# claims

claim_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2:claim:c811b10e47782f6d8990
claim_id: claim:c811b10e47782f6d8990
paper_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2
span_literal: groups 1 and 2) that expressed mesenchymal markers PDGFRa , PDGFRb , and SCA1
summary:
In Homo sapiens subcutaneous adipose tissue, mesenchymal cell groups 1 and 2 express the mesenchymal markers platelet-derived growth factor receptor alpha, platelet-derived growth factor receptor beta, and stem cell antigen 1.


claim_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2:claim:5bf4478d95af6d28c495
claim_id: claim:5bf4478d95af6d28c495
paper_key: hca:0176_10.1126_science.aav2501_7c9d3a1bd2
span_literal:
However, murine group 3 markers CD142, CLEC11A , and FMO2 were broadly expressed across human groups 1 and 2

summary:
In Homo sapiens subcutaneous adipose tissue, CD142, CLEC11A, and FMO2 are broadly expressed across both group 1 interstitial progenitor cells and group 2 committed preadipocytes, rather than marking a distinct population.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:6ec40decbc0384e76900
claim_id: claim:6ec40decbc0384e76900
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
CD patients were uniquely characterized by the massive expansion of CD4 + Trm ( fig. 1 A and C and SI Appendix , fig. S2 A ), which were defined by the high expression of the resident marker CD103 and the low expression of the effector memory markers CCR7 and CD27

summary:
In Homo sapiens, CD4+ tissue-resident memory T cells are defined by high expression of CD103 and low expression of CCR7 and CD27.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:fec9d8e13591842e4833
claim_id: claim:fec9d8e13591842e4833
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
Heat maps of the mean expression levels of T cell markers revealed that a particular fraction of CD4 + Trm abundant in the gut of CD exhibited high CD161 and CCR5 compared with other T cell fractions

summary:
In Homo sapiens, a fraction of CD4+ tissue-resident memory T cells in the gut of Crohn's disease patients exhibited high CD161 and CCR5 compared with other T cell fractions.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:c8f402d040e2e4321aa1
claim_id: claim:c8f402d040e2e4321aa1
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
CD4 + Trm showed higher expression of CCR5, CD161, CD127, CD69, and CCR6 accompanied by lower expression of CCR7 and CD27 when compared with the other CD4 + T cell subsets

summary:
In Homo sapiens, CD4+ tissue-resident memory T cells showed higher expression of CCR5, CD161, CD127, CD69, and CCR6 and lower expression of CCR7 and CD27 compared with other CD4+ T cell subsets.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:cbc7383dba2c7c60b3f7
claim_id: claim:cbc7383dba2c7c60b3f7
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
Tem, naive T cells, and Tcm were annotated based on the combination of expression levels of CD45RA and CCR7 : CD45RA − CCR7 − T cells as Tem, CD45RA + CCR7 + as naive T cells, and CD45RA − CCR7 + as Tcm.

summary:
In Homo sapiens, effector memory T cells are defined as CD45RA-negative CCR7-negative, naive T cells as CD45RA-positive CCR7-positive, and central memory T cells as CD45RA-negative CCR7-positive.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:fc90f69486208cc6eafe
claim_id: claim:fc90f69486208cc6eafe
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal: The largest T cell subpopulation was CD161 high CD4 + Tem (clusters 1, 5, and 6)
summary:
In Homo sapiens, the largest T cell subpopulation in the gut was CD161-high CD4+ effector memory T cells.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:e9d8e0937ee42789ff8a
claim_id: claim:e9d8e0937ee42789ff8a
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
summary: In Homo sapiens, cytolytic CD4+ T cells are enriched in cytotoxic genes such as GZMs and NKGs.
span_literal:
Cluster 21 was enriched in cytotoxic genes such as GZMs and NKGs , implying the cytotoxic nature of this cluster, which was compatible with cytolytic CD4 + T cells (CD4 + CTL)


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:c4e991b4ca847329e62d
claim_id: claim:c4e991b4ca847329e62d
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
summary: In Homo sapiens, T follicular helper cells highly express BCL6, TCF7, and CXCL13.
span_literal:
Furthermore, Tfh (cluster 8) highly expressing master transcription factor transcripts BCL6 and TCF7 ( 31 – 33 ) together with CXCL13 , encoding a ligand for CXCR5 ( 34 ), tended to increase in UC.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:bd8f507feb670b17bf20
claim_id: claim:bd8f507feb670b17bf20
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
PRDM1 encoding B Lymphocyte-Induced Maturation Protein (BLIMP-1), which is dominantly expressed in effector T cells ( 35 ) and regulates a transcriptional program of tissue residency ( 36 ), was up-regulated in CD compared with the level in UC.

summary:
In Homo sapiens, PRDM1 encoding B Lymphocyte-Induced Maturation Protein 1 is dominantly expressed in effector T cells and was up-regulated in Crohn's disease CD4+ lymphocytes compared with ulcerative colitis.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:b88b07e19d0733e0eb47
claim_id: claim:b88b07e19d0733e0eb47
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal: Cells within the CDpop highly expressed GZMA and IFNG under unstimulated conditions
summary:
In Homo sapiens, CD103+CD161+CCR5+ CD4+ tissue-resident memory T cells (CDpop) highly expressed GZMA and IFNG under unstimulated conditions.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:9e1066e8c59cefd96b5c
claim_id: claim:9e1066e8c59cefd96b5c
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
Genes differentially expressed between CDpop and the rest of the CD4 + T cells revealed that transcripts of chemokines and IFNG were significantly up-regulated in CDpop, whereas genes related to a resting phenotype were up-regulated in the rest of the CD4 + T cells

summary:
In Homo sapiens, IFNG and chemokine transcripts were significantly up-regulated in CD103+CD161+CCR5+ CD4+ tissue-resident memory T cells (CDpop) compared with the rest of CD4+ T cells.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:a5e5143a9f5d2abdc292
claim_id: claim:a5e5143a9f5d2abdc292
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal: CDtrm displayed the higher expression of GZMA and IFNG than the rest of CDpop
summary:
In Homo sapiens, Crohn's disease-specific CD4+ tissue-resident memory T cells (CDtrm) displayed higher expression of GZMA and IFNG than the rest of CDpop.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:204198c74f6ef370b93d
claim_id: claim:204198c74f6ef370b93d
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
Genes differentially expressed between CDtrm and the rest of CDpop revealed that IFNG and a substantial number of natural cytotoxicity-related genes were up-regulated in CDtrm

summary:
In Homo sapiens, IFNG and natural cytotoxicity-related genes were up-regulated in Crohn's disease-specific CD4+ tissue-resident memory T cells (CDtrm) compared with the rest of CDpop.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:180a42e3ac0c6337f67a
claim_id: claim:180a42e3ac0c6337f67a
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal:
UC samples were significantly enriched in CD45RA + CCR7 + -naive CD4 + T cells and CXCR5 + CD4 + T follicular helper cells (Tfh)

summary:
In Homo sapiens, naive CD4+ T cells are defined by CD45RA and CCR7 expression, and T follicular helper cells are defined by CXCR5 expression.


claim_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212:claim:2323e8774dde8c961e4c
claim_id: claim:2323e8774dde8c961e4c
paper_key: hca:0177_10.1073_pnas.2204269120_58cc2f2212
span_literal: CD25 high CD127 − regulatory T cells (Treg) were elevated in both subtypes of IBD
summary:
In Homo sapiens, regulatory T cells are defined by high CD25 expression and negative CD127 expression.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:05ca59aeddc3b078be7e
claim_id: claim:05ca59aeddc3b078be7e
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal: DNAJB1 was significantly associated with Cluster 0
summary:
In Homo sapiens, DNAJB1 expression is a marker of synovial fibroblast cluster 0, which is predominant in fibroblasts from painful sites in end-stage osteoarthritis.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:9991a026012643d199b4
claim_id: claim:9991a026012643d199b4
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
Expression of RARRES1 and TYPMS were significantly associated with Cluster 1 and Cluster 6 respectively, clusters predominant in fibroblasts from non-painful sites in early OA.

summary:
In Homo sapiens, RARRES1 expression is a marker of synovial fibroblast cluster 1, which is predominant in fibroblasts from non-painful sites in early osteoarthritis.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:bea986cf9819c873de98
claim_id: claim:bea986cf9819c873de98
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
Expression of RARRES1 and TYPMS were significantly associated with Cluster 1 and Cluster 6 respectively, clusters predominant in fibroblasts from non-painful sites in early OA.

summary:
In Homo sapiens, TYPMS expression is a marker of synovial fibroblast cluster 6, which is predominant in fibroblasts from non-painful sites in early osteoarthritis.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:502a1717ece5a6ddaab8
claim_id: claim:502a1717ece5a6ddaab8
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
Expression of PTGDS (Cluster 2), CXCL3 (Cluster 3), RSPO3 (Cluster 4), and NRN1 (Cluster 5) were all significantly associated with specific fibroblasts clusters predominantly found in early OA painful synovial sites

summary:
In Homo sapiens, PTGDS expression is a marker of synovial fibroblast cluster 2, which is predominantly found in early osteoarthritis painful synovial sites.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:4f9b86d0f1a4e34fa7c2
claim_id: claim:4f9b86d0f1a4e34fa7c2
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
Expression of PTGDS (Cluster 2), CXCL3 (Cluster 3), RSPO3 (Cluster 4), and NRN1 (Cluster 5) were all significantly associated with specific fibroblasts clusters predominantly found in early OA painful synovial sites

summary:
In Homo sapiens, CXCL3 expression is a marker of synovial fibroblast cluster 3, which is predominantly found in early osteoarthritis painful synovial sites.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:e54f49f169c2ac528437
claim_id: claim:e54f49f169c2ac528437
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
Expression of PTGDS (Cluster 2), CXCL3 (Cluster 3), RSPO3 (Cluster 4), and NRN1 (Cluster 5) were all significantly associated with specific fibroblasts clusters predominantly found in early OA painful synovial sites

summary:
In Homo sapiens, RSPO3 expression is a marker of synovial fibroblast cluster 4, which is predominantly found in early osteoarthritis painful synovial sites.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:c93063a8913c660af740
claim_id: claim:c93063a8913c660af740
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
summary:
In Homo sapiens, NRN1 expression is a marker of synovial fibroblast cluster 5, which is predominantly found in early osteoarthritis painful synovial sites.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:d7af2c3c319cd5c48194
claim_id: claim:d7af2c3c319cd5c48194
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
fibroblasts from early OA painful synovial sites exhibited high gene expression of NFKBIA, CXCL2, GEM, VCAM1, LIF, IL-6 and INHBA, whilst fibroblasts from end-stage OA painful synovial sites were characterised by high expression of HSPA1A, DNAJB1, SLC39A8, HTRA3, ATF3, PTGIS and BNIP3

summary:
In Homo sapiens, synovial fibroblasts from early osteoarthritis painful synovial sites are characterized by high expression of NFKBIA, CXCL2, GEM, VCAM1, LIF, IL-6, and INHBA, while synovial fibroblasts from end-stage osteoarthritis painful synovial sites are characterized by high expression of HSPA1A, DNAJB1, SLC39A8, HTRA3, ATF3, PTGIS, and BNIP3.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:ed44192d652b3d5157d6
claim_id: claim:ed44192d652b3d5157d6
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
fibroblasts from early OA painful synovial sites exhibited high gene expression of NFKBIA, CXCL2, GEM, VCAM1, LIF, IL-6 and INHBA, whilst fibroblasts from end-stage OA painful synovial sites were characterised by high expression of HSPA1A, DNAJB1, SLC39A8, HTRA3, ATF3, PTGIS and BNIP3

summary:
In Homo sapiens, synovial fibroblasts from end-stage osteoarthritis painful synovial sites are characterized by high expression of HSPA1A, DNAJB1, SLC39A8, HTRA3, ATF3, PTGIS, and BNIP3.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:3c711e539b5351d23482
claim_id: claim:3c711e539b5351d23482
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
End-stage OA fibroblasts were also characterised by high expression of the stress-response genes ATF3, HSPA1A and DNAJB1

summary:
In Homo sapiens, end-stage osteoarthritis synovial fibroblasts are characterized by high expression of the stress-response genes ATF3, HSPA1A, and DNAJB1.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:718ca7ddeeb217d661c1
claim_id: claim:718ca7ddeeb217d661c1
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
End-stage OA pain fibroblasts also exhibited high expression of HTRA3, a serine proteinase implicated in the degradation of extracellular matrix

summary:
In Homo sapiens, end-stage osteoarthritis pain-associated synovial fibroblasts exhibit high expression of HTRA3, a serine proteinase implicated in extracellular matrix degradation.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:8200e46cb3cacc6d6122
claim_id: claim:8200e46cb3cacc6d6122
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
our finding that painful synovial tissue sites in early OA contain fibroblast subsets with high expression of pro-inflammatory mediators including CXCL1, CXCL2, IL-6 and LIF provides further evidence for the role of synovial inflammation in the development of early OA pain

summary:
In Homo sapiens, synovial fibroblast subsets from painful synovial tissue sites in early osteoarthritis exhibit high expression of the pro-inflammatory mediators CXCL1, CXCL2, IL-6, and LIF.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:e34992aeefe640a6204f
claim_id: claim:e34992aeefe640a6204f
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
These data are further supported by our finding of increased KCNMA1 and decreased ACKR4 expression in fibroblast subsets from painful synovial sites in early OA patients.

summary:
In Homo sapiens, synovial fibroblast subsets from painful synovial sites in early osteoarthritis patients show increased KCNMA1 expression and decreased ACKR4 expression.


claim_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2:claim:3dbbceaf47f965ae4582
claim_id: claim:3dbbceaf47f965ae4582
paper_key: hca:0178_10.1016_j.ebiom.2021.103618_7744ce01c2
span_literal:
This specific fibroblast subset exhibited high expression of neuritin 1 and sulfatase 1, which are known promoters of neuronal survival, development and outgrowth

summary:
In Homo sapiens, the neuritogenesis-associated synovial fibroblast subset (cluster 5) exhibits high expression of neuritin 1 and sulfatase 1, which are known promoters of neuronal survival, development, and outgrowth.


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:7eee5618a5d97fb52746
claim_id: claim:7eee5618a5d97fb52746
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
summary: In Homo sapiens brain organoids, radial glial progenitor cells are marked by PAX6.
span_literal:
Without Shh signaling, organoids exhibited cortical characteristics including expression of the apical and basal radial glial progenitor marker PAX6, the intermediate progenitor marker TBR2 (EOMES), deep cortical plate markers including TBR1, CTIP2 (BCL11B), and BHLHB5 (BHLHE22), and superficial layer markers such as SATB2, and BRN2 (POU3F2)


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:6fb1a7afc282025d9a0f
claim_id: claim:6fb1a7afc282025d9a0f
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
span_literal:
Without Shh signaling, organoids exhibited cortical characteristics including expression of the apical and basal radial glial progenitor marker PAX6, the intermediate progenitor marker TBR2 (EOMES), deep cortical plate markers including TBR1, CTIP2 (BCL11B), and BHLHB5 (BHLHE22), and superficial layer markers such as SATB2, and BRN2 (POU3F2)

summary:
In Homo sapiens brain organoids, deep cortical plate neurons are marked by TBR1, CTIP2 (BCL11B), and BHLHB5 (BHLHE22).


