209
paper_key: biorxiv:4d508308-6c00-1014-97df-8810bda21050
span_literal:
STAT3+ cells in the BZLF1+ abortive lytic state (cluster C) notably co-expressed BCL2A1 and other NF-κB pathway target genes

summary:
In Homo sapiens, STAT3-positive abortive lytic cells co-express BCL2A1 and other NF-κB pathway target genes.


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:7cc09bc70bafd1799fa7
claim_id: claim:7cc09bc70bafd1799fa7
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
span_literal:
In contrast, CoPhaser identifies genes such as KRT14 as being constitutively overexpressed in TN cells (Fig. 3F), consistent with their role as known markers of TN breast cancer [33].

summary:
In Homo sapiens, KRT14 is a known marker of triple-negative breast cancer, being constitutively overexpressed in triple-negative breast cancer cells.


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:1847af7669d267299605
claim_id: claim:1847af7669d267299605
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
span_literal:
This analysis revealed an upregulation of cell cycle–associated genes, most notably the proliferation marker BIRC5 (Fig. S5H, I), suggesting that the classifier identifies a G0-like state.

summary:
In Homo sapiens, BIRC5 is a proliferation marker upregulated in cycling G0/G1 breast cancer cells compared to non-cycling cells.


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:569a7d0ffa31602b426a
claim_id: claim:569a7d0ffa31602b426a
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
span_literal:
Feature attribution via Integrated Gradients [31] between cells in G1 and cells classified as non-cycling, displayed shared negative markers between subtypes consisting mostly of cell cycle regulators, as well as fewer positive markers, among which epithelial markers such as keratins (Fig. S5D–F).

summary:
In Homo sapiens, keratins are positive epithelial markers distinguishing G1 cycling cells from non-cycling cells in breast cancer.


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:44ea134048a28b99b3cc
claim_id: claim:44ea134048a28b99b3cc
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
summary: In Homo sapiens, triple-negative breast cancer cells display elevated expression of CDC20.
span_literal:
Analysis of inferred mean shifts further revealed that TN cells display elevated expression of CDC20 (Fig. 3E), consistent with prior reports [32].


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:eca3d52b8ed89a7c056b
claim_id: claim:eca3d52b8ed89a7c056b
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
span_literal:
The original study described a distinct population of eStromal cells marked by high expression of matrix metalloproteinases (MMPs).

summary:
In Homo sapiens, a distinct population of endometrial stromal cells is marked by high expression of matrix metalloproteinases.


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:38050f277cf421e1db43
claim_id: claim:38050f277cf421e1db43
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
summary: In Homo sapiens, endometrial perivascular cell group 1b is annotated based on STC2 expression.
span_literal:
Notably, a subtype of endometrial perivascular cells (ePVs), annotated as “group 1b” based on STC2 expression, also appears highly proliferative.


claim_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db:claim:386a1ed3e3fd00d668f0
claim_id: claim:386a1ed3e3fd00d668f0
paper_key: biorxiv:4efb5f41-6da6-1014-a51d-ce90ae1a09db
span_literal:
In contrast, analysis of inferred mean shifts revealed that PAEP is consistently more highly expressed in subjects with endometriosis compared to controls (Fig. 5G).

summary:
In Homo sapiens, PAEP is consistently more highly expressed in endometrial stromal cells from subjects with endometriosis compared to controls.


claim_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7:claim:17a2014cad1aa19e526c
claim_id: claim:17a2014cad1aa19e526c
paper_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7
span_literal:
This approach identified two subtypes of cortical GABAergic interneurons (PVALB and TOX-expressing neurons; and ADARB2 and RELN-expressing neurons) and oligodendrocytes (OPALIN, FCHSD2, and LAMA2 -expressing oligodendrocytes) as associated with ALS risk (Fig. 5, C).

summary:
In Homo sapiens, a subtype of cortical GABAergic interneuron is identified by expression of PVALB and TOX in the cortex.


claim_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7:claim:a74c3c51d43726cb1ab7
claim_id: claim:a74c3c51d43726cb1ab7
paper_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7
span_literal:
This approach identified two subtypes of cortical GABAergic interneurons (PVALB and TOX-expressing neurons; and ADARB2 and RELN-expressing neurons) and oligodendrocytes (OPALIN, FCHSD2, and LAMA2 -expressing oligodendrocytes) as associated with ALS risk (Fig. 5, C).

summary:
In Homo sapiens, a subtype of cortical GABAergic interneuron is identified by expression of ADARB2 and RELN in the cortex.


claim_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7:claim:fbad4db5f0a941e90d53
claim_id: claim:fbad4db5f0a941e90d53
paper_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7
span_literal:
This approach identified two subtypes of cortical GABAergic interneurons (PVALB and TOX-expressing neurons; and ADARB2 and RELN-expressing neurons) and oligodendrocytes (OPALIN, FCHSD2, and LAMA2 -expressing oligodendrocytes) as associated with ALS risk (Fig. 5, C).