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:31d70cd74fe2338674d7
claim_id: claim:31d70cd74fe2338674d7
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
span_literal:
Shh pathway-stimulated organoids by contrast expressed canonical GE progenitor and migratory interneuron markers such as NKX2.1, DLX1, DLX2, and OLIG2.

summary:
In Homo sapiens brain organoids, ganglionic eminence progenitor and migratory interneuron cells express NKX2.1, DLX1, DLX2, and OLIG2.


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:9fa3af28f99610f7b399
claim_id: claim:9fa3af28f99610f7b399
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
summary: In Homo sapiens brain organoids, GABAergic inhibitory neurons are marked by GAD65 (GAD2).
span_literal:
Over time in culture, many neurons within GE organoids expressed GABAergic inhibitory neuron markers such as GAD65 (GAD2) and GABA along with a variety of interneuron subtype markers


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:a08bf5c41046e6c7905d
claim_id: claim:a08bf5c41046e6c7905d
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
span_literal:
We plotted the expression of canonical markers associated with each of these clusters (e.g., GAD1 with interneurons or SATB2 with excitatory clusters) including many of the markers we had used for immunohistochemical analyses of neuronal subtypes

summary:
In Homo sapiens brain organoids, interneurons are marked by GAD1 and excitatory neurons are marked by SATB2.


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:da0b9e1b52db7a1591d1
claim_id: claim:da0b9e1b52db7a1591d1
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
span_literal:
Genes associated with astrocyte progenitors and maturing astrocytes (e.g., GFAP , FGFR3 , AQP4 , and ALDH1L1 expression) overlapped with the oRG cluster,

summary:
In Homo sapiens brain organoids, astrocyte progenitors and maturing astrocytes express GFAP, FGFR3, AQP4, and ALDH1L1.


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:2289522024ed865ae684
claim_id: claim:2289522024ed865ae684
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
span_literal:
We found 7 major subclusters defined by their distinct profile of interneuron-associated genes such as SST , NPY , CALB1 , and CALB2 , vasoactive intestinal polypeptide ( VIP ), and parvalbumin ( PVALB ), and variable expression of additional genes such as DLX2, DLX5, GAD2, SLC6A1, SLC32A1, LAMP5, SCGN, and TAC1

summary:
In Homo sapiens brain organoids, interneuron subtypes are defined by expression of SST, NPY, CALB1, CALB2, vasoactive intestinal polypeptide (VIP), parvalbumin (PVALB), DLX2, DLX5, GAD2, SLC6A1, SLC32A1, LAMP5, SCGN, and TAC1.


claim_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4:claim:77425afe01fb826307be
claim_id: claim:77425afe01fb826307be
paper_key: hca:0179_10.1038_s41593-021-00906-5_f703d212e4
span_literal:
Significant reductions in PVALB + interneurons have been seen in the prefrontal cortex of autistic individuals

summary:
In Homo sapiens, PVALB-positive interneurons are found in the prefrontal cortex and are significantly reduced in autistic individuals.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:17ac1c8bf8a845d7f153
claim_id: claim:17ac1c8bf8a845d7f153
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal: cluster 2 was associated with IFN-response genes (e.g. ISG15 )
summary:
In Homo sapiens, interferon-response CD8-positive T cells (cluster 2) are marked by expression of ISG15.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:3710d468ca63a5be5ca5
claim_id: claim:3710d468ca63a5be5ca5
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
summary: In Homo sapiens, exhausted CD8-positive T cells express PDCD1, CTLA4, and HAVCR2.
span_literal:
clusters 3 and 4 expressed checkpoint markers associated with exhaustion (e.g. PDCD1 [gene for PD-1], CTLA4 and HAVCR2 [gene for TIM3])


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:8849b6afc2f8e91c7dac
claim_id: claim:8849b6afc2f8e91c7dac
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal: cluster 6 expressed markers associated with naïve or memory cells (e.g. CCR7 and CD27 )
summary:
In Homo sapiens, naïve or memory CD8-positive T cells (cluster 6) are marked by expression of CCR7 and CD27.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:adb11bc58447cce6fc9c
claim_id: claim:adb11bc58447cce6fc9c
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal: cluster 7 expressed genes associated with early activation (e.g. JUNB and FOSB )
summary:
In Homo sapiens, early activated CD8-positive T cells (cluster 7) are marked by expression of JUNB and FOSB.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:bb896bfb85679f831459
claim_id: claim:bb896bfb85679f831459
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal: cluster 8 expressed genes associated with effector function (e.g. KLRG1 and GZMH )
summary:
In Homo sapiens, effector CD8-positive T cells (cluster 8) are marked by expression of KLRG1 and GZMH.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:456bdb556ec1a3f1faaf
claim_id: claim:456bdb556ec1a3f1faaf
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
DC1 was strongly associated with a terminally differentiated phenotype, with progression along DC1 associated with increased co-expression of inhibitory receptors such as LAG3 , CTLA4 , PDCD1 (gene for PD1) and HAVCR2 (gene for TIM3)

summary:
In Homo sapiens, terminally differentiated CD8-positive T cells co-express the inhibitory receptors LAG3, CTLA4, PDCD1, and HAVCR2.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:30491d9511f60addd3b1
claim_id: claim:30491d9511f60addd3b1
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
We also found high expression of ENTPD1 (gene for CD39) and CXCL13 by these terminally differentiated CD8 + T cells, suggestive of a role of these cells in adenosine metabolism

summary:
In Homo sapiens, terminally differentiated CD8-positive T cells express high levels of ENTPD1 and CXCL13.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:804644ec85e385331076
claim_id: claim:804644ec85e385331076
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
DC2 was associated with a memory phenotype ( Figure S3C ), governed by co-expression of CD27 , CCR7 , EOMES and other genes associated with memory formation

summary:
In Homo sapiens, memory CD8-positive T cells are characterized by co-expression of CD27, CCR7, and EOMES.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:167dc61fcdc8218c24d4
claim_id: claim:167dc61fcdc8218c24d4
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
we found that TNFRSF18 (GITR), TNFRSF9 (CD137; 4-1BB) and TNFRSF4 (OX40) were positively correlated with DC1 and were co-expressed at late DPT

summary:
In Homo sapiens, effector regulatory T cells co-express TNFRSF18, TNFRSF9, and TNFRSF4 at late differentiation pseudotime.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:e5a11ca28b95353f8205
claim_id: claim:e5a11ca28b95353f8205
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
we found that IFN-response genes IFITM1 , IFIT1 , IFIT3 , and ISG20 were expressed at early DPT and were turned off as pseudotime progressed

summary:
In Homo sapiens, early activated regulatory T cells express the interferon-response genes IFITM1, IFIT1, IFIT3, and ISG20, which are turned off as differentiation progresses.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:627926c31a77cde4823d
claim_id: claim:627926c31a77cde4823d
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
This led to identification of cluster 2 as CD16 + monocytes, and two clusters of CD14 + monocytes (clusters 3 and 4).

summary:
In Homo sapiens, CD16-positive monocytes (cluster 2) are identified by FCGR3A expression, and CD14-positive monocytes are identified in clusters 3 and 4.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:65afe0d7ab740e6d0a4e
claim_id: claim:65afe0d7ab740e6d0a4e
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
span_literal:
Cluster 1 had high expression of IDO1 , CCL17 and CCR7 , cluster 6 expressed CD1C (consistent with conventional DCs) and cluster 8 expressed complement.

summary:
In Homo sapiens, IDO1-positive dendritic cells (cluster 1) express IDO1, CCL17, and CCR7, while conventional dendritic cells (cluster 6) express CD1C.


claim_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1:claim:15b44ea31ae8257e3beb
claim_id: claim:15b44ea31ae8257e3beb
paper_key: hca:0180_10.1016_j.immuni.2019.11.014_dd3bbb9bc1
summary: In Homo sapiens, M2-like macrophages (cluster 8) express the canonical marker MRC1.
span_literal:
Cluster 8 also expressed the canonical M2 marker MRC1 (gene for CD206), although it was not among the top differentially expressed genes.


claim_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538:claim:b771c69bc14fb3e59a21
claim_id: claim:b771c69bc14fb3e59a21
paper_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538
span_literal:
cluster 0 [ITGAE (CD103) hi ZNF683 (HOBIT) hi ], composed of conventional CD103 + T RM cells; cluster 1 (EOMES hi ), composed of CD69 + CD103 −/low T RM cells; and cluster 2, CD8 + T cells expressing high levels CXCR6, PRF1, and TNF

summary:
In Homo sapiens, respiratory CD8+ T cell cluster 0 (conventional CD103+ tissue-resident memory cell) is marked by high expression of ITGAE and ZNF683.


claim_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538:claim:1f07bc73c89a866f3bee
claim_id: claim:1f07bc73c89a866f3bee
paper_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538
span_literal:
cluster 0 [ITGAE (CD103) hi ZNF683 (HOBIT) hi ], composed of conventional CD103 + T RM cells; cluster 1 (EOMES hi ), composed of CD69 + CD103 −/low T RM cells; and cluster 2, CD8 + T cells expressing high levels CXCR6, PRF1, and TNF

summary:
In Homo sapiens, respiratory CD69+ CD103−/low tissue-resident memory T cell (cluster 1) is marked by high expression of EOMES.


claim_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538:claim:91344e3e44b096dd2a2a
claim_id: claim:91344e3e44b096dd2a2a
paper_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538
span_literal:
cluster 0 [ITGAE (CD103) hi ZNF683 (HOBIT) hi ], composed of conventional CD103 + T RM cells; cluster 1 (EOMES hi ), composed of CD69 + CD103 −/low T RM cells; and cluster 2, CD8 + T cells expressing high levels CXCR6, PRF1, and TNF

summary:
In Homo sapiens, respiratory CD8+ T cell cluster 2 is marked by high expression of CXCR6, PRF1, and TNF.


claim_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538:claim:debd253797646a74e944
claim_id: claim:debd253797646a74e944
paper_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538
span_literal:
Cluster 1 CD103 −/low T RM cells also expressed higher levels of NKG7, a cytotoxic molecule that can promote lethal inflammation after infection ( 22 ), and granzyme K, an inflammatory granzyme that promotes fibroblast activation

summary:
In Homo sapiens, CD103-/low tissue-resident memory T cell cluster 1 expresses higher levels of NKG7 and granzyme K compared to conventional tissue-resident memory T cells.


claim_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538:claim:a5ad5d96d7d248acda11
claim_id: claim:a5ad5d96d7d248acda11
paper_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538
span_literal:
Compared with CD103 + T RM cells, CD69 + CD103 − T cells expressed higher levels of EOMES, granzyme B, granzyme K, CXCR4, and KLRG1

summary:
In Homo sapiens, CD69+ CD103- T cells express higher levels of EOMES, granzyme B, granzyme K, CXCR4, and KLRG1 compared to CD103+ tissue-resident memory T cells.


claim_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538:claim:be8e51918a91adbee8d1
claim_id: claim:be8e51918a91adbee8d1
paper_key: hca:0182_10.1126_sciimmunol.abk1741_33c534a538
span_literal:
aged COVID-19 convalescents had increased presence of cluster 2 CD4 + T cells, which expressed genes associated with myeloid cell inflammation including Lyz, S100 A8, and S100 A9

summary:
In Homo sapiens, cluster 2 CD4+ T cells express genes associated with myeloid cell inflammation including LYZ, S100A8, and S100A9.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:237da989b1503b78e3b4
claim_id: claim:237da989b1503b78e3b4
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal: basal cells by their expression of TP63, KRT15, and KRT5
summary:
In Homo sapiens, basal cells are identified by expression of TP63, KRT15, and KRT5, and mitotic basal cells are identified by expression of MKI67 and TOP2A.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:bdeb52cc2d0bdaa6572a
claim_id: claim:bdeb52cc2d0bdaa6572a
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
We resolved large populations of secretory cells and goblet cells ( KRT7 , CXCL17, F3, AQP5, CP) ; despite strong transcriptional similarity, we distinguished between goblet and secretory cells based on expression of MUC5AC- expressing goblet, and BPIFA1- expressing secretory cells.

summary:
In Homo sapiens, secretory cells and goblet cells express KRT7, CXCL17, F3, AQP5, and CP; goblet cells are distinguished by MUC5AC expression and secretory cells by BPIFA1 expression.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:9a69773b3c6801d554e8
claim_id: claim:9a69773b3c6801d554e8
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
We resolved large populations of secretory cells and goblet cells ( KRT7 , CXCL17, F3, AQP5, CP) ; despite strong transcriptional similarity, we distinguished between goblet and secretory cells based on expression of MUC5AC- expressing goblet, and BPIFA1- expressing secretory cells.

summary:
In Homo sapiens, secretory cells express KRT7, CXCL17, F3, AQP5, CP, and BPIFA1, and are distinguished from goblet cells.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:bcd11d73a73916bdcd1a
claim_id: claim:bcd11d73a73916bdcd1a
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
summary: In Homo sapiens, ciliated cells are marked by expression of FOXJ1, DLEC1, DNAH11, and CFAP43.
span_literal:
Ciliated cells ( FOXJ1 and a ciliogenesis gene program, e.g., DLEC1, DNAH11, CFAP43 ) were the most numerous epithelial cell type recovered.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:0d0099869762c7dcfe8f
claim_id: claim:0d0099869762c7dcfe8f
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
one, termed “developing ciliated cells,” expressed canonical ciliated cell genes such as FOXJ1 , CAPSL , and PIFO at lower levels than mature ciliated cells and lacked expression of cilia-forming genes

summary:
In Homo sapiens, developing ciliated cells express FOXJ1, CAPSL, and PIFO at lower levels than mature ciliated cells.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:7ca673f389629e8469c7
claim_id: claim:7ca673f389629e8469c7
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal: we also resolved deuterosomal cells ( DEUP1, CCNO, CDC20B, FOXN4, HES6 )
summary:
In Homo sapiens, deuterosomal cells are identified by expression of DEUP1, CCNO, CDC20B, FOXN4, and HES6.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:504418e0573d6fb05460
claim_id: claim:504418e0573d6fb05460
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
Among lymphoid cells, we recovered T cells ( CD3E, CD2, TRBC2 ) and B cells ( MS4A1, CD79A, CD79B ).

summary:
In Homo sapiens, T cells are marked by CD3E, CD2, and TRBC2, and B cells are marked by MS4A1, CD79A, and CD79B.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:9cb592d10ee9753277c2
claim_id: claim:9cb592d10ee9753277c2
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
Among myeloid cell types, we recovered a large population of macrophages ( CD14, FCGR3A, VCAN ), dendritic cells ( CCR7, CD86 ), and plasmacytoid DCs ( IRF7, IL3RA ).

summary:
In Homo sapiens, macrophages are marked by CD14, FCGR3A, and VCAN; dendritic cells by CCR7 and CD86; and plasmacytoid dendritic cells by IRF7 and IL3RA.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:2da0ddf9019a73dc0086
claim_id: claim:2da0ddf9019a73dc0086
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
Basal cells represent the main stem/progenitor cells of the nasal epithelium, and are classically defined by TP63 , KRT5 , and KRT15 expression

summary:
In Homo sapiens, basal cells of the nasal epithelium are classically defined by TP63, KRT5, and KRT15 expression.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:6b8f7c57cfa5a2425ddd
claim_id: claim:6b8f7c57cfa5a2425ddd
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
Secretory cells are a distinct exocrine cell of the nasal epithelium, and are distinguished from goblet cells by the absence of mucin production and preferential expression of antimicrobial molecules (e.g., BPIFA1)

summary:
In Homo sapiens, secretory cells of the nasal epithelium are distinguished from goblet cells by preferential expression of BPIFA1.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:96d98f56eca01fe5dce9
claim_id: claim:96d98f56eca01fe5dce9
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
FFAR4 high macrophages are defined by expression of FFAR4 , MRC1 , CHIT1 , and SIGLEC11 , as well as chemotactic factors including CCL18 , CCL15 , genes involved in leukotriene synthesis ( ALOX5, ALOX5AP, LTA4H ), and toll-like receptors TLR8 and TLR2

summary:
In Homo sapiens, FFAR4 high macrophages are defined by expression of FFAR4, MRC1, CHIT1, SIGLEC11, CCL18, CCL15, ALOX5, ALOX5AP, LTA4H, TLR8, and TLR2.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:10e794dccd1167aac423
claim_id: claim:10e794dccd1167aac423
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
Interferon responsive macrophages are distinguished by elevated expression of anti-viral genes such as IFIT3, IFIT2, ISG15, and MX1 , akin to the epithelial subsets labeled “interferon responsive,” along with CXCL9 , CXCL10 , CXCL11 , which are likely indicative of IFNγ stimulation.

summary:
In Homo sapiens, interferon responsive macrophages are distinguished by elevated expression of IFIT3, IFIT2, ISG15, MX1, CXCL9, CXCL10, and CXCL11.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:785c05a8c2be5a1b020d
claim_id: claim:785c05a8c2be5a1b020d
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
MSR1 high C1QB high macrophages are defined by cathepsin expression ( CTSD, CTSL, CTSB ) and elevated expression of complement ( C1QB, C1QA, C1QC ), and lipid binding proteins ( APOE, APOC, and NPC2 ).

summary:
In Homo sapiens, MSR1 high C1QB high macrophages are defined by expression of CTSD, CTSL, CTSB, C1QB, C1QA, C1QC, APOE, APOC, and NPC2.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:d25fa604644f0a784ff1
claim_id: claim:d25fa604644f0a784ff1
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
summary: In Homo sapiens, inflammatory macrophages uniquely express CCL3, CCL3L1, IL1B, CXCL2, and CXCL3.
span_literal:
inflammatory macrophages,” which uniquely express inflammatory cytokines such as CCL3, CCL3L1, IL1B, CXCL2, and CXCL3


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:9a5e42d1fa0f08b44957
claim_id: claim:9a5e42d1fa0f08b44957
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
The remaining “ ITGAX high ” macrophages are distinguished from other immune cell types by ITGAX , VCAN, PSAP, FTL, FTH1 and CD163

summary:
In Homo sapiens, ITGAX high macrophages are distinguished from other immune cell types by ITGAX, VCAN, PSAP, FTL, FTH1, and CD163.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:563b59cb247130f057e7
claim_id: claim:563b59cb247130f057e7
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
T cells are largely CD69 and CD8A positive, with significantly-enriched expression of ITGAE , ITGB7 and CD44 , consistent with a T resident memory-like phenotype

summary:
In Homo sapiens, T cells in the nasopharynx are positive for CD69, CD8A, ITGAE, ITGB7, and CD44, consistent with a T resident memory-like phenotype.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:37ea0b28fe3ec274c349
claim_id: claim:37ea0b28fe3ec274c349
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
the other termed “interferon responsive cytotoxic CD8 T cells,” defined by granzyme and perforin expression ( GZMB, GZMA, GNLY, PRF1, GZMH ), anti-viral genes ( ISG20, IFIT3, APOBEC3C, GBP5 ) and genes associated with effector CD8 T cell function ( LAG3, IL2RB, IKZF3, TBX21 ).

summary:
In Homo sapiens, interferon responsive cytotoxic CD8 T cells are defined by expression of GZMB, GZMA, GNLY, PRF1, GZMH, ISG20, IFIT3, APOBEC3C, GBP5, LAG3, IL2RB, IKZF3, and TBX21.


claim_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088:claim:7bbb1dd738e046467e95
claim_id: claim:7bbb1dd738e046467e95
paper_key: hca:0184_10.1016_j.cell.2021.07.023_f621bea088
span_literal:
We also recovered a very small population of cells we term “enteroendocrine cells,” based on unique expression of gastric inhibitory polypeptide ( GIP ), which is typically produced by intestinal and gastric enteroendocrine cells and LGR5 , which classically marks stem cell populations in the gastrointestinal mucosa

summary:
In Homo sapiens, enteroendocrine cells are identified by unique expression of gastric inhibitory polypeptide (GIP) and LGR5.


claim_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45:claim:1d1fee9f254d0c7d2ede
claim_id: claim:1d1fee9f254d0c7d2ede
paper_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45
span_literal:
Expression of ACTA2 , COL1A1 and COL3A1 (markers of myofibroblast transdifferentiation 29 , 30 ) were significantly increased in fibroblasts grown in 2D

summary:
In Homo sapiens, ACTA2, COL1A1, and COL3A1 are positive markers of myofibroblast transdifferentiation.


claim_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45:claim:4b9fcc00367e0288598a
claim_id: claim:4b9fcc00367e0288598a
paper_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45
summary: In Homo sapiens, IL6 is a positive marker of inflammatory fibroblasts.
span_literal:
whereas expression of IL6 (a marker of ‘inflammatory’ fibroblasts 31 ) was significantly increased in 3D


claim_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45:claim:8dd03ff333babe51724e
claim_id: claim:8dd03ff333babe51724e
paper_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45
span_literal:
culturing these cells in 3D resulted in significantly increased expression of IL6 , which may be indicative of an ‘inflammatory’ CAF phenotype 31

summary:
In Homo sapiens, IL6 is a positive marker indicative of an inflammatory cancer-associated fibroblast phenotype.


claim_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45:claim:f986f8fa19a4acd5f283
claim_id: claim:f986f8fa19a4acd5f283
paper_key: hca:0185_10.1038_s41598-019-45842-4_2aeb7a4d45
summary: In Homo sapiens, DCN is identified as a pan-fibroblast marker used to identify fibroblasts.
span_literal:
Ex vivo fibroblasts were filtered by DCN expression (identified as a pan-fibroblast marker; cells with a DCN expression level of less than 1 were excluded) to exclude any misclassified cells.


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:7c4bd4fdd9455176e535
claim_id: claim:7c4bd4fdd9455176e535
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
summary: In Homo sapiens, basal stem cells in the lung are marked by the transcription factor TP63.
span_literal:
In the lung, basal stem cells reside on the basolateral surface of the pseudostratified epithelium and are marked by the transcription factor TP63, which is essential for basal cell fate determination and function


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:1d14cdd2eb9d0123dfe1
claim_id: claim:1d14cdd2eb9d0123dfe1
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
summary: In Homo sapiens, bud tip progenitor cells express the markers SFTPC, ID2, and HMGA1.
span_literal:
bud tip progenitor organoid cells exhibited low cellular heterogeneity and expressed human bud tip progenitor markers SFTPC, ID2 and HMGA1


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:bac625741fcdeed9fd65
claim_id: claim:bac625741fcdeed9fd65
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
summary: In Homo sapiens, TP63 is a marker of mature basal cells and KRT5 is a marker of mature basal cells.
span_literal:
Interestingly, while TP63 is a marker of mature basal cells, lineage tracing in mice using the Tp63 -cre ER has shown that Cre activation prior to E10.5 leads to labeling of the entire lung epithelium and labeling of TP63+ cells that are negative for the mature basal cell marker KRT5


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:45b5eba3013c256de025
claim_id: claim:45b5eba3013c256de025
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
span_literal:
we first identified basal cells as cells within cluster 7 based on expression of the canonical basal cell markers TP63 and KRT5

summary:
In Homo sapiens, basal cells in the developing lung are identified by expression of the canonical markers TP63 and KRT5.


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:5865e1912b7ff99b7845
claim_id: claim:5865e1912b7ff99b7845
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
span_literal: this cluster highly expressed a set of genes including KRT15, IL33 , S100A2 , F3, EGFR , and PDPN
summary:
In Homo sapiens, the basal cell cluster in the developing lung highly expresses KRT15, IL33, S100A2, F3, EGFR, and PDPN.


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:85980263f6b96c83bc16
claim_id: claim:85980263f6b96c83bc16
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
span_literal:
Cluster 6 bud tip adjacent cells co-expressed a unique combination of genes including bud tip progenitor markers (low SFTPC , ID2 ) as well as canonical AECI markers such as HOPX , PDPN and AGER

summary:
In Homo sapiens, bud tip adjacent cells co-express low levels of bud tip progenitor markers SFTPC and ID2 as well as canonical alveolar epithelial cell type 1 markers HOPX, PDPN, and AGER.


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:64d85fd0f6e0eb4652e5
claim_id: claim:64d85fd0f6e0eb4652e5
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
span_literal:
Cells in cluster 4 express high levels of SCGB3A2 , SFTPB and CFTR , were molecularly distinct from other secretory cell populations; for example, they did not express the club cell marker SCGB1A1

summary:
In Homo sapiens, secretory progenitor cells express high levels of SCGB3A2, SFTPB, and CFTR, and do not express the club cell marker SCGB1A1.


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:e0235f195a09c9275910
claim_id: claim:e0235f195a09c9275910
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
span_literal:
Of the basal cell enriched genes, EGFR and F3 were surface markers uniquely co-expressed in basal cells.

summary:
In Homo sapiens, EGFR and F3 are surface markers uniquely co-expressed in basal cells of the developing lung.


claim_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e:claim:1a411b02edea31d4f9c8
claim_id: claim:1a411b02edea31d4f9c8
paper_key: hca:0186_10.1016_j.devcel.2020.01.033_6afe089f1e
summary: In Homo sapiens, fetal airway secretory cells express SCGB3A2 and SFTPB.
span_literal:
Organoids showed expression of fetal airway secretory cells (SCGB3A2+/SFTPB+, see also Figure 3 ) multiciliated cells (FOXJ1+, ACTUB+), club cells (SCGB1A1+), goblet cells (MUC5AC+) and neuroendocrine cells (CHGA+, SYN+), in addition to TP63+ cells and a subset of TP63+/KRT5+ basal-like cells


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:4c0ae0b0beeecc053239
claim_id: claim:4c0ae0b0beeecc053239
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal:
KLRC2 , which encodes the NK activating receptor NKG2C was negatively associated with this continuum, while the signaling adaptor FCER1G was positively associated

summary:
In Homo sapiens, natural killer cells exhibit KLRC2 expression negatively associated with the CD38-defined gradient and FCER1G expression positively associated with the CD38-defined gradient.


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:322bff2f0f9ccde59dc1
claim_id: claim:322bff2f0f9ccde59dc1
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal:
we found that ATAC-seq peaks accessible in MAIT cells were highly enriched for motifs for the pro-inflammatory transcription factor RORγt

summary:
In Homo sapiens, mucosal associated invariant T cells show enrichment for the pro-inflammatory transcription factor RORγt motifs in accessible chromatin regions.


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:7ed2851a62faa373bd12
claim_id: claim:7ed2851a62faa373bd12
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
summary: In Homo sapiens, plasmacytoid dendritic cells are marked by CD123 positivity.
span_literal:
We confirmed that this marker discovery procedure identifies effective panels for well-characterized populations (plasmacytoid DC [pDC]: CD123 + ; MAIT cells: CD3 + CD161 + TCRvɑ7.2 + ; CD4 naive: CD4 + CD45RA + CD45RB + )


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:8ebee373d2f62d4fc490
claim_id: claim:8ebee373d2f62d4fc490
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal:
We confirmed that this marker discovery procedure identifies effective panels for well-characterized populations (plasmacytoid DC [pDC]: CD123 + ; MAIT cells: CD3 + CD161 + TCRvɑ7.2 + ; CD4 naive: CD4 + CD45RA + CD45RB + )

summary:
In Homo sapiens, mucosal associated invariant T cells are marked by CD3, CD161, and TCRvα7.2 positivity.


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:891212f05685abff36a1
claim_id: claim:891212f05685abff36a1
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal: Both populations did not express the canonical resident marker CD69
summary:
In Homo sapiens, CD8+ CD103+ T cells and CD8+ CD49a+ T cells do not express the canonical resident marker CD69.


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:ab93cbb2360e33f1b7cf
claim_id: claim:ab93cbb2360e33f1b7cf
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
summary: In Homo sapiens, regulatory T cells express CD25 protein.
span_literal:
For example, cells that were annotated as regulatory T cells expressed CD25 in the CITE-seq data, and we observed similar results for MAIT cells (CD161 + ), memory (CD45RA − CD45RO + ) and naive (CD45RA + CD45RO − ) T cells, and circulating ILC (CD117 + CD25 + )


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:900f1976a43eaaafe968
claim_id: claim:900f1976a43eaaafe968
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal:
we identified Siglec-1 (CD169) as a protein response biomarker that was robustly induced only in day 3 samples

summary:
In Homo sapiens, Siglec-1 (CD169) is a protein biomarker induced in myeloid cells in response to vaccination.