summary:
In Homo sapiens, a subtype of oligodendrocyte is identified by expression of OPALIN, FCHSD2, and LAMA2 in the cortex.


claim_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7:claim:55d33a0da9cbe2da06b4
claim_id: claim:55d33a0da9cbe2da06b4
paper_key: biorxiv:5183da06-6c7a-1014-bb2c-9a559be552c7
span_literal:
Our modeling in this second human dataset confirmed our previous findings: PVALB-expressing GABAergic neurons and oligodendrocytes were significantly enriched in ALS risk (see SI Appendix, Fig. S3).

summary:
In Homo sapiens, PVALB-expressing GABAergic neurons are a cell type confirmed to be enriched in amyotrophic lateral sclerosis risk, with PVALB as a marker gene.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:c7bcdb1f0d0eeaea1374
claim_id: claim:c7bcdb1f0d0eeaea1374
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal:
Notably, the UMAP projection for IRF2 indicates a high activity pattern within Natural Killer cells and CD8 T cells (Figure 4B).

summary:
In Homo sapiens, IRF2 shows high transcription factor activity in natural killer cells and CD8 T cells in peripheral blood mononuclear cells.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:41b959b927aff3e87462
claim_id: claim:41b959b927aff3e87462
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal:
Notably, the UMAP projection for IRF2 indicates a high activity pattern within Natural Killer cells and CD8 T cells (Figure 4B).

summary:
In Homo sapiens, IRF2 shows high transcription factor activity in CD8 T cells in peripheral blood mononuclear cells.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:68104de46e83f3764c40
claim_id: claim:68104de46e83f3764c40
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal: Additionally, SMAD5 is predicted as highly active in B cells.
summary:
In Homo sapiens, SMAD5 is predicted as highly active in B cells within peripheral blood mononuclear cells.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:a1ed8d1bc2ab99532ad8
claim_id: claim:a1ed8d1bc2ab99532ad8
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal: For example, within B cells we observe high activity for the TF PAX5.
summary:
In Homo sapiens, PAX5 shows high transcription factor activity in B cells within peripheral blood mononuclear cells.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:6fdfd5a1fea65d37954d
claim_id: claim:6fdfd5a1fea65d37954d
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal:
Dendritic cells, the marker gene HLA-DQA1 is predicted to be regulated by the TFs SMAD1 and RFX5; the marker gene HLA-DPA1 is predicted to be regulated by ZNF2 and RFX5; and the marker gene HLA-DRB1

summary:
In Homo sapiens, HLA-DQA1, HLA-DPA1, and HLA-DRB1 are marker genes of dendritic cells in peripheral blood mononuclear cells.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:347c81e74eb74bda3380
claim_id: claim:347c81e74eb74bda3380
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal: Within Natural Killer cells, the marker gene PRF1 is predicted to be regulated by ZNF626.
summary:
In Homo sapiens, PRF1 is a marker gene of natural killer cells in peripheral blood mononuclear cells.


claim_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec:claim:d6ad6b2b4249f2e641b8
claim_id: claim:d6ad6b2b4249f2e641b8
paper_key: biorxiv:51fac41a-6c0a-1014-9c40-ecb16ebed7ec
span_literal:
Finally, within B cells, the marker gene BANK1 is predicted to be regulated by the TFs ZNF792, EBF1, PAX8, and PAX5; and the marker gene HLA-DQA1 is predicted to be regulated by the TF SMAD1.

summary:
In Homo sapiens, BANK1 and HLA-DQA1 are marker genes of B cells in peripheral blood mononuclear cells.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:27d4f3c2c623a2137f49
claim_id: claim:27d4f3c2c623a2137f49
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary: In Homo sapiens, CD163 is a marker of Hofbauer cells in the human placenta.
span_literal:
The CD163 receptor (CD163, 1.29) is a gram-positive and gram-negative bacteria sensor36 and inducer of local inflammation by producing cytokines, e.g., IL-6 and IL-10. In the human placenta, CD163 was detected in Hofbauer cells.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:2a5b2c0e8cce7d1fcab5
claim_id: claim:2a5b2c0e8cce7d1fcab5
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal: TLR7 is detected in first-trimester cytotrophoblast and second-trimester Hofbauer cells43.
summary:
In Homo sapiens, toll-like receptor 7 (TLR7) is detected in cytotrophoblast in the first trimester and in Hofbauer cells in the second trimester.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:0b1faf11b4d2dcaa0048
claim_id: claim:0b1faf11b4d2dcaa0048
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal: DEFB 1 is mainly expressed in epithelial and immune cells of the reproductive tract55,56.
summary:
In Homo sapiens, beta-defensin 1 (DEFB1) is mainly expressed in epithelial cells of the reproductive tract.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:38db46911de72c9dd6ea
claim_id: claim:38db46911de72c9dd6ea
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal: DEFB 1 is mainly expressed in epithelial and immune cells of the reproductive tract55,56.
summary:
In Homo sapiens, beta-defensin 1 (DEFB1) is mainly expressed in immune cells of the reproductive tract.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:a4377233ffc9e26c97ec
claim_id: claim:a4377233ffc9e26c97ec
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary: In Homo sapiens, S100A8 and S100A9 are constitutively expressed in neutrophils and monocytes.
span_literal:
The genes S100A8 (1.87) and S100A9 (1.70) encode proteins constitutively expressed in neutrophils and monocytes.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:b66064d4ab40fe050c9d
claim_id: claim:b66064d4ab40fe050c9d
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
In the human placenta, IL-690 and IL-6R91 were detected in the syncytiotrophoblast and extravillous trophoblast, suggesting trophoblast response for IL-6/IL-6R interaction.