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:d586de7c7ebd66a107d0
claim_id: claim:d586de7c7ebd66a107d0
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal: MAIT cells were identified by expression of CD3, CD161, and TCR Vα 7.2 as shown in Figure S7
summary:
In Homo sapiens, mucosal associated invariant T cells are identified by expression of CD3, CD161, and TCR Vα7.2.


claim_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19:claim:265d1b4dae2ae3ae332c
claim_id: claim:265d1b4dae2ae3ae332c
paper_key: hca:0187_10.1016_j.cell.2021.04.048_58f6b9bb19
span_literal:
B cell states are subdivided by their mutually exclusive expression of kappa or lambda light chain, with distinguishing markers including IGKC, IGLC3, IGLC3.

summary:
In Homo sapiens, B cell states are subdivided by mutually exclusive expression of kappa or lambda light chain, with distinguishing markers including IGKC and IGLC3.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:4b59c49a15fc43cd411b
claim_id: claim:4b59c49a15fc43cd411b
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
summary: In Homo sapiens, pro-inflammatory endothelial cells express IL6 and RELB.
span_literal:
EC3 exhibited a pro-inflammatory signature, expressing cytokines such as IL6 and the gene encoding the NFκB family transcription factor RELB


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:16c9da0cafaab85c28b9
claim_id: claim:16c9da0cafaab85c28b9
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
summary: In Homo sapiens, a subset of endothelial cells from dilated cardiomyopathy expresses KIT.
span_literal:
EC5 was derived from a patient with DCM and comprised a small cluster of endothelial cells expressing KIT


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:87e8ea094887bd4291f4
claim_id: claim:87e8ea094887bd4291f4
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
summary: In Homo sapiens, activated cardiac fibroblasts are marked by expression of FAP and POSTN.
span_literal:
CF3 included cells from control, DCM and Neo-HLHS hearts, and exhibited gene-expression signatures consistent with cardiac fibroblast activation, as indicated by expression of the cardiac fibroblast activation markers FAP and POSTN


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:e3e651eaf7e10b61f39d
claim_id: claim:e3e651eaf7e10b61f39d
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal:
CF4 included increased expression of canonical YAP target genes such as CYR61 (also known as CCN1 ), FAT1 , THBS1 , CCL2 , AMOTL1 and PTX3

summary:
In Homo sapiens, cardiac fibroblast cluster 4 is marked by increased expression of CYR61, FAT1, THBS1, CCL2, AMOTL1, and PTX3.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:1e0f6a5749879204aef6
claim_id: claim:1e0f6a5749879204aef6
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal: DEGs in CM2 included cardiac stress markers such as NPPA , THBS1 , ANKRD1 and NPPB
summary:
In Homo sapiens, cardiomyocyte cluster 2 is marked by expression of the cardiac stress markers NPPA, THBS1, ANKRD1, and NPPB.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:34362b96e733f3c2ea2e
claim_id: claim:34362b96e733f3c2ea2e
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal:
Cell annotation based on known marker-gene expression revealed 12 clusters of circulating immune cells, including MS4A1 + B cells, CD14 + monocytes and KLRF1 + natural killer (NK) cells

summary:
In Homo sapiens, B cells are marked by MS4A1, monocytes are marked by CD14, and natural killer cells are marked by KLRF1.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:6c45723c40273e6e0d9f
claim_id: claim:6c45723c40273e6e0d9f
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal:
Cells in the NK2 cluster expressed the chemokines XCL1 and XCL2, which are known inducers of monocyte-derived dendritic cells and markers of activated NK cells

summary:
In Homo sapiens, activated natural killer cells in the NK2 cluster are marked by expression of XCL1 and XCL2.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:a20d6d816ea215ea5aea
claim_id: claim:a20d6d816ea215ea5aea
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal: CORIN expression was reduced in the CHD-enriched clusters CM2 and CM3 compared with CM1
summary:
In Homo sapiens, CORIN expression is reduced in cardiomyocyte cluster 2 and cardiomyocyte cluster 3 compared with cardiomyocyte cluster 1.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:296a84277abb7560b949
claim_id: claim:296a84277abb7560b949
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal: CORIN expression was reduced in the CHD-enriched clusters CM2 and CM3 compared with CM1
summary:
In Homo sapiens, CORIN expression is reduced in cardiomyocyte cluster 3 compared with cardiomyocyte cluster 1.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:a5f2bad173dab9ca34a9
claim_id: claim:a5f2bad173dab9ca34a9
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
summary: In Homo sapiens, CRIM1 is enriched in cardiomyocyte cluster 2 and cardiomyocyte cluster 3.
span_literal:
CRIM1 is enriched in CM2 and CM3, is likely to modulate TGFβ signalling, and has been suggested as a biomarker for heart failure in adults


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:bd59a5967679535f96f4
claim_id: claim:bd59a5967679535f96f4
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal: RYR2 (cardiomyocyte
summary:
In Homo sapiens, RYR2 is a canonical cardiomyocyte marker expressed in cardiomyocyte cluster 1, cardiomyocyte cluster 2, and cardiomyocyte cluster 3.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:8468f0a805939b127094
claim_id: claim:8468f0a805939b127094
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal:
In addition, CF4 was marked by the expression of KDM6B , which encodes a histone demethylase important for the profibrotic cardiac fibroblast phenotype

summary:
In Homo sapiens, cardiac fibroblast cluster 4 is marked by expression of KDM6B, which encodes a histone demethylase.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:b44ce6b342a8150a24cc
claim_id: claim:b44ce6b342a8150a24cc
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal: THBS1 -expressing cells in the CD14–1 cluster
summary:
In Homo sapiens, CD14-1 monocytes enriched in congenital heart disease peripheral blood mononuclear cells express THBS1.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:d3d4c238ff7fa88e1db2
claim_id: claim:d3d4c238ff7fa88e1db2
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
span_literal:
Monocytes in the CD14–2 cluster were enriched in control PBMCs and expressed pro-inflammatory factors, including CCL3 , CXCl8 and IL1B , which expressed at much lower levels in CHD-enriched CD14–1 monocytes

summary:
In Homo sapiens, CD14-2 monocytes express the pro-inflammatory factors CCL3, CXCL8, and IL1B, which are expressed at much lower levels in CD14-1 monocytes.


claim_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e:claim:c684242d3e7fc006d657
claim_id: claim:c684242d3e7fc006d657
paper_key: hca:0188_10.1038_s41586-022-04989-3_7ea3ee9a4e
summary: In Homo sapiens, macrophage clusters are distinguished by expression of CD68, CD14, and CD163.
span_literal:
Macrophages separated into 3 clusters (MΦ1–MΦ3), distinguished by expression of CD68, CD14 and CD163, and were localized to perivascular fibrotic areas


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:ae3000ab5acde8523ce8
claim_id: claim:ae3000ab5acde8523ce8
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: αβ T cells ( CD3E , LCK , TRAC , and TRAJ16
summary:
In Homo sapiens, alpha-beta T cells are identified by expression of CD3E, LCK, TRAC, and TRAJ16 in blood and cerebrospinal fluid leukocytes.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:c91ef73bffc0f4adf318
claim_id: claim:c91ef73bffc0f4adf318
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: regulatory T cells ( FOXP3 and CTLA4
summary:
In Homo sapiens, regulatory T cells are identified by expression of FOXP3 and CTLA4 in blood and cerebrospinal fluid leukocytes.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:d4ee55314f376977ff9f
claim_id: claim:d4ee55314f376977ff9f
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: γδ T cells ( TRDC
summary:
In Homo sapiens, gamma-delta T cells are identified by expression of TRDC in blood and cerebrospinal fluid leukocytes.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:a542429eb1fd2342a095
claim_id: claim:a542429eb1fd2342a095
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: natural killer (NK) cell clusters ( GNLY and NKG7
summary:
In Homo sapiens, natural killer cell clusters are identified by expression of GNLY and NKG7, with the CD56dim subset (NK1) marked by FCGR3A and PRF1, and the CD56bright subset (NK2) marked by SELL and XCL1.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:171cb28b386099dc5ea8
claim_id: claim:171cb28b386099dc5ea8
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: B lineage clusters ( CD74 , CD79A
summary:
In Homo sapiens, B lineage cells are identified by expression of CD74, CD79A, and IGH gene family members.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:027f3124f952938881d3
claim_id: claim:027f3124f952938881d3
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: plasma blasts (plasma; IGHG , CD38 , and TNFRSF17 /CD269; negative for MS4A1 /CD20 and SDC1
summary:
In Homo sapiens, plasmablasts are marked by IGHG, CD38, and TNFRSF17, and are negative for MS4A1 and SDC1.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:088e208c0826256d5ada
claim_id: claim:088e208c0826256d5ada
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: mDC1 cells expressed markers indicating cross-presenting capacity ( XCR1 and WDFY4
summary:
In Homo sapiens, myeloid dendritic cell type 1 expresses XCR1 and WDFY4, indicating cross-presenting capacity.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:a4112e21781177a72854
claim_id: claim:a4112e21781177a72854
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: naive-like ( SELL and CCR7
summary:
In Homo sapiens, naive-like CD4-positive T cells are marked by SELL and CCR7, while memory-like CD4-positive T cells are marked by CD44.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:bc67f8c09bd176dcd2ee
claim_id: claim:bc67f8c09bd176dcd2ee
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal:
Memory cells further separated into subsets with mostly effector memory-like ( CD69 ; CD4Tc #3,0,4) and central memory-like ( CD27 ; CD4Tc #7,6,9) phenotype.

summary:
In Homo sapiens, effector memory-like CD4-positive T cells are marked by CD69, while central memory-like CD4-positive T cells are marked by CD27.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:9d53091c6f19f5d20b78
claim_id: claim:9d53091c6f19f5d20b78
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal: Treg identity ( FOXP3 and CTLA4
summary:
In Homo sapiens, a regulatory T cell cluster (CD4Tc #10) is identified by expression of FOXP3 and CTLA4.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:bcc3d116e48793290f86
claim_id: claim:bcc3d116e48793290f86
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal:
This cluster expressed multiple genes associated with cytotoxic function ( GZMB , PRF1 , and CCL5 ) despite similar levels of CD4 + T cell marker genes ( CD4 and IL7R ), low doublet probability (predicted doublet t -test p value 0.68), and absence of CD8 or NK cell markers ( CD8B and NKG7 ; Fig. 3e ) in this population.

summary:
In Homo sapiens, cytotoxic CD4-positive T cells (CD4Tc #0) express GZMB, PRF1, and CCL5, along with CD4-positive T cell markers CD4 and IL7R, while lacking CD8B and NKG7.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:cf080e02a6da0a5466b5
claim_id: claim:cf080e02a6da0a5466b5
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal:
mDC1 cells abundant in the CSF-expressed markers of cross-presenting capacity ( XCR1 and WDFY4 (ref. 19 )), while NK2 cells in the CSF expressed the corresponding ligands ( XCL1 and XCL2 ) indicating that cell types equipped for cross-presentation and antiviral defence circulate the CSF.

summary:
In Homo sapiens, myeloid dendritic cell type 1 in the cerebrospinal fluid expresses XCR1 and WDFY4, while CD56bright natural killer cells (NK2) express XCL1 and XCL2.


claim_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea:claim:575833192f46619197e1
claim_id: claim:575833192f46619197e1
paper_key: hca:0190_10.1038_s41467-019-14118-w_eee71dc5ea
span_literal:
mDC1 cells abundant in the CSF-expressed markers of cross-presenting capacity ( XCR1 and WDFY4 (ref. 19 )), while NK2 cells in the CSF expressed the corresponding ligands ( XCL1 and XCL2 ) indicating that cell types equipped for cross-presentation and antiviral defence circulate the CSF.

summary:
In Homo sapiens, CD56bright natural killer cells (NK2) in the cerebrospinal fluid express XCL1 and XCL2.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:47381d0979c350b6af11
claim_id: claim:47381d0979c350b6af11
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
two populations of Tfh cells, with one population expressing high levels of CXCL13 , CD200 and IL21 , likely representing GC Tfh

summary:
In Homo sapiens, germinal center T follicular helper cells express high levels of CXCL13, CD200, and IL21.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:d6abee240fd8e29a80ae
claim_id: claim:d6abee240fd8e29a80ae
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
We also found a small cluster of B cells expressing markers of type I interferon response genes such as IFI44L , XAF1 , and MX1

summary:
In Homo sapiens, interferon-responsive B cells express type I interferon response genes such as IFI44L, XAF1, and MX1.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:e8167cbce18df3b2858d
claim_id: claim:e8167cbce18df3b2858d
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
Our analysis also revealed shared regulatory TF activities between similar cell states, such as those active in naïve, activated and memory B cells (KLF2, BCL11A, ELF2, ETV6, ELK4) or GC B cells (EBF1, REST, POU2F1, PKNOX1)

summary:
In Homo sapiens, naïve, activated, and memory B cells show regulatory activity of KLF2, BCL11A, ELF2, ETV6, and ELK4.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:669a8970f5909c689b87
claim_id: claim:669a8970f5909c689b87
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
Our analysis also revealed shared regulatory TF activities between similar cell states, such as those active in naïve, activated and memory B cells (KLF2, BCL11A, ELF2, ETV6, ELK4) or GC B cells (EBF1, REST, POU2F1, PKNOX1)

summary:
In Homo sapiens, germinal center B cells show regulatory activity of EBF1, REST, POU2F1, and PKNOX1.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:14d93e17b3a86f366d9a
claim_id: claim:14d93e17b3a86f366d9a
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
We also found highly cell type-specific activities, such as for EOMES, IRF1/2 and RUNX1/3 in cytotoxic lymphocytes, and ID3, ASCL2, NFIA and TCF12 in Tfh cells

summary:
In Homo sapiens, cytotoxic lymphocytes show cell type-specific transcription factor activity of EOMES, IRF1, IRF2, RUNX1, and RUNX3.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:0fada74d7a085da531bd
claim_id: claim:0fada74d7a085da531bd
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
We also found highly cell type-specific activities, such as for EOMES, IRF1/2 and RUNX1/3 in cytotoxic lymphocytes, and ID3, ASCL2, NFIA and TCF12 in Tfh cells

summary:
In Homo sapiens, T follicular helper cells show cell type-specific transcription factor activity of ID3, ASCL2, NFIA, and TCF12.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:48994063ee648b7ea5f7
claim_id: claim:48994063ee648b7ea5f7
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal:
TNFRSF13B (encoding TACI) was most highly expressed in memory B cells, particularly tonsillar FCRL4 + memory B cells.

summary:
In Homo sapiens, TNFRSF13B (encoding TACI) is most highly expressed in memory B cells, particularly tonsillar FCRL4-positive memory B cells.


claim_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105:claim:59af34e8c593df579285
claim_id: claim:59af34e8c593df579285
paper_key: hca:0191_10.1126_sciimmunol.abh3768_bc0f7a7105
span_literal: CTLA4 expression peaked in Tfh and Treg populations as expected.
summary:
In Homo sapiens, CTLA4 expression peaks in T follicular helper cell and regulatory T cell populations.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:cd745b1a5b8524c12d09
claim_id: claim:cd745b1a5b8524c12d09
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
We generated subsets of the whole lung parenchyma datasets for COL1A2+ stromal cells (Fig 1C and Appendix Fig S1C–E ), EPCAM+ epithelial cells (Fig 1D and Appendix Fig S1F–H ), CLDN5+ endothelial cells (Fig 1E and Appendix Fig S1I –K), and CD45+ leukocytes (Fig 1F and Appendix Fig S1L–N ).

summary:
In Homo sapiens lung, COL1A2 is a marker of stromal cells, EPCAM is a marker of epithelial cells, CLDN5 is a marker of endothelial cells, and CD45 (PTPRC) is a marker of leukocytes.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:b677c33e607c72d989e1
claim_id: claim:b677c33e607c72d989e1
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
summary: In Homo sapiens, KRT17 is a marker for aberrant basaloid cells in idiopathic pulmonary fibrosis.
span_literal:
The upregulated KRT17 gene (Fig 2F ) in alveolar epithelial cells was recently defined as a marker for the novel aberrant basaloid cells in IPF (Adams et al , 2020 ; Habermann et al , 2020 ).


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:1541e94b01ad0452cb04
claim_id: claim:1541e94b01ad0452cb04
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
summary: In Homo sapiens, aberrant basaloid cells feature high expression of CDKN2A (encoding p16).
span_literal:
These fibrosis‐specific cells feature a cellular senescence signature (Kobayashi et al , 2020 ), including high expression of CDKN2A (encoding for p16; Fig 2F ).


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:f5de4bf69f4048433438
claim_id: claim:f5de4bf69f4048433438
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
In macrophages (Fig 2H ), the normal alveolar macrophage phenotype that is marked by high FABP4 expression is replaced by an ILD‐associated cell state that features high expression of SPP1 (Osteopontin) (Morse et al , 2019 ), which we termed activated AM.

summary:
In Homo sapiens, the normal alveolar macrophage phenotype is marked by high FABP4 expression, while the activated alveolar macrophage state features high expression of SPP1 (Osteopontin).


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:8b4b647d7eb6c197863d
claim_id: claim:8b4b647d7eb6c197863d
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
In macrophages (Fig 2H ), the normal alveolar macrophage phenotype that is marked by high FABP4 expression is replaced by an ILD‐associated cell state that features high expression of SPP1 (Osteopontin) (Morse et al , 2019 ), which we termed activated AM.

summary:
In Homo sapiens, the activated alveolar macrophage state features high expression of SPP1 (Osteopontin).


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:44bfbaf2ad0544ee8137
claim_id: claim:44bfbaf2ad0544ee8137
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
In the COL1A2+ cells, the CFHR1 expression was further limited to an activated PDGFRB+ pericyte state that was mainly found in ILD patients (Fig 7B ).

summary:
In Homo sapiens, CFHR1 expression is limited to an activated PDGFRB-positive pericyte state found mainly in interstitial lung disease patients.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:2b832d95b927a7158a1b
claim_id: claim:2b832d95b927a7158a1b
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
The correlation analysis revealed a large cluster of genes that was strongly associated with SSTR2 in pericytes, including CFHR1 , CFH , CXCL2/3 , CD36, and YAP1 (Fig 7E ).

summary:
In Homo sapiens, SSTR2 expression in pericytes is strongly associated with CFHR1, CFH, CXCL2/3, CD36, and YAP1.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:7802919f39adec837db3
claim_id: claim:7802919f39adec837db3
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
SSTR2+/PDGFRB+/DES− pericytes were found around remodeled vessels that had a thickened layer of DES+/PDGFRB+ smooth muscle cells in ILD.

summary:
In Homo sapiens, pericytes are positive for SSTR2 and PDGFRB and negative for DES (desmin), while smooth muscle cells are positive for DES and PDGFRB.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:b8c0679f37e10e4a0424
claim_id: claim:b8c0679f37e10e4a0424
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
Our model confirmed the gradual upregulation of SSTR2 and CFHR1 with their correlating genes (Fig 7E ) concurrent with downregulation of several pericyte marker genes such as PDGFRB (Fig 7M ).

summary:
In Homo sapiens, PDGFRB is a pericyte marker gene, and SSTR2 and CFHR1 are upregulated during pericyte state change in interstitial lung disease.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:f594489ddaae56ac96b8
claim_id: claim:f594489ddaae56ac96b8
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
Our single‐cell atlas revealed specific expression of CRTAC1 in lung lymphatic endothelium, airway club cells, and most prominently in alveolar type‐2 epithelial (AT2) cells (Fig 8B , Appendix Fig S7B ).

summary:
In Homo sapiens lung, CRTAC1 is specifically expressed in lymphatic endothelium, airway club cells, and most prominently in alveolar type-2 epithelial cells.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:96e81e5933c9ef3f93e9
claim_id: claim:96e81e5933c9ef3f93e9
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
summary: In Homo sapiens, alveolar type-2 epithelial cells are positive for SFTPC.
span_literal:
To identify gene programs within AT2 cells that are associated with CRTAC1 expression, we performed gene–gene correlation analysis within SFTPC+ AT2 cells.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:eecf76b40a8385286bac
claim_id: claim:eecf76b40a8385286bac
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
A novel SSTR2+ pericyte state correlated with disease severity and was reflected in lavage fluid by increased levels of the complement regulatory factor CFHR1.

summary:
In Homo sapiens, a novel SSTR2-positive pericyte state is correlated with disease severity and reflected by increased CFHR1 levels in lavage fluid.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:c0909f8acf52c04a09f5
claim_id: claim:c0909f8acf52c04a09f5
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
We show that the main source of CRTAC1 in the human body is the alveolar AT2 cell and that CRTAC1 is downregulated early in a de‐differentiation trajectory of AT2 cells toward the aberrant basaloid state.

summary:
In Homo sapiens, the main source of CRTAC1 is the alveolar type-2 epithelial cell, and CRTAC1 is downregulated early in de-differentiation toward the aberrant basaloid cell state.


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:692cfdd6501c0f5f73ef
claim_id: claim:692cfdd6501c0f5f73ef
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
summary: In Homo sapiens, activated alveolar macrophages express higher levels of CCL7.
span_literal:
These cells also express higher levels of the CCR2 ligand CCL7, which is a chemoattractant potentially involved in the recruitment of fibrocytes and profibrotic macrophages (Moore et al , 2005 ; Osterholzer et al , 2012 , 2013 ).


claim_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f:claim:11e0d76a337357d52725
claim_id: claim:11e0d76a337357d52725
paper_key: hca:0193_10.15252_emmm.202012871_3b35c5fb8f
span_literal:
In this work, we discover a highly disease‐specific SSTR2+/CFHR1+ pericyte state that features a pro‐inflammatory phenotype with expression of various chemokines.

summary:
In Homo sapiens, a disease-specific pericyte state is positive for SSTR2 and CFHR1 and features a pro-inflammatory phenotype.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:49130ef8877a830034b3
claim_id: claim:49130ef8877a830034b3
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
the distinct HS3ST5 − PCP4 + ( Ex5a ), HS3ST5 + PCP4 − ( Ex5b ) and HTR2C + PCP4 + TLE4 + ( Ex6a ) subpopulations in layer 5, the latter bordering on a HTR2C − TLE4 + ( Ex6b ) layer 6 population ( Fig. 2C )

summary:
In Homo sapiens, excitatory neuron subtype 5a is marked by negative expression of HS3ST5 and positive expression of PCP4.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:659143341fae53a9a2e9
claim_id: claim:659143341fae53a9a2e9
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
the distinct HS3ST5 − PCP4 + ( Ex5a ), HS3ST5 + PCP4 − ( Ex5b ) and HTR2C + PCP4 + TLE4 + ( Ex6a ) subpopulations in layer 5, the latter bordering on a HTR2C − TLE4 + ( Ex6b ) layer 6 population ( Fig. 2C )

summary:
In Homo sapiens, excitatory neuron subtype 5b is marked by positive expression of HS3ST5 and negative expression of PCP4.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:10136349bd306e7fa5e0
claim_id: claim:10136349bd306e7fa5e0
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
the distinct HS3ST5 − PCP4 + ( Ex5a ), HS3ST5 + PCP4 − ( Ex5b ) and HTR2C + PCP4 + TLE4 + ( Ex6a ) subpopulations in layer 5, the latter bordering on a HTR2C − TLE4 + ( Ex6b ) layer 6 population ( Fig. 2C )

summary:
In Homo sapiens, excitatory neuron subtype 6a is marked by positive expression of HTR2C, PCP4, and TLE4.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:2b9878691ecf1c30a3d8
claim_id: claim:2b9878691ecf1c30a3d8
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
summary:
In Homo sapiens, excitatory neuron subtype 6b is marked by negative expression of HTR2C and positive expression of TLE4.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:3a1051d30ac2c11b9ea8
claim_id: claim:3a1051d30ac2c11b9ea8
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
summary: In Homo sapiens, excitatory neuron subtype 3b is marked by positive expression of RORB and PCP4.
span_literal:
the RORB + PCP4 + Ex3b , RORB + NEFM hi Ex3c , and RORB + PHACTR2 + EYA4 + Ex3d sub-populations ( Fig. 2C )


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:4315f93bde19a556c497
claim_id: claim:4315f93bde19a556c497
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
the RORB + PCP4 + Ex3b , RORB + NEFM hi Ex3c , and RORB + PHACTR2 + EYA4 + Ex3d sub-populations ( Fig. 2C )

summary:
In Homo sapiens, excitatory neuron subtype 3c is marked by positive expression of RORB and high expression of NEFM.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:69bd39a9316079e25a96
claim_id: claim:69bd39a9316079e25a96
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
the RORB + PCP4 + Ex3b , RORB + NEFM hi Ex3c , and RORB + PHACTR2 + EYA4 + Ex3d sub-populations ( Fig. 2C )

summary:
In Homo sapiens, excitatory neuron subtype 3d is marked by positive expression of RORB, PHACTR2, and EYA4.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:1019647a7624427a5634
claim_id: claim:1019647a7624427a5634
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
that showed distinct profiles of canonical interneuron markers (e.g. VIP, RELN, PVALB, SST ) as well as sub-type restricted expression (e.g. THSD7B, CA8, GLCE )

summary:
In Homo sapiens, inhibitory neuron subtypes showed distinct profiles of canonical interneuron markers VIP, RELN, PVALB, SST as well as sub-type restricted expression of THSD7B, CA8, GLCE.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:4a528e1e2a5b49ba7139
claim_id: claim:4a528e1e2a5b49ba7139
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal: layer 1 RELN + CCK + CNR1 + In1a
summary:
In Homo sapiens, inhibitory neuron subtype 1a is marked by positive expression of RELN, CCK, and CNR1.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:c5303f9ec9edcf810713
claim_id: claim:c5303f9ec9edcf810713
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal: upper layer VIP + CALB2 + TAC3 + In1d
summary:
In Homo sapiens, inhibitory neuron subtype 1d is marked by positive expression of VIP, CALB2, and TAC3.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:f9a553038b424415dd0d
claim_id: claim:f9a553038b424415dd0d
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal: PVALB + CA8 + In6a concentrated around layer 4, as well as the more peripheral PVALB + TAC1 + In6b
summary:
In Homo sapiens, inhibitory neuron subtype 6a is marked by positive expression of PVALB and CA8, while inhibitory neuron subtype 6b is marked by positive expression of PVALB and TAC1.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:dc1db3868a4ea72fdf0a
claim_id: claim:dc1db3868a4ea72fdf0a
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
two distinct SST positive subtypes, including the upper layer SST + CALB1 + ( In7 ) and lower layer SST + CALB1 − ( In8 ) subpopulations ( Fig. S8 )

summary:
In Homo sapiens, inhibitory neuron subtype 7 is marked by positive expression of SST and CALB1, while inhibitory neuron subtype 8 is marked by positive expression of SST and negative expression of CALB1.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:632fd52bcbfc8503c28e
claim_id: claim:632fd52bcbfc8503c28e
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
two distinct SST positive subtypes, including the upper layer SST + CALB1 + ( In7 ) and lower layer SST + CALB1 − ( In8 ) subpopulations ( Fig. S8 )

summary:
In Homo sapiens, inhibitory neuron subtype 8 is marked by positive expression of SST and negative expression of CALB1.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:be1d0cc7fbedf13b7b7b
claim_id: claim:be1d0cc7fbedf13b7b7b
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
we find two distinct Purk neuron populations expressing inhibitory markers GAD1/GAD2 ( Fig. 2F , Fig. S9 ) distinguishable by expression of SORCS3 ( Fig. 2H )

summary:
In Homo sapiens, Purkinje neuron populations express inhibitory markers GAD1 and GAD2 and are distinguishable by expression of SORCS3.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:177621e45f322eaab144
claim_id: claim:177621e45f322eaab144
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
Ast_Cer, marked by expression of ALDH1A1 ( Fig. 2G ), showed enriched expression of the AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor-encoding gene GRIA1 ( GluA1 in mouse) and SLC1A3 (or GLAST ) characteristic of Bergmann Glia

summary:
In Homo sapiens, cerebellar astrocytes (Bergmann Glia) are marked by expression of ALDH1A1, GRIA1, and SLC1A3.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:f7cb66091326065a4d36
claim_id: claim:f7cb66091326065a4d36
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
we resolved two distinct populations of OPCs , a LUZP2 + CASK + population showing a general transcriptomic signature resembling the cortical OPCs , and an ORAOV1 + LRP6 + RCN2 + population ( OPC_Cer ) specifically found in the cerebellum ( Fig. 2F–G , Fig. S9 )

summary:
In Homo sapiens, oligodendrocyte precursor cells are marked by positive expression of LUZP2 and CASK, while cerebellar oligodendrocyte precursor cells are marked by positive expression of ORAOV1, LRP6, and RCN2.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:ac0213f31534ed841d46
claim_id: claim:ac0213f31534ed841d46
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
we resolved two distinct populations of OPCs , a LUZP2 + CASK + population showing a general transcriptomic signature resembling the cortical OPCs , and an ORAOV1 + LRP6 + RCN2 + population ( OPC_Cer ) specifically found in the cerebellum ( Fig. 2F–G , Fig. S9 )

summary:
In Homo sapiens, cerebellar oligodendrocyte precursor cells are marked by positive expression of ORAOV1, LRP6, and RCN2.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:3c4a5708fc7b7f8c79b3
claim_id: claim:3c4a5708fc7b7f8c79b3
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
our human OPC population expressed markers associated with mouse OPCs ( PDGFRA , CSPG4, SOX6, VCAN ), yet they also expressed markers for more committed mouse progenitors ( ITPR2, NEU4 )

summary:
In Homo sapiens, oligodendrocyte precursor cells express PDGFRA, CSPG4, SOX6, VCAN, ITPR2, and NEU4.


claim_key: hca:0195_10.1038_nbt.4038_23df984b1c:claim:784fd4f9714cf3460493
claim_id: claim:784fd4f9714cf3460493
paper_key: hca:0195_10.1038_nbt.4038_23df984b1c
span_literal:
the mature Oli ( mOli ) population, expressed markers associated with myelin formation ( PLP1, MBP, MOG )

summary:
In Homo sapiens, mature oligodendrocytes express markers associated with myelin formation including PLP1, MBP, and MOG.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:f11a7f1485b71e8df3fc
claim_id: claim:f11a7f1485b71e8df3fc
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
span_literal: Our census revealed that enterocytes expressing BEST4 are distinct from other epithelial cells
summary:
In Homo sapiens, BEST4+ enterocytes are distinguished from other epithelial cells by expression of BEST4.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:3c08328d91f77099de0c
claim_id: claim:3c08328d91f77099de0c
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, BEST4+ enterocytes are enriched for otopetrin 2 (OTOP2) and otopetrin 3 (OTOP3).
span_literal:
This includes the otopetrins 2 and 3 ( OTOP2 / 3 ), proton channels that detect pH and underlie sour taste perception


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:236157deeb27451d0b14
claim_id: claim:236157deeb27451d0b14
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
span_literal:
carbonic anhydrase VII ( CA7 ), which catalyzes bicarbonate formation; and bestrophin-4 ( BEST4 ), which may export bicarbonate

summary:
In Homo sapiens, BEST4+ enterocytes are enriched for carbonic anhydrase VII (CA7) and bestrophin-4 (BEST4).