summary:
In Homo sapiens, interleukin-6 (IL-6) and interleukin-6 receptor (IL-6R) are detected in the syncytiotrophoblast in the human placenta.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:d5abc63ea8cd1aa17a34
claim_id: claim:d5abc63ea8cd1aa17a34
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
In the human placenta, IL-690 and IL-6R91 were detected in the syncytiotrophoblast and extravillous trophoblast, suggesting trophoblast response for IL-6/IL-6R interaction.

summary:
In Homo sapiens, interleukin-6 (IL-6) and interleukin-6 receptor (IL-6R) are detected in the extravillous trophoblast in the human placenta.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:e3e61751986fded2e782
claim_id: claim:e3e61751986fded2e782
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
In contrast, IL-27, IL-35, and IL-39 cytokines share the EBI3 subunit encoded by Epstein-Barr virus-induced gene 3 (EBI3, 1.89), which is expressed by the syncytiotrophoblast and extravillous trophoblast throughout pregnancy94,,99.

summary:
In Homo sapiens, Epstein-Barr virus-induced gene 3 (EBI3) is expressed by the syncytiotrophoblast and extravillous trophoblast throughout pregnancy.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:f441ac25c4ca55146527
claim_id: claim:f441ac25c4ca55146527
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
In contrast, IL-27, IL-35, and IL-39 cytokines share the EBI3 subunit encoded by Epstein-Barr virus-induced gene 3 (EBI3, 1.89), which is expressed by the syncytiotrophoblast and extravillous trophoblast throughout pregnancy94,,99.

summary:
In Homo sapiens, Epstein-Barr virus-induced gene 3 (EBI3) is expressed by the extravillous trophoblast throughout pregnancy.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:4fcca1ac0c3e2f3d9bb3
claim_id: claim:4fcca1ac0c3e2f3d9bb3
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary: In Homo sapiens, FCGR2B is expressed in endothelial cells of villous vessels in the placenta.
span_literal:
FCGR2B is expressed in the endothelium of villous vessels104 while LAIR1 — by Hofbauer cells, dendritic cells, macrophages, monocytes, granulocytes, and NK cells [HPA].


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:0d518aca8ab29b88cd35
claim_id: claim:0d518aca8ab29b88cd35
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
FCGR2B is expressed in the endothelium of villous vessels104 while LAIR1 — by Hofbauer cells, dendritic cells, macrophages, monocytes, granulocytes, and NK cells [HPA].

summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is expressed by Hofbauer cells.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:19ac5bb737d957ac0885
claim_id: claim:19ac5bb737d957ac0885
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
FCGR2B is expressed in the endothelium of villous vessels104 while LAIR1 — by Hofbauer cells, dendritic cells, macrophages, monocytes, granulocytes, and NK cells [HPA].

summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is expressed by dendritic cells.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:3d3ca1ba953e59ce4d9a
claim_id: claim:3d3ca1ba953e59ce4d9a
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is expressed by macrophages.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:dec43b894baa51750506
claim_id: claim:dec43b894baa51750506
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is expressed by monocytes.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:e061f77f34da6a8c99a8
claim_id: claim:e061f77f34da6a8c99a8
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is expressed by granulocytes.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:34ec921d0866e3e35a71
claim_id: claim:34ec921d0866e3e35a71
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary:
In Homo sapiens, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is expressed by natural killer cells.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:f6e6202c14afc2ca1d2b
claim_id: claim:f6e6202c14afc2ca1d2b
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
The gene GPR183 (1.54) is tissue-specifically highly expressed by immune cells in the human placenta and brain.

summary:
In Homo sapiens, GPR183 is tissue-specifically highly expressed by immune cells in the human placenta and brain.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:3568ce90b828a1a318e4
claim_id: claim:3568ce90b828a1a318e4
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary: In Homo sapiens, CCL2 is localized in trophoblast cells in the placenta.
span_literal:
CCL2, localized in trophoblast and decidual cells, may attract macrophages, T cells, basophils, mast cells, and NK cells.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:98cfc8208bb941dbb410
claim_id: claim:98cfc8208bb941dbb410
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
summary: In Homo sapiens, CXCL13 is expressed in decidual stromal cells.
span_literal:
СXCL13 is expressed in decidual stromal cells, fetal membranes, and the umbilical vein, where it may recruit T and B cells and regulate the adaptive immune response.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:4d31968ccc0e48b1e016
claim_id: claim:4d31968ccc0e48b1e016
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
NGAL is a neutrophil attractant, involved in apoptosis, innate immunity, and kidney development, and found in neutrophil and macrophage granules63.