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:ab8a4a63eab0e512c53b
claim_id: claim:ab8a4a63eab0e512c53b
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
span_literal:
Some are enriched for WNT2B , WNT4 , and DKK3 , suggesting they reside near the crypt, whereas others are enriched for BMP4 , BMP5 , and WNT5A / B , and may reside near the villus

summary:
In Homo sapiens, some fibroblast subsets in the colon are enriched for WNT2B, WNT4, and DKK3, while others are enriched for BMP4, BMP5, and WNT5A/WNT5B.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:c6a1bb85c635d0ee4911
claim_id: claim:c6a1bb85c635d0ee4911
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
span_literal:
IAFs are enriched for expression of many genes associated with colitis, fibrosis, and cancer, including IL11 , IL24 , and IL13RA2

summary:
In Homo sapiens, inflammation-associated fibroblasts are enriched for expression of IL11, IL24, and IL13RA2.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:24ef63271f4e093e54d6
claim_id: claim:24ef63271f4e093e54d6
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, inflammation-associated fibroblasts express FAP, TWIST1, and WNT2.
span_literal:
IAFs express markers of cancer-associated fibroblasts (CAFs) ( Figure 1G ), including FAP , TWIST1 , and WNT2


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:f7bc77b79eb9f8b0d75a
claim_id: claim:f7bc77b79eb9f8b0d75a
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, microfold-like cells highly express CCL20 and CCL23.
span_literal:
They highly express several chemokines ( e.g ., CCL20 , CCL23 ; Figure 1G ), suggesting involvement in recruiting immune cells to sites of inflammation.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:f50ef6e6cdb83370591a
claim_id: claim:f50ef6e6cdb83370591a
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
span_literal: OSM was most enriched in inflammatory monocytes and DC2s, while OSMR was most enriched in IAFs
summary:
In Homo sapiens, oncostatin M (OSM) is most enriched in inflammatory monocytes, while OSMR is most enriched in inflammation-associated fibroblasts.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:0bec8793f54360256d86
claim_id: claim:0bec8793f54360256d86
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, IL13RA2, TNFRSF11B, and IL11 are markers of inflammation-associated fibroblasts.
span_literal:
The three genes most associated with drug resistance — IL13RA2 , TNFRSF11B , and IL11 — are IAF markers that are rarely expressed in other cells


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:342c71bccbc9e6a8e3e1
claim_id: claim:342c71bccbc9e6a8e3e1
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, intelectin 1 (ITLN1) is enriched in immature goblet cells.
span_literal:
intelectin 1 ( ITLN1 ), a lipid raft protein that localizes to the epithelial brush border ( Wrackmeyer et al., 2006 ), is enriched in immature goblet cells


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:8446fa00aa649284a62b
claim_id: claim:8446fa00aa649284a62b
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
span_literal:
Notably, M-like cells express many risk genes at higher levels than other cells ( e.g ., NR5A2 , CCL20 , JAK2 ; Figure 7A , Table S6 )

summary:
In Homo sapiens, microfold-like cells express NR5A2, CCL20, and JAK2 at higher levels than other cells.


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:5823a91e1be0385847bf
claim_id: claim:5823a91e1be0385847bf
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, a subset of regulatory T cells co-express TNFRSF4 (OX40) and TNFRSF18 (GITR).
span_literal:
T regs co-expressing TNFRSF4 / OX40 and TNFRSF18 / GITR , which may reflect activated vs . resting T regs


claim_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587:claim:2a8b2515edd319b266f2
claim_id: claim:2a8b2515edd319b266f2
paper_key: hca:0196_10.1016_j.cell.2019.06.029_0759da9587
summary: In Homo sapiens, regulatory T cells are marked by FOXP3, CTLA4, and IL10.
span_literal:
they are still more enriched for T reg markers ( e.g ., FOXP3 , CTLA4 , IL10 ) than TNF – T reg cells


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:fe2d73179672eb417235
claim_id: claim:fe2d73179672eb417235
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
It was reported that ICAM-1 is highly expressed in endothelial cells of HBV-MN, IgA nephropathy and lupus nephritis ( 59 , 60 ).

summary:
In Homo sapiens, ICAM1 is highly expressed in endothelial cells in HBV-associated membranous nephropathy, IgA nephropathy, and lupus nephritis.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:794bc344beffcc77e95c
claim_id: claim:794bc344beffcc77e95c
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
HSPA5 , an endoplasmic reticulum stress protein gene in podocytes, was upregulated by HBV infection, indicating the increase of endoplasmic reticulum stress in MN ( 41 ).

summary:
In Homo sapiens, HSPA5, an endoplasmic reticulum stress protein gene, is upregulated in podocytes in HBV-associated membranous nephropathy.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:e5c98f6863c683839585
claim_id: claim:e5c98f6863c683839585
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Endothelial cells and proximal tubule cells highly expressed the A20 (TNFAIP3), an NF-kappaB-dependent stress response gene in ECs and SMCs with potent anti-inflammatory effects in both cell types through blockade of NF-kappaB pathway ( 51 ).

summary:
In Homo sapiens, endothelial cells highly express TNFAIP3 (A20), an NF-kappaB-dependent stress response gene with anti-inflammatory effects.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:ebab9346956630acfa2d
claim_id: claim:ebab9346956630acfa2d
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Endothelial cells and proximal tubule cells highly expressed the A20 (TNFAIP3), an NF-kappaB-dependent stress response gene in ECs and SMCs with potent anti-inflammatory effects in both cell types through blockade of NF-kappaB pathway ( 51 ).

summary:
In Homo sapiens, proximal tubule cells highly express TNFAIP3 (A20), an NF-kappaB-dependent stress response gene.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:a60697b2f6281c3a40b3
claim_id: claim:a60697b2f6281c3a40b3
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
In addition, SELE was reported as an inflammatory marker, and played a role in kidney dysfunction with type 1 diabetes ( 97 ), which was overexpressed in the endothelial cells in HBV-associated MN patients.

summary:
In Homo sapiens, SELE is overexpressed in endothelial cells in HBV-associated membranous nephropathy patients.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:172b9eb61c82fbacf310
claim_id: claim:172b9eb61c82fbacf310
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Interestingly, the elevated expression of Leucine-rich alpha-2-glycoprotein 1 ( LRG1 ) was displayed in HBV-MN endothelial cells ( Supplementary Table 4 ).

summary:
In Homo sapiens, leucine-rich alpha-2-glycoprotein 1 (LRG1) shows elevated expression in endothelial cells in HBV-associated membranous nephropathy.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:65ff4605ddd86fc6446e
claim_id: claim:65ff4605ddd86fc6446e
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Also, NFKBIZ , a gene highly expressed in endothelial cells in HBV-MN, which is a member of the IkappaB family of NF-kB regulators.

summary:
In Homo sapiens, NFKBIZ is highly expressed in endothelial cells in HBV-associated membranous nephropathy.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:b900fd2652a4520ae368
claim_id: claim:b900fd2652a4520ae368
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Moreover, we found that DEGs included overexpressed cellular proliferation-related genes such as HSPA1A and IRF1 in kidney endothelial cells of HBV-MN ( Supplementary Table 4 ).

summary:
In Homo sapiens, HSPA1A and IRF1 are overexpressed in kidney endothelial cells in HBV-associated membranous nephropathy.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:cbdf98f895ef28ad3bc7
claim_id: claim:cbdf98f895ef28ad3bc7
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
It was reported for the first time in our study that several genes including HSPA5, CTGF , and EDIL3 were overexpressed in podocytes of HBV-MN ( Figure 2A ).

summary:
In Homo sapiens, HSPA5, CTGF, and EDIL3 are overexpressed in podocytes of HBV-associated membranous nephropathy.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:cad67cde14b3fdf3f65e
claim_id: claim:cad67cde14b3fdf3f65e
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
FOS was significantly overexpressed in proximal tubule cells of HBV-MN, which plays a crucial role in mesangial proliferation and glomerular sclerosis ( 53 ).

summary:
In Homo sapiens, FOS is significantly overexpressed in proximal tubule cells of HBV-associated membranous nephropathy.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:9881db61737a0dc6abe9
claim_id: claim:9881db61737a0dc6abe9
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
scRNA-seq was applied in this study and the analysis proved that GLG1 expressed in mesangial cells, principal cells and proximal tubular cells, interacting with SELE in endothelial dysfunction ( 82 , 83 , 99 ).

summary:
In Homo sapiens, GLG1 is expressed in mesangial cells, interacting with SELE in endothelial dysfunction.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:c3b447a657c543ec512c
claim_id: claim:c3b447a657c543ec512c
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
scRNA-seq was applied in this study and the analysis proved that GLG1 expressed in mesangial cells, principal cells and proximal tubular cells, interacting with SELE in endothelial dysfunction ( 82 , 83 , 99 ).

summary:
In Homo sapiens, GLG1 is expressed in principal cells, interacting with SELE in endothelial dysfunction.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:d0e5f822e99328687344
claim_id: claim:d0e5f822e99328687344
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
scRNA-seq was applied in this study and the analysis proved that GLG1 expressed in mesangial cells, principal cells and proximal tubular cells, interacting with SELE in endothelial dysfunction ( 82 , 83 , 99 ).

summary:
In Homo sapiens, GLG1 is expressed in proximal tubular cells, interacting with SELE in endothelial dysfunction.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:af917b0fc6bad2d12b77
claim_id: claim:af917b0fc6bad2d12b77
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Through intercellular receptor-ligand analysis, we found that CCL3L1 was highly expressed in macrophages and interacted with DPP4 in MESs.

summary:
In Homo sapiens, CCL3L1 is highly expressed in macrophages and interacts with DPP4 in mesangial cells.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:c65446aec4ed8a50667b
claim_id: claim:c65446aec4ed8a50667b
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Macrophages highly express TGF-β and become interaction pairs with TGFBR3 in MESs ( Figure 5G ), possibly involved in cell recruitment and metastasis ( 58 ).

summary:
In Homo sapiens, macrophages highly express TGF-beta, which interacts with TGFBR3 in mesangial cells.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:e8e380a6e65e0c2e5c3d
claim_id: claim:e8e380a6e65e0c2e5c3d
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Mesangial cells and proximal cells expressing CXCL1 and CCL2, interact with ACKR1 in endothelial cells ( Figures 5D,E ), possibly promoting neutrophil/macrophage infiltration.

summary:
In Homo sapiens, mesangial cells express CXCL1 and CCL2, which interact with ACKR1 in endothelial cells.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:ca18dd8feec696e45445
claim_id: claim:ca18dd8feec696e45445
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Mesangial cells and proximal cells expressing CXCL1 and CCL2, interact with ACKR1 in endothelial cells ( Figures 5D,E ), possibly promoting neutrophil/macrophage infiltration.

summary:
In Homo sapiens, proximal cells express CXCL1 and CCL2, which interact with ACKR1 in endothelial cells.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:43d53fa085c16bbe5873
claim_id: claim:43d53fa085c16bbe5873
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
Mesangial cells and proximal cells expressing CXCL1 and CCL2, interact with ACKR1 in endothelial cells ( Figures 5D,E ), possibly promoting neutrophil/macrophage infiltration.

summary:
In Homo sapiens, endothelial cells express ACKR1, which interacts with CXCL1 and CCL2 from mesangial cells and proximal cells.


claim_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76:claim:857e467c6e1cc8f29741
claim_id: claim:857e467c6e1cc8f29741
paper_key: hca:0197_10.3389_fmed.2022.869284_8494fa8c76
span_literal:
MESs, PCs, and PTs expressed GLG1 , a self-glycosylating protein that primes glycogen synthesis ( 56 ), may interact with SELE from ECs, respectively ( Figures 5D–F ).

summary:
In Homo sapiens, mesangial cells, principal cells, and proximal tubule cells express GLG1, which may interact with SELE from endothelial cells.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:56face918f75cc2ae785
claim_id: claim:56face918f75cc2ae785
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
we identified four major subtypes of T cells based on marker expression: naive-like T cells (Cluster 3, 5, 7, 8: SELL + , IL7R high , immune checkpoint receptor (ICR) negative/low )

summary:
In Homo sapiens head and neck squamous cell carcinoma, naive-like CD8+ T cells are marked by positive expression of SELL and high IL7R, with negative/low immune checkpoint receptor expression.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:39eb28dbbc5760ebe57b
claim_id: claim:39eb28dbbc5760ebe57b
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: cytotoxic T cells [Cluster 1, 4, 5, 11, 12: GNLY high , KLRG1 + , ICR low/intermediate ]
summary:
In Homo sapiens head and neck squamous cell carcinoma, cytotoxic T cells are marked by high GNLY and positive KLRG1 expression.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:ce0a77f2c77a172bfc4e
claim_id: claim:ce0a77f2c77a172bfc4e
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: pre-dysfunctional (Cluster 1, 9, 10: GZMK high , CXCL13 low , LYAR + )
summary:
In Homo sapiens head and neck squamous cell carcinoma, pre-dysfunctional CD8+ T cells are marked by high GZMK, low CXCL13, and positive LYAR expression.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:117f470b91672a479ac5
claim_id: claim:117f470b91672a479ac5
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: terminally dysfunctional cells (Cluster 0, 2: GZMK low , CXCL13 high , ENTPD1 + )
summary:
In Homo sapiens head and neck squamous cell carcinoma, terminally dysfunctional CD8+ T cells are marked by low GZMK, high CXCL13, and positive ENTPD1 expression.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:66f7b7b677dc3a22c54c
claim_id: claim:66f7b7b677dc3a22c54c
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
We also identified two clusters of cycling CD8 + T cells (clusters 6 and 13), expressing Ki67 (gene MKI67 ) and genes associated with the formation of the mitotic spindle apparatus ( TUBA1B , STMN1 )

summary:
In Homo sapiens head and neck squamous cell carcinoma, cycling CD8+ T cells express MKI67, TUBA1B, and STMN1.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:cf8adfa992e78fa5b2cd
claim_id: claim:cf8adfa992e78fa5b2cd
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
Hallmark genes of activated, pro-tumor type-2 pericytes, such as ACTA2 (encodes α-smooth muscle actin) and RGS5 (encodes regulator of G-protein signaling-5) were observed

summary:
In Homo sapiens head and neck squamous cell carcinoma, activated pro-tumor type-2 pericytes express ACTA2 (alpha-smooth muscle actin) and RGS5 (regulator of G-protein signaling 5).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:a14981b70a16267765cf
claim_id: claim:a14981b70a16267765cf
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
Clusters 0, 1, 2, 3, 4, 5, and 6 show expression of classical cancer-associated fibroblast (CAF) markers ( FAP , PDGFRA , LOX, and metalloproteinases, Fig. 5B and Supplementary Fig. 6A ).

summary:
In Homo sapiens head and neck squamous cell carcinoma, cancer-associated fibroblasts express classical markers FAP, PDGFRA, and LOX.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:1a9d8bab978851170df2
claim_id: claim:1a9d8bab978851170df2
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
One sub-state previously not described in HNSCC TME scRNAseq studies were fibroblasts expressing elastic fiber differentiation genes (cluster 7; Supplementary Fig. 6B and Supplementary Data 1 ), with increased expression of tropoelastin ( ELN ), fibrillin-1 ( FBLN1 ), and Microfibril Associated Protein 4 ( MFAP4 )

summary:
In Homo sapiens head and neck squamous cell carcinoma, fibroblasts with elastic fiber differentiation express tropoelastin (ELN), fibrillin-1 (FBLN1), and microfibril associated protein 4 (MFAP4).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:5068177e1458b3e0447b
claim_id: claim:5068177e1458b3e0447b
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: The main contributors of PD-L1 (Gene: CD274 ) in the TME were DC and macrophages.
summary:
In Homo sapiens head and neck squamous cell carcinoma tumor microenvironment, dendritic cells and macrophages are the main contributors of CD274 (PD-L1).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:6294cdf86a4110604168
claim_id: claim:6294cdf86a4110604168
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: The main contributors of PD-L1 (Gene: CD274 ) in the TME were DC and macrophages.
summary:
In Homo sapiens head and neck squamous cell carcinoma tumor microenvironment, macrophages are the main contributors of CD274 (PD-L1).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:65d274887c6645f4447e
claim_id: claim:65d274887c6645f4447e
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: In contrast, highest levels of PD-L2 (Gene: PDCD1LG2 ) were detected in DC and fibroblasts.
summary:
In Homo sapiens head and neck squamous cell carcinoma, dendritic cells express the highest levels of PDCD1LG2 (PD-L2).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:368566f32b0aaa00f2ff
claim_id: claim:368566f32b0aaa00f2ff
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: In contrast, highest levels of PD-L2 (Gene: PDCD1LG2 ) were detected in DC and fibroblasts.
summary:
In Homo sapiens head and neck squamous cell carcinoma, fibroblasts express the highest levels of PDCD1LG2 (PD-L2).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:e73ab97c0dea811f9c13
claim_id: claim:e73ab97c0dea811f9c13
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
Low expression levels of FGL1 (encodes fibrinogen-like protein 1), a major inhibitory LAG3 ligand 35 , were detected in fibroblasts.

summary:
In Homo sapiens head and neck squamous cell carcinoma, fibroblasts express low levels of FGL1 (fibrinogen-like protein 1).


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:cb2f8e05d33871d48085
claim_id: claim:cb2f8e05d33871d48085
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
Low levels of CD155 (Gene: PVR ), a high-affinity TIGIT ligand 36 , were primarily observed in endothelial cells.

summary:
In Homo sapiens head and neck squamous cell carcinoma, endothelial cells express low levels of PVR (CD155), a high-affinity TIGIT ligand.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:6fdb570c72e6f8afab22
claim_id: claim:6fdb570c72e6f8afab22
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal:
It is especially interesting that terminally exhausted T cells seem to express the B-cell attracting chemokine CXCL13 , suggesting that these cells may play a role in the development of mature tertiary lymphoid structures

summary:
In Homo sapiens head and neck squamous cell carcinoma, terminally exhausted T cells express the B-cell attracting chemokine CXCL13.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:20669b7a3f593fa9a8dd
claim_id: claim:20669b7a3f593fa9a8dd
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: Cluster 2 mainly expressed MMP1 , while cluster 1 expressed MMP11 (Supplementary Fig. 6A )
summary:
In Homo sapiens head and neck squamous cell carcinoma, cancer-associated fibroblast cluster 2 mainly expresses MMP1, while cancer-associated fibroblast cluster 1 expresses MMP11.


claim_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3:claim:ee6fbfc92c1ba26fc63e
claim_id: claim:ee6fbfc92c1ba26fc63e
paper_key: hca:0198_10.1038_s41467-021-27619-4_12529026b3
span_literal: Cluster 2 mainly expressed MMP1 , while cluster 1 expressed MMP11 (Supplementary Fig. 6A )
summary:
In Homo sapiens head and neck squamous cell carcinoma, cancer-associated fibroblast cluster 1 expresses MMP11.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:2febb7fbaf4b906f6820
claim_id: claim:2febb7fbaf4b906f6820
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal: The formation of glomeruli was evident from positive staining for NPHS1 and MAFB
summary:
In Homo sapiens kidney micro-organoids, podocytes forming glomeruli are marked by positive expression of NPHS1 and MAFB.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:45be53d2aeb160bcd536
claim_id: claim:45be53d2aeb160bcd536
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
Proximal nephron segments were EpCAM + and stained positive for Lotus tetragonolobus lectin (LTL), CUBN, LRP2 and HNF4A

summary:
In Homo sapiens kidney micro-organoids, proximal tubule cells are marked by positive expression of EpCAM, CUBN, LRP2, and HNF4A.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:7bc32df2ad67e29263b6
claim_id: claim:7bc32df2ad67e29263b6
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
Distal nephron segments were stained with ECAD (CDH1) and EpCAM, whereas a presumptive collecting duct/connecting segment was ECAD + /GATA3 +

summary:
In Homo sapiens kidney micro-organoids, distal tubule cells are marked by positive expression of CDH1 and EpCAM, whereas collecting duct cells are marked by positive expression of CDH1 and GATA3.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:75718e1a96b6051237d0
claim_id: claim:75718e1a96b6051237d0
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
Distal nephron segments were stained with ECAD (CDH1) and EpCAM, whereas a presumptive collecting duct/connecting segment was ECAD + /GATA3 +

summary:
In Homo sapiens kidney micro-organoids, collecting duct cell is marked by positive expression of CDH1 and GATA3.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:badf73544992cf7bce35
claim_id: claim:badf73544992cf7bce35
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal: The presence of endothelial cells (PECAM1 + /SOX17 + )
summary:
In Homo sapiens kidney micro-organoids, endothelial cells are marked by positive expression of PECAM1 and SOX17.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:12fef03c114401edeffd
claim_id: claim:12fef03c114401edeffd
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
epithelial cell Cluster 5 also showed expression of distal tubule/collecting duct markers such as GFRA1

summary:
In Homo sapiens kidney micro-organoids, distal tubule/collecting duct epithelial cells express the marker GFRA1.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:8a43090951748f699e9f
claim_id: claim:8a43090951748f699e9f
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
Cluster 2 showed expression of the nephron progenitor markers SIX1 , SIX2 and CITED1 , as well as the stromal marker PAX3 that has previously been associated with myogenic Wilms' tumours

summary:
In Homo sapiens kidney micro-organoids, nephron progenitor cells express the markers SIX1, SIX2, and CITED1.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:063874385b804dabf6cf
claim_id: claim:063874385b804dabf6cf
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
Cells in Cluster 2 also expressed markers of myogenic fate such as MYF5 and MYF6 , but not PAX7 , MYOD1 and TBX6

summary:
In Homo sapiens kidney micro-organoids, cells in Cluster 2 express MYF5 and MYF6 but do not express PAX7, MYOD1, or TBX6.


claim_key: hca:0200_10.1242_dev.172361_e8969b05b0:claim:70df3debea894689ff18
claim_id: claim:70df3debea894689ff18
paper_key: hca:0200_10.1242_dev.172361_e8969b05b0
span_literal:
Cluster 0 (430 cells), the largest cluster, showed a more committed nephron progenitor signature, with expression of early renal vesicle markers PAX2 , PAX8 , LHX1 and JAG1 as well as the human NP markers LYPD1 and DAPL1

summary:
In Homo sapiens kidney micro-organoids, committed nephron progenitor cells express the early renal vesicle markers PAX2, PAX8, LHX1, and JAG1, as well as the nephron progenitor markers LYPD1 and DAPL1.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:3ffbabf89e87056251d1
claim_id: claim:3ffbabf89e87056251d1
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens, SLC12A3 is a canonical marker of the distal convoluted tubule.
span_literal:
There was no cluster enriched for SLC12A3 (Na-Cl symporter; Supplementary Fig. 2 ), a canonical marker of the distal convoluted tubule (DCT).


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:85abad55c924eb19563b
claim_id: claim:85abad55c924eb19563b
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
We identified data-derived markers (Supplementary Table 2 ), including osteopontin ( SPP1 ) 22 in the proximal tubular cell cluster, and WFDC2 23 and MAL 24 in the distal nephron cluster (Fig. 1d and Supplementary Fig. 3A ), in line with scRNA-seq studies of human adult and fetal kidney 25 .

summary:
In Homo sapiens kidney organoids, SPP1 (osteopontin) is a marker of the proximal tubular cell cluster, while WFDC2 and MAL are markers of the distal nephron cluster.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:f539aee393c3f714fdea
claim_id: claim:f539aee393c3f714fdea
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
off-target populations 17 , absent in adult human kidney (Fig. 1c , Supplementary Fig. 3B ), were found in D29 organoids, including melanoma-like cells ( PMEL ), SOX2 -positive(+) neuronal precursors, STMN2 + neuron-like cells, and MYOG + muscle-like cells, as reported previously 14 – 18 .

summary:
In Homo sapiens kidney organoids, melanoma-like cells are marked by PMEL, neuronal precursors are marked by SOX2, neuron-like cells are marked by STMN2, and muscle-like cells are marked by MYOG.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:b458a9850d3cf11ac726
claim_id: claim:b458a9850d3cf11ac726
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens kidney organoids, nephron progenitor cells are enriched for PAX2, LHX1, and PAX8.
span_literal:
D29 organoids also contained nephron progenitor cells (NPC) enriched in PAX2 , LHX1 and PAX8 (top cluster-specific differentially expressed (DE) genes).


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:f0b1f097734c30158594
claim_id: claim:f0b1f097734c30158594
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens developing kidney, fetal mesangial cells are marked by MGP, GAS2, PRXX2, and FOXP2.
span_literal:
mesenchymal-2 cells in organoids were enriched for MGP , GAS2 , PRXX2 and FOXP2 30 , known markers of fetal mesangial cells in the developing kidney.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:efdae77eca1e61644bf0
claim_id: claim:efdae77eca1e61644bf0
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
NPHS1 (podocyte cluster), colocalized with the podocyte-specific marker synaptopodin (SYNPO) (Fig. 2d )

summary:
In Homo sapiens kidney organoids, NPHS1 and the podocyte-specific marker synaptopodin (SYNPO) are markers of the podocyte cluster.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:7637d667c738cac29c44
claim_id: claim:7637d667c738cac29c44
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens kidney organoids, LRP2 is a marker of the proximal tubule cluster.
span_literal:
LRP2 (proximal tubule cluster), colocalized with LTL, a lectin specific to the proximal tubule (Fig. 2e )


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:04c4020452b8346df511
claim_id: claim:04c4020452b8346df511
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens kidney organoids, MEIS1 is a gene enriched in kidney mesenchymal cells.
span_literal:
We also validated MEIS1, a gene enriched in kidney mesenchymal cells, by IF staining, where it was shown to localize appropriately to the interstitium, defined as the cellular space outside laminin (LAMA1) positive basement membrane structures (Fig. 2f ).


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:9bda8515fe48daa941bb
claim_id: claim:9bda8515fe48daa941bb
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
At D15 we first observed a SOX17 -positive endothelial progenitor cell population that persisted in D29 (Fig. 4a , Supplementary Fig. 9C ).

summary:
In Homo sapiens kidney organoids, SOX17 is a positive marker of the endothelial progenitor cell population.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:c7e8880fc1254d056883
claim_id: claim:c7e8880fc1254d056883
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
FOXC2 and WT1 were prominent in podocytes, whereas IRX3 and POU3F3 had a distinct distal pattern (Fig. 4a , Supplementary Fig. 15A ).

summary:
In Homo sapiens kidney organoids, FOXC2 and WT1 are prominently expressed in podocytes, whereas IRX3 and POU3F3 have a distinct distal nephron pattern.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:982e9250cecc7f5e16d7
claim_id: claim:982e9250cecc7f5e16d7
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
FOXC2 and WT1 were prominent in podocytes, whereas IRX3 and POU3F3 had a distinct distal pattern (Fig. 4a , Supplementary Fig. 15A ).

summary:
In Homo sapiens kidney organoids, IRX3 and POU3F3 are markers with a distinct distal nephron cell pattern.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:33592f764e4e6b9e29d1
claim_id: claim:33592f764e4e6b9e29d1
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
Of several data-derived markers enriched in the podocyte population at D15 ( CTGF , CLDN5 , SOST , SPARC ; Fig. 4b , Supplementary Fig. 15B ), we validated CLDN5 (claudin 5, an integral membrane protein controlling tight junctions 45 in many cells including podocytes 46 ) in nephrin (NPHS1) and WT1-positive podocytes of D15 organoids (Fig. 4c ).

summary:
In Homo sapiens kidney organoids, CTGF, CLDN5, SOST, and SPARC are data-derived markers enriched in the podocyte population.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:7b4e5bcc566f2eed49ba
claim_id: claim:7b4e5bcc566f2eed49ba
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens kidney organoids, SOX17 and CD31 are markers of endothelial precursor cells.
span_literal:
To validate the endothelial precursors identified in our analysis of D15 organoids, we stained for SOX17 (localized to EC nuclei) and showed that it colocalized with CD31, a classical endothelial marker (Fig. 4d ).


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:225caaea3fb727644ad1
claim_id: claim:225caaea3fb727644ad1
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
For example, PTPRO (from CKD GWAS and monogenic glomerular diseases) was appropriately expressed in D29 and adult human podocytes 50 (Supplementary Figs. 18 , 19 ).

summary:
In Homo sapiens, PTPRO is appropriately expressed in podocytes in both kidney organoids and adult human kidney.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:8bf919e644920408e648
claim_id: claim:8bf919e644920408e648
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
span_literal:
Similarly, PAX2 and MUC1 (from CAKUT and cystic diseases, respectively) were highly expressed in D29 distal tubules, similar to their human adult expression pattern 51 (Fig. 5a, b ; Supplementary Figs. 16 , 17 ).

summary:
In Homo sapiens, PAX2 and MUC1 are highly expressed in distal tubule cells in kidney organoids, similar to their adult expression pattern.


claim_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead:claim:6e2af5173cb33d645864
claim_id: claim:6e2af5173cb33d645864
paper_key: hca:0201_10.1038_s41467-019-13382-0_3e98068ead
summary: In Homo sapiens kidney organoids, HES1 is expressed in MAL-positive distal tubular cells.
span_literal:
the Notch effector HES1 , which plays a role in proximal to distal patterning in kidney nephrogenesis 61 , in MAL + distal tubular cells (Fig. 6e ).


claim_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902:claim:965918723777ad592d9b
claim_id: claim:965918723777ad592d9b
paper_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902
summary: In Homo sapiens nasal mucosa, ionocytes are identified by expression of CFTR.
span_literal:
We also classified six distinct immune cell types which were: monocytes, conventional dendritic cells (cDCs), plasmacystoid dendritic cells (pDCs), B cells, Mast cells, and T cells. Additionally, we were able to identify CFTR expressing ionocytes


claim_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902:claim:bcd25b0267c5136a8371
claim_id: claim:bcd25b0267c5136a8371
paper_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902
span_literal:
With this increased resolution, we found that these NM T cells were primarily CD8 positive and expressed genes encoding CCL5 and interferon gamma, TNF, PRF, granzymes, and killer-like receptors that are important for T cell effector function and antiviral activity.

summary:
In Homo sapiens nasal mucosa, resident T cells are positive for CD8, CCL5, interferon gamma, TNF, PRF, granzymes, and killer-like receptors.


claim_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902:claim:1c78e149038d0fd3a8ed
claim_id: claim:1c78e149038d0fd3a8ed
paper_key: hca:0203_10.1038_s41598-021-95532-3_bdd0d22902
span_literal:
Additionally, these cells are strongly enriched for expression of tissue residency markers such as ITGAE (CD103), ITGA1 (CD49a) and CD69 , and are void of expression of CCR7 , which is necessary for lymphocyte homing (Fig. 3 C).

summary:
In Homo sapiens nasal mucosa, resident T cells are positive for tissue residency markers ITGAE (CD103), ITGA1 (CD49a), and CD69, and are negative for CCR7.