summary:
In Homo sapiens, neutrophil gelatinase-associated lipocalin (NGAL, also known as LCN2) is found in neutrophil granules.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:9389000e6ae510a9acdf
claim_id: claim:9389000e6ae510a9acdf
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
NGAL is a neutrophil attractant, involved in apoptosis, innate immunity, and kidney development, and found in neutrophil and macrophage granules63.

summary:
In Homo sapiens, neutrophil gelatinase-associated lipocalin (NGAL, also known as LCN2) is found in macrophage granules.


claim_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b:claim:047982bd5d2c2d6f84d4
claim_id: claim:047982bd5d2c2d6f84d4
paper_key: biorxiv:5200cce7-72d7-1014-98f6-994ae061fa4b
span_literal:
CXCL4 and CXCL7 mRNAs originate from maternal platelets adhering to the surface of the placental syncytiotrophoblast83.

summary:
In Homo sapiens, CXCL4 and CXCL7 mRNAs originate from maternal platelets adhering to the placental syncytiotrophoblast.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:75f63e091abedbc71d59
claim_id: claim:75f63e091abedbc71d59
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
span_literal:
Boolean implication analysis identified WWC1 (WW domain containing protein-1) as a novel high confidence cone photoreceptor gene.

summary:
In Homo sapiens, WWC1 (WW domain containing protein-1) is identified as a novel high confidence marker gene for cone photoreceptor cells.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:cb98023258b6c9e35c1b
claim_id: claim:cb98023258b6c9e35c1b
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
span_literal:
Boolean implication analysis of rods also identified two novel rod-specific genes: CASZ1 (Castor zinc finger 1) (Fig. 3E-F) and PPEF2 (Protein Phosphatase with EF-Hand Domain 2) (Fig. 3G-H).

summary:
In Homo sapiens, CASZ1 (Castor zinc finger 1) and PPEF2 (Protein Phosphatase with EF-Hand Domain 2) are identified as novel rod photoreceptor cell-specific genes.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:386b3d3229157523e050
claim_id: claim:386b3d3229157523e050
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
summary: In Homo sapiens, WWC1 is identified as a novel marker gene for cone photoreceptor cells.
span_literal:
Boolean implication analysis provided more accurate insight into high confidence genes, and led to the identification of WWC1 as a novel marker gene for cone photoreceptors.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:47a833a439ff3046317b
claim_id: claim:47a833a439ff3046317b
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
span_literal:
Application of our method to retinal organoid datasets identified novel high confidence cell type-specific genes such as WWC1 for cones and CASZ1 and PPEF2 for rods.

summary:
In Homo sapiens, WWC1 is identified as a cell type-specific gene for cone photoreceptor cells, and CASZ1 and PPEF2 are identified as cell type-specific genes for rod photoreceptor cells.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:0f8efc40d3dc1c4e22bf
claim_id: claim:0f8efc40d3dc1c4e22bf
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
span_literal:
Application of our method to retinal organoid datasets identified novel high confidence cell type-specific genes such as WWC1 for cones and CASZ1 and PPEF2 for rods.

summary:
In Homo sapiens, CASZ1 and PPEF2 are identified as cell type-specific genes for rod photoreceptor cells.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:17cdd31001f591917cd2
claim_id: claim:17cdd31001f591917cd2
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
summary: In Homo sapiens, CERKL is a gene specific to cone photoreceptor cells.
span_literal:
we found small differences in expression patterns in the mouse vs. human retina, such as CERKL, a gene specific to human cone photoreceptors, but expressed in both cone and rod photoreceptors in mice.


claim_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f:claim:7b0abde3d945dadcf6df
claim_id: claim:7b0abde3d945dadcf6df
paper_key: biorxiv:5337c5de-6d7b-1014-83c4-bb815278a53f
summary: In Homo sapiens, CRX, GNB3, and GNAT2 are used as bait marker genes for cone photoreceptor cells.
span_literal:
We also performed SRCCA and Boolean implication analysis for cone photoreceptors using the same three bait genes: CRX, GNB3 and GNAT2.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:414bcf378d24ad874579
claim_id: claim:414bcf378d24ad874579
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal: ITLN1, CD24, and GATA3 in colon adenocarcinoma
summary:
In Homo sapiens, ITLN1 is a marker gene associated with colon adenocarcinoma, serving as an independent favorable prognostic factor with roles including inhibiting tumor angiogenesis.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:9ea9bceb21bc686d5f70
claim_id: claim:9ea9bceb21bc686d5f70
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal: CD2437 can be used to identify colorectal cancer stem cells
summary:
In Homo sapiens, CD24 is a positive marker used to identify colorectal cancer stem cells, which are associated with tumor formation, chemotherapy resistance, and metastatic disease.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:179e7e4fa0d2085bbafe
claim_id: claim:179e7e4fa0d2085bbafe
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal:
GATA3 is a transcription factor that can be detected in cell nuclei of normal and neoplastic epithelial cells in the breast, that is used as lineage- and differentiation marker in IDC.

summary:
In Homo sapiens, GATA3 is a transcription factor detected in neoplastic epithelial cells in the breast and is used as a lineage and differentiation marker in invasive ductal carcinoma.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:5f8cf7b037554d484f63
claim_id: claim:5f8cf7b037554d484f63
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal:
The marker genes for the READ dataset include: OLFM4, PLA2G2A, PLA2G2D, MMP1, MMP11, MMP12, SMAD4, MUC13, SLC26A3, ZG16 and NDRG1.

summary:
In Homo sapiens, OLFM4, PLA2G2A, PLA2G2D, MMP1, MMP11, MMP12, SMAD4, MUC13, SLC26A3, ZG16, and NDRG1 are marker genes for rectal adenocarcinoma.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:f866a48a26118ca340a6
claim_id: claim:f866a48a26118ca340a6
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal: The marker genes for the IDC dataset include MKI67, ERBB2, PRF1, ESR1, PGR, GATA3, AR and EGFR.
summary:
In Homo sapiens, MKI67, ERBB2, PRF1, ESR1, PGR, GATA3, AR, and EGFR are marker genes for invasive ductal carcinoma.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:4d94d01257db11f1b11a
claim_id: claim:4d94d01257db11f1b11a
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal: The marker genes for PSC include CYP3A4, VWF, KRT7, ACTA2, and DCN.
summary:
In Homo sapiens, CYP3A4, VWF, KRT7, ACTA2, and DCN are marker genes for primary sclerosing cholangitis.


claim_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682:claim:6a08e17b3699e2d51abb
claim_id: claim:6a08e17b3699e2d51abb
paper_key: biorxiv:53d5ed42-720c-1014-8ae0-cec2222d6682
span_literal:
For the evaluation of marker genes and genes influencing disease progression, the following genes are included in our study: ZNF276, ZNF750, YBX1, VHL, RUNX2, RND, ERCC4, PADI2, S100A8, and S100A6.

summary:
In Homo sapiens, ZNF276, ZNF750, YBX1, VHL, RUNX2, RND, ERCC4, PADI2, S100A8, and S100A6 are marker genes for invasive ductal carcinoma in axillary lymph nodes.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:fde15345bc44820347ed
claim_id: claim:fde15345bc44820347ed
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
The human PDGFRAhigh FOXL1+ cluster expressed BMP5 and BMP7, consistently with SEMF/telocyte identity shared with mouse cells.

summary:
In Homo sapiens, PDGFRAhigh FOXL1-positive subepithelial myofibroblasts express BMP5 and BMP7, consistent with subepithelial myofibroblast/telocyte identity.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:05370a64004d94df6063
claim_id: claim:05370a64004d94df6063
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
summary: In Homo sapiens, PDGFRAlow PI16-negative mucosa-associated fibroblasts express CCL8.
span_literal:
The human PDGFRAlow PI16-cells also expressed several marker genes shared with their mouse counterparts, including e.g., CCL8, a cytokine previously reported as a colon fibroblast subset-specific marker [4].


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:8c3b5c925bedff0056b4
claim_id: claim:8c3b5c925bedff0056b4
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
Unlike in mice, the human PDGFRAlow cells did not show differential expression of CD81, but expression of markers such as ACKR4, C3, and PCOLCE2 suggested shared identity of PDGFRAlow PI16+ cells with the mouse Pdgfralow Pi16+ Cd81+ cells (Fig 1F, S2H Fig).

summary:
In Homo sapiens, PDGFRAlow PI16-positive submucosa-associated fibroblasts express ACKR4, C3, and PCOLCE2.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:5d34500edeced5f02257
claim_id: claim:5d34500edeced5f02257
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
summary: In Homo sapiens, PDGFRAlow PI16-positive submucosa-associated fibroblasts express GREM1 and RSPO3.
span_literal:
while in humans GREM1 and RSPO3 were primarily derived from PDGFRAlow PI16+ cells, and the PDGFRAlow PI16-cells instead expressed the canonical Wnt ligand WNT2B (Fig 1d).


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:d990f67191b38ea204e9
claim_id: claim:d990f67191b38ea204e9
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
the PDGFRAhigh FOXL1+ cells were enriched directly beneath the epithelial cells, especially in the luminal side of colonic mucosa, and expressed the myofibroblast marker ACTG2 (S2D Fig), confirming the SEMF identity (Fig 1G).

summary:
In Homo sapiens, PDGFRAhigh FOXL1-positive subepithelial myofibroblasts express the myofibroblast marker ACTG2.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:a63062b11d96b31a4156
claim_id: claim:a63062b11d96b31a4156
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
Consistent with the mouse analysis, the dataset included HHIP+ cells, interpreted as mucosal myocytes, and GREM1+ GREM2+ RSPO2+ cells representing MM-SMCs (Fig 3E and 3F).

summary:
In Homo sapiens, mucosal myocytes express HHIP, while muscularis mucosae smooth muscle cells express GREM1, GREM2, and RSPO2.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:0a13d17d86455a59dfa9
claim_id: claim:0a13d17d86455a59dfa9
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
For example, DES, encoding for Desmin, was highly expressed in MM-SMCs and MP-SMCs but not in myocytes, indicating DES as a marker for non-mucosal SMCs in humans (Fig 3E).

summary:
In Homo sapiens, DES (encoding Desmin) is a positive marker for muscularis mucosae smooth muscle cells and muscularis propria smooth muscle cells, and is not expressed in myocytes.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:e580e3ae2d33ff5201c5
claim_id: claim:e580e3ae2d33ff5201c5
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
For example, DES, encoding for Desmin, was highly expressed in MM-SMCs and MP-SMCs but not in myocytes, indicating DES as a marker for non-mucosal SMCs in humans (Fig 3E).

summary:
In Homo sapiens, DES (encoding Desmin) is a positive marker for muscularis propria smooth muscle cells and is not expressed in myocytes.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:86e58b9a9c3b61b49ec6
claim_id: claim:86e58b9a9c3b61b49ec6
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
For example, DES, encoding for Desmin, was highly expressed in MM-SMCs and MP-SMCs but not in myocytes, indicating DES as a marker for non-mucosal SMCs in humans (Fig 3E).

summary:
In Homo sapiens, DES (encoding Desmin) is a negative marker for myocytes, distinguishing them from smooth muscle cells.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:774b75216cafbedfed51
claim_id: claim:774b75216cafbedfed51
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
ICCs also clustered among the SMCs but were distinguishable based on expression of KIT and lack of SMC markers (Fig 3E and 3F).

summary:
In Homo sapiens, interstitial cells of Cajal are distinguished from smooth muscle cells by expression of KIT.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:5a1ec612cbfcb7d40b21
claim_id: claim:5a1ec612cbfcb7d40b21
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
summary: In Homo sapiens, muscle-embedded interstitial fibroblasts express PDGFRA.
span_literal:
Interestingly, MIFs did not resemble any of the previously identified colon fibroblast subclusters and, despite clustering with fibroblasts and expressing PDGFRA, also expressed a set of unique genes absent from all other fibroblast populations (Fig 4A and 4E).


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:3c49436c4d02704b85a1
claim_id: claim:3c49436c4d02704b85a1
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
Tissue staining confirmed specific KCNN3 expression in the PDGFRA+ cells exclusively in the MP in the mouse (Fig 4C) and human colon (Fig 4H), as well as in the mouse small intestine (Fig 4D), consistent with the spatial transcriptomics data (Fig 1G).

summary:
In Homo sapiens, muscle-embedded interstitial fibroblasts in the muscularis propria of the colon express KCNN3 and PDGFRA.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:b17e56fca59c0e0cbb67
claim_id: claim:b17e56fca59c0e0cbb67
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
One of the CAF populations specifically expressed MMP1, CXCL1, and IL6 as well as other inflammatory genes, closely aligning with the previously described inflammatory CAFs (iCAFs) [66–69] (Fig 5D, S6A Fig).

summary:
In Homo sapiens, inflammatory cancer-associated fibroblasts specifically express MMP1, CXCL1, and IL6.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:0616f8674de3ee989fdb
claim_id: claim:0616f8674de3ee989fdb
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
summary: In Homo sapiens, matrix cancer-associated fibroblasts express MMP11, HOPX, COL10A1, and COL11A1.
span_literal:
We also identified a cluster expressing the myofibroblast/matrix CAFs (mCAFs) genes, such as MMP11, HOPX, COL10A1, and COL11A1 (Fig 5D, S6B Fig) [67, 70].


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:850b701673d060601864
claim_id: claim:850b701673d060601864
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
summary: In Homo sapiens, cancer-associated fibroblasts express the marker FAP.
span_literal:
The cancer-specific fibroblast clusters were named CAFs, consistent with their expression of the CAF marker FAP [65] (Fig 5D).


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:d9df62767868059ecb7a
claim_id: claim:d9df62767868059ecb7a
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
In addition to FAP, we identified CTHRC1, INHBA, THBS2 and WNT2 as the most specific and sensitive markers for CRC CAFs.

summary:
In Homo sapiens, CTHRC1, INHBA, THBS2, and WNT2 are identified as specific and sensitive markers for colorectal cancer cancer-associated fibroblasts, in addition to FAP.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:d195c626e199a38d2f81
claim_id: claim:d195c626e199a38d2f81
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
Transcription factors PRRX1, MAFB, and TWIST1 were uncovered as potential regulators of CAF identity and CTHRC1 was identified as a specific and sensitive pan-CAF marker in CRC.

summary:
In Homo sapiens, CTHRC1 is identified as a specific and sensitive pan-cancer-associated fibroblast marker in colorectal cancer, and PRRX1, MAFB, and TWIST1 are potential regulators of cancer-associated fibroblast identity.


claim_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679:claim:50694b90b59412e5a37b
claim_id: claim:50694b90b59412e5a37b
paper_key: biorxiv:53fe4c58-6d7e-1014-9234-a9ab6cb90679
span_literal:
pericytes are commonly annotated as fibroblasts or CAFs in the CRC field despite their distinct transcriptional signature (RGS5, NOTCH3, PDGFRB, NDUFA4L2

summary:
In Homo sapiens, pericytes have a distinct transcriptional signature including RGS5, NOTCH3, PDGFRB, and NDUFA4L2.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:f3d6af6a79a7f4411e92
claim_id: claim:f3d6af6a79a7f4411e92
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
Each cluster was identified as GSCCs or macrophages based on the expression of SOX2 and CD68 respectively (Fig S2B-C).

summary:
In Homo sapiens, glioblastoma stem cells were identified by expression of SOX2, and macrophages were identified by expression of CD68.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:ed0b3d5218cfaee24394
claim_id: claim:ed0b3d5218cfaee24394
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
MC1 consisted of macrophages that expressed high levels of immunosuppressive genes HS3ST2 and MS4A6A.

summary:
In Homo sapiens, macrophage cluster 1 expressed high levels of the immunosuppressive genes HS3ST2 and MS4A6A.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:2b1a33fcfdd48c1b3342
claim_id: claim:2b1a33fcfdd48c1b3342
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
MC2 contained macrophages that express AKR1B1 (Fig 3C), which is commonly associated with an inflammatory profile (Erbel et al, 2016; Cheng et al, 2021).

summary:
In Homo sapiens, macrophage cluster 2 expressed AKR1B1, which is commonly associated with an inflammatory profile.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:ee3f8a24c05fb8ab97a2
claim_id: claim:ee3f8a24c05fb8ab97a2
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
MC3 macrophages expressed high levels of CHIT1 (and CHI3L1) and lower levels of the mature macrophage markers CD68, CD163, CD204/MSR1, and CD206/MRC1 (Fig 3B-C).

summary:
In Homo sapiens, macrophage cluster 3 (transitioning monocytes) expressed high levels of CHIT1 and CHI3L1 and lower levels of the mature macrophage markers CD68, CD163, MSR1, and MRC1.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:ccdb5f702bffeb386831
claim_id: claim:ccdb5f702bffeb386831
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
As such, we identified MC3 as transitioning monocytes (TransMos) as it has been demonstrated that CHIT1 expression increases exponentially over time in monocytes during the transition to macrophages (di Rosa et al, 2013).

summary:
In Homo sapiens, transitioning monocytes were identified by CHIT1 expression, which increases exponentially during the transition from monocytes to macrophages.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:d9e6138dff89f066ac79
claim_id: claim:d9e6138dff89f066ac79
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal: We found LGALS1 to be significantly downregulated in LBT003 (Fig 8A-B).
summary:
In Homo sapiens, LGALS1 was significantly downregulated in LBT003 glioblastoma stem cells compared to other glioblastoma stem cell cultures.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:9f14642e977031473f8e
claim_id: claim:9f14642e977031473f8e
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
Similarly, we found that CLU is expressed at significantly lower levels in LBT003 compared to the other GSCCs (Fig 8A + S8A).

summary:
In Homo sapiens, CLU was expressed at significantly lower levels in LBT003 glioblastoma stem cells compared to the other glioblastoma stem cell cultures.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:d647256ba1041b73835e
claim_id: claim:d647256ba1041b73835e
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
For instance, immunostimulatory genes like AKR1B1 and CCL4 gradually decreased in expression along the trajectory (Fig S4C-D).

summary:
In Homo sapiens, immunostimulatory genes AKR1B1 and CCL4 gradually decreased in expression along the trajectory from inflammatory macrophage cluster 2 to immunosuppressive macrophage cluster 1.


claim_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b:claim:594503f764fabb899f73
claim_id: claim:594503f764fabb899f73
paper_key: biorxiv:54c905c7-6e9f-1014-9168-935cc2dc841b
span_literal:
MSR1, LIPA and LGALS1, genes that have previously been shown to be upregulated in immunosuppressive macrophages (Huang et al, 2014), were initially downregulated and increased in expression along the trajectory (Fig S4E-G).

summary:
In Homo sapiens, MSR1, LIPA, and LGALS1 are upregulated in immunosuppressive macrophages and increased in expression along the trajectory toward immunosuppressive macrophage cluster 1.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:07ea92b9fc014582ac84
claim_id: claim:07ea92b9fc014582ac84
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Closer inspection revealed characteristic SMC genes: myosin heavy chain (MYH11), smooth muscle alpha actin (ACTA2) and transgelin (TAGLN) to be highest expressed in the contractile cluster, markedly decreased in the synthetic cluster, and lowest in the macrophage-like cluster

summary:
In Homo sapiens, contractile smooth muscle cells express high levels of myosin heavy chain 11 (MYH11), smooth muscle alpha actin (ACTA2), and transgelin (TAGLN), which are markedly decreased in synthetic smooth muscle cells and lowest in macrophage-like smooth muscle cells.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:ab842203cd30a8f3b955
claim_id: claim:ab842203cd30a8f3b955
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Closer inspection revealed characteristic SMC genes: myosin heavy chain (MYH11), smooth muscle alpha actin (ACTA2) and transgelin (TAGLN) to be highest expressed in the contractile cluster, markedly decreased in the synthetic cluster, and lowest in the macrophage-like cluster

summary:
In Homo sapiens, macrophage-like smooth muscle cells have the lowest expression of MYH11, ACTA2, and TAGLN compared to contractile smooth muscle cells.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:70daee5a5c61a9b5a254
claim_id: claim:70daee5a5c61a9b5a254
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
In contrast, the synthetic gene osteopontin (SPP1) and macrophage markers galectin 3 (LGALS3) and CD68 were lowest in the contractile cluster, elevated in the progressive switch to synthetic, and highest in the macrophage-like cluster.

summary:
In Homo sapiens, macrophage-like smooth muscle cells have the highest expression of osteopontin (SPP1), galectin 3 (LGALS3), and CD68, compared to contractile smooth muscle cells where they are lowest.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:bf00387eefef40726a52
claim_id: claim:bf00387eefef40726a52
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
In contrast, the synthetic gene osteopontin (SPP1) and macrophage markers galectin 3 (LGALS3) and CD68 were lowest in the contractile cluster, elevated in the progressive switch to synthetic, and highest in the macrophage-like cluster.

summary:
In Homo sapiens, contractile smooth muscle cells have the lowest expression of SPP1, LGALS3, and CD68.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:49ea9851f613427eb74e
claim_id: claim:49ea9851f613427eb74e
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Unexpectedly, we noted a similar gene expression pattern in genes of the iron regulation pathway: ferritin light-chain (FTL) and heavy chain (FTH1), and transferrin receptor 1 (TFRC), transitioning through the synthetic to macrophage-like cell clusters.

summary:
In Homo sapiens, ferritin light-chain (FTL), ferritin heavy chain (FTH1), and transferrin receptor 1 (TFRC) are progressively upregulated from synthetic smooth muscle cells to macrophage-like smooth muscle cells.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:7dd2d949853083bcf561
claim_id: claim:7dd2d949853083bcf561
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
SMC8-Mac showed downregulated contractile genes (ACA2, MYH11, TAGLN) compared to the other SMC clusters, and instead, upregulated synthetic (COL1A1, SPP1), foam cell (CD68, LGALS3, AIF1, MSR1, PLIN2), and iron regulation genes (TFRC, SLCO2B1, SLC11A2, SLC40A1, FTL, FTH1, NFE2L2, NCOA4, STEAP3, ACSL4, SAT1, DPP4, CTSB), mirroring the expression pattern of the macrophage cluster.

summary:
In Homo sapiens, macrophage-like smooth muscle cell 8 (SMC8-Mac) shows downregulated ACTA2, MYH11, and TAGLN compared to other smooth muscle cell clusters, and upregulated COL1A1, SPP1, CD68, LGALS3, AIF1, MSR1, PLIN2, TFRC, SLCO2B1, SLC11A2, SLC40A1, FTL, FTH1, NFE2L2, NCOA4, STEAP3, ACSL4, SAT1, DPP4, and CTSB.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:c423a31b16d8cfcf61bb
claim_id: claim:c423a31b16d8cfcf61bb
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Whereas TFRC appears as the primary iron uptake receptor upregulated in SMC8-Mac and macrophages, SLC39A14 was primarily expressed for iron uptake in SMC-Fibro.

summary:
In Homo sapiens, TFRC is the primary iron uptake receptor upregulated in macrophage-like smooth muscle cell 8 (SMC8-Mac), while SLC39A14 is primarily expressed in fibroblast-like smooth muscle cells (SMC-Fibro).


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:58b5b028835c2f3e72c6
claim_id: claim:58b5b028835c2f3e72c6
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Whereas TFRC appears as the primary iron uptake receptor upregulated in SMC8-Mac and macrophages, SLC39A14 was primarily expressed for iron uptake in SMC-Fibro.

summary:
In Homo sapiens, SLC39A14 is primarily expressed for iron uptake in fibroblast-like smooth muscle cells.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:ae1a2544fdb58b8ea713
claim_id: claim:ae1a2544fdb58b8ea713
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Among all SMC cell states, the comparison between SMC8-Mac and SMC1-Con revealed distinct upregulation of foam cell markers (MSR1, CD14, SPP1, TREM2, FOLR2), markers of lipid metabolism (APOC1, PLTP), inflammation (FCGR2A, TYROBP, GPNMB, FOLR2, LSP1, CFD) and extracellular matrix (ECM) regulation (LUM)

summary:
In Homo sapiens, macrophage-like smooth muscle cell 8 (SMC8-Mac) shows distinct upregulation of MSR1, CD14, SPP1, TREM2, FOLR2, APOC1, PLTP, FCGR2A, TYROBP, GPNMB, LSP1, CFD, and LUM compared to contractile smooth muscle cell 1 (SMC1-Con).