claim_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa:claim:26511ee8fd72e7bc354a
claim_id: claim:26511ee8fd72e7bc354a
paper_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa
span_literal:
Cluster annotation was carried out by combining expression patterns of canonical cell type markers, for example, NES , DCX , SIX6 , AIF1 , DCN and EPCAM

summary:
In Homo sapiens cerebral organoids, NES is used as a canonical cell type marker for neural progenitor cells.


claim_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa:claim:ea65f61f979436c75f0a
claim_id: claim:ea65f61f979436c75f0a
paper_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa
summary:
In Homo sapiens cerebral organoids, DCN is used as a canonical cell type marker for mesenchymal cells.


claim_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa:claim:c05e496b9031cd4712df
claim_id: claim:c05e496b9031cd4712df
paper_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa
summary:
In Homo sapiens cerebral organoids, EPCAM is used as a canonical cell type marker for epithelial cells.


claim_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa:claim:6572e653158e06fe0b11
claim_id: claim:6572e653158e06fe0b11
paper_key: hca:0204_10.1038_s41592-021-01344-8_b3626153aa
summary: In Homo sapiens, SOX2 and OCT-4 are pluripotency markers of induced pluripotent stem cells.
span_literal:
The cell line was tested for the proper expression of pluripotency markers SOX2, OCT-4, TRA1-60 and SSEA.


claim_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540:claim:bf4637c04b973b8c6e29
claim_id: claim:bf4637c04b973b8c6e29
paper_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540
summary: In Homo sapiens, pericytes are characterized by the coexpression of TAGLN, ACTA2, and RGS5.
span_literal:
Pericytes were characterized by the coexpression of contractile genes ( TAGLN , ACTA2 ) and RGS5 (ref. 20 )


claim_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540:claim:1aaac0da89ad787d3a4f
claim_id: claim:1aaac0da89ad787d3a4f
paper_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540
span_literal:
vascular smooth muscle cells by contractile and cytoskeletal gene expression ( TAGLN , ACTA2 , MYH11 , SYNPO2 , CNN1 and DES ) 21

summary:
In Homo sapiens, vascular smooth muscle cells are characterized by expression of TAGLN, ACTA2, MYH11, SYNPO2, CNN1, and DES.


claim_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540:claim:c2f675373b390356df1a
claim_id: claim:c2f675373b390356df1a
paper_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540
summary: In Homo sapiens, endothelial cell clusters are characterized by expression of ENG and PECAM1.
span_literal:
Endothelial cell clusters were characterized by ENG and PECAM1 gene expression without fibroblast markers 23


claim_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540:claim:551230d8a34fbb326557
claim_id: claim:551230d8a34fbb326557
paper_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540
span_literal:
we identified a highly proliferative cell population with overexpression of survivin (coded by BIRC5 ) and CKS1B as a unique tumor-derived cluster (proliferative endothelial cells, cluster 23 in Supplementary Fig. 6d and Fig. 3b )

summary:
In Homo sapiens, proliferative endothelial cells are characterized by overexpression of BIRC5 and CKS1B.


claim_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540:claim:d2f4582667be6d816677
claim_id: claim:d2f4582667be6d816677
paper_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540
summary: In Homo sapiens, conventional dendritic cells express CD1C and FCER1A.
span_literal:
The dendritic cell cluster expressed transcripts for CD1C and FCER1A , consistent with conventional dendritic cells 38


claim_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540:claim:2f9610f66cbe7b43ada6
claim_id: claim:2f9610f66cbe7b43ada6
paper_key: hca:0205_10.1038_s41588-020-0636-z_f39ba80540
summary: In Homo sapiens, SPP1-positive macrophages express apolipoprotein E (APOE).
span_literal:
However, SPP1 + macrophages also express apolipoprotein E ( APOE ), which is associated with an anti-inflammatory phenotype 35


claim_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82:claim:de172378256597929c8f
claim_id: claim:de172378256597929c8f
paper_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82
summary: In Homo sapiens, Hillock-like cells are marked by KRT14, KRT6A, and KRT13.
span_literal:
The latter are all marked by KRT14 , KRT6A and KRT13 , which form a distinct differentiation trajectory (Fig. 1d ) similar to the one reported in mice


claim_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82:claim:89999d98ae0e30a21227
claim_id: claim:89999d98ae0e30a21227
paper_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82
summary: In Homo sapiens, IL-6-positive monocytes are marked by IL6 expression in the airways.
span_literal:
Moreover, monocytes fall into clearly distinct clusters, annotated by their highly expressed markers, IL-6 + monocytes, GPBAR1 + monocytes and CXCL10 + monocytes, and were mostly derived from neonates with COVID-19


claim_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82:claim:d9b9da3ea76ad1eb5eb4
claim_id: claim:d9b9da3ea76ad1eb5eb4
paper_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82
span_literal: The neutrophil recruitment signature was driven by S100A8 and S100A9 expression (calprotectin)
summary:
In Homo sapiens, transit epithelial cells express S100A8 and S100A9 (calprotectin), driving a neutrophil recruitment signature.


claim_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82:claim:e265be6b67acd397163e
claim_id: claim:e265be6b67acd397163e
paper_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82
span_literal:
SARS-CoV-2 uses a host cell-surface protein, angiotensin-converting enzyme 2 (ACE2), as a receptor for cellular entry

summary:
In Homo sapiens, angiotensin-converting enzyme 2 (ACE2) serves as the cell-surface receptor for SARS-CoV-2 cellular entry.


claim_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82:claim:efd60e56e66e12480ff9
claim_id: claim:efd60e56e66e12480ff9
paper_key: hca:0206_10.1038_s41586-021-04345-x_4379471b82
span_literal:
This list includes BST2 , CMPK2 , EIF2AK2 , EPSTI1 , HERC5 , IFI35 , IFI44L , IFI6 , IFIT3 , ISG15 , LY6E , MX1 , MX2 , OAS1 , OAS2 , PARP9 , PLSCR1 , SAMD9 , SAMD9L , SP110 , STAT1 , TRIM22 , UBE2L6 , XAF1 and IRF7

summary:
In Homo sapiens, interferon-stimulated subpopulations in peripheral blood mononuclear cells are defined by expression of BST2, CMPK2, EIF2AK2, EPSTI1, HERC5, IFI35, IFI44L, IFI6, IFIT3, ISG15, LY6E, MX1, MX2, OAS1, OAS2, PARP9, PLSCR1, SAMD9, SAMD9L, SP110, STAT1, TRIM22, UBE2L6, XAF1, and IRF7.


claim_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861:claim:cc4e8dd37fb59a4c059b
claim_id: claim:cc4e8dd37fb59a4c059b
paper_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861
summary: In Homo sapiens, monocytes are identified by expression of CD14, ITGAM, S100A8, and S100A9.
span_literal:
In general, monocytes ( CD14, ITGAM, S100A8 and A100A9), granulocytes ( FCGR3B ), erythroid cells ( HBA1, HBA2 and HBB ), NK cells ( GNLY, NCAM1 ), proliferative lymphocytes ( MKI67 and TUBA1B ), CD4 + T cells ( CD3G, CD4 and CCR7 ), CD8 + T cells ( CD3G and CD8A ), dendritic cells ( PLD4, IL3RA and LILRA4 ), B cells ( CD19 ), plasmablasts ( CD27 , CD38 and MZB1 ), megakaryocytes ( ITGA2B, TUBB1 and GP9 ) and cell precursors ( CD34, ITGA4 and TUBA1A ), such as, hematopoietic stem cells (HSCs), megakaryocyte-erythroid progenitor cells (MEPs), common myeloid progenitors (CMPs) and granulocytes-macrophage progenitors (GMPs).


claim_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861:claim:ead69f1fc6f11731dff8
claim_id: claim:ead69f1fc6f11731dff8
paper_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861
summary:
In Homo sapiens, cell precursors including hematopoietic stem cells are identified by expression of CD34, ITGA4, and TUBA1A.


claim_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861:claim:2a642e1452c242e82c53
claim_id: claim:2a642e1452c242e82c53
paper_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861
summary: In Homo sapiens, memory B cells are identified by expression of NT5E (CD73).
span_literal:
B cell compartment clusters were assigned based on expression of marker genes, with memory B cell expressing CD73/NT5E , naive B cells expressing IGHD and CD185/CXCR5 , transitional B cells expressing CD9 , plasmablasts expressing CD27 and CD38 ) and neutrophil-like cell expressing ELANE, MPO and CAMP ( Glass et al., 2020 ).


claim_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861:claim:19ef60c41026fb75326d
claim_id: claim:19ef60c41026fb75326d
paper_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861
span_literal:
We could distinguish a smaller cluster of PBs, which expressed genes associated with neutrophils (e.g., ELANE , MPO , and CAMP )

summary:
In Homo sapiens, a smaller cluster of plasmablasts expressed neutrophil-associated genes ELANE, MPO, and CAMP.


claim_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861:claim:0e24d41077d2f7ae3f25
claim_id: claim:0e24d41077d2f7ae3f25
paper_key: hca:0207_10.1016_j.immuni.2020.11.017_b182001861
summary: In Homo sapiens, plasmablasts are marked by expression of CD27, CD38, and TNFRSF17.
span_literal:
PB-specific UMAP highlighted neutrophil-like cells (NL). Smaller UMAPs corresponding to expression of PB markers ( CD27 , CD38 , and TNFRSF17 ) and neutrophil-like markers ( ELANE , MPO , and CAMP ).


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:f3771601beff3559ce99
claim_id: claim:f3771601beff3559ce99
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
Cells in groups I and II expressed high levels of neuroepithelial markers, including VIM, SOX2, and PAX6 .

summary:
In Homo sapiens developing cerebral cortex, neuroepithelial cells express high levels of VIM, SOX2, and PAX6.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:bf6cb721f3d756e1d8ec
claim_id: claim:bf6cb721f3d756e1d8ec
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
cells in group I also expressed high levels of proliferative markers CDK1 and ASPM , while cells in group II expressed high levels of mature radial glial markers SLC1A3 and HES1 .

summary:
In Homo sapiens developing cerebral cortex, dividing neural progenitors express high levels of the proliferative markers CDK1 and ASPM.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:f59e8b4132d941cd85a7
claim_id: claim:f59e8b4132d941cd85a7
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
cells in group I also expressed high levels of proliferative markers CDK1 and ASPM , while cells in group II expressed high levels of mature radial glial markers SLC1A3 and HES1 .

summary:
In Homo sapiens developing cerebral cortex, radial glia express high levels of the mature radial glial markers SLC1A3 and HES1.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:9dff14cdb71ce9df1cd8
claim_id: claim:9dff14cdb71ce9df1cd8
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
cells in groups III–IV expressed the pan-neuronal marker DCX , and cells in group IV also expressed many markers of neuronal maturation, including MEF2C , SATB2 and SNAP25

summary:
In Homo sapiens developing cerebral cortex, newborn neurons and maturing neurons express the pan-neuronal marker DCX.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:967a121aa8d072cd3545
claim_id: claim:967a121aa8d072cd3545
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
cells in groups III–IV expressed the pan-neuronal marker DCX , and cells in group IV also expressed many markers of neuronal maturation, including MEF2C , SATB2 and SNAP25

summary:
In Homo sapiens developing cerebral cortex, maturing neurons express markers of neuronal maturation including MEF2C, SATB2, and SNAP25.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:26ed6b1ff7a23634e8c2
claim_id: claim:26ed6b1ff7a23634e8c2
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
Cells in group IIIb expressed canonical markers of inhibitory interneurons GAD1 and DLX genes, as well as novel markers such as PDZRN3

summary:
In Homo sapiens developing cerebral cortex, inhibitory interneurons express canonical markers GAD1 and DLX genes, as well as the novel marker PDZRN3.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:c031fae7c6a467824d6c
claim_id: claim:c031fae7c6a467824d6c
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal: while the remaining cells in group III expressed proneural genes NEUROD1 and NEUROD6.
summary:
In Homo sapiens developing cerebral cortex, newborn excitatory neurons express the proneural genes NEUROD1 and NEUROD6.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:9257b83183b1157e198c
claim_id: claim:9257b83183b1157e198c
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
summary: In Homo sapiens developing cerebral cortex, newborn neurons express UNC5D, ROBO2, and NTM.
span_literal:
group III cells expressed UNC5D, a gene transiently up-regulated in newly-generated mouse excitatory neurons required for the earliest phases of migration 12 , and other genes such as ROBO2 and NTM


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:ed7b027180f04dfeb796
claim_id: claim:ed7b027180f04dfeb796
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
Group IV could be further divided into maturing neurons expressing high levels of CAMKV and cells expressing high levels of ADRA2A

summary:
In Homo sapiens developing cerebral cortex, maturing neurons can be divided into subtypes expressing high levels of CAMKV or ADRA2A.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:175b8ab145f1cc7bae64
claim_id: claim:175b8ab145f1cc7bae64
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
Candidate mitotic markers CKS2 and HMGB2 were detected specifically in a subset of human radial glia undergoing cell division at the edge of the lateral ventricle

summary:
In Homo sapiens, the candidate mitotic markers CKS2 and HMGB2 are detected specifically in a subset of radial glia undergoing cell division.


claim_key: hca:0208_10.1038_nbt.2967_18c9fd3939:claim:dabe342c08102dc4ed2c
claim_id: claim:dabe342c08102dc4ed2c
paper_key: hca:0208_10.1038_nbt.2967_18c9fd3939
span_literal:
we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia.

summary:
In Homo sapiens, EGR1 and FOS are identified as previously unreported candidate targets of Notch signaling in radial glia.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:661954eaf8b403c70be6
claim_id: claim:661954eaf8b403c70be6
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
An analogous population of cells characterized by the expression of TP63 , KRT5 , KRT17 , LAMB3, LAMC2 , VIM , CHD2 , FN1 , COL1A1 , TNC , and HMGA2 and several senescence markers ( CDKN1A , CDKN2A , CCND1 , CCND2 , MDM2 , and SERPINE1 ) accumulates during pulmonary fibrosis in humans.

summary:
In Homo sapiens, a transitional epithelial cell population accumulating during pulmonary fibrosis is characterized by expression of TP63, KRT5, KRT17, LAMB3, LAMC2, VIM, CHD2, FN1, COL1A1, TNC, HMGA2, CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and SERPINE1.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:bacccdae54845af114db
claim_id: claim:bacccdae54845af114db
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
These cells have been suggested to contribute to disease pathogenesis through expression of TGFB1 , ITGAV , and ITGB6 (the KRT5 − KRT17 + epithelial cell cluster in the Habermann et al . dataset)

summary:
In Homo sapiens, the KRT5-negative KRT17-positive epithelial cell cluster expresses TGFB1, ITGAV, and ITGB6, and is characterized by positive KRT17 and negative KRT5.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:9fcecfb938b6d78dd4c6
claim_id: claim:9fcecfb938b6d78dd4c6
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
Human profibrotic monocyte-derived alveolar macrophages are characterized by expression of SPP1 , ILRN , MMP9 , CHI3L1, and PLA2G7 and reduced expression of FABP4 , INHBA , and PPARG, which mark tissue-resident homeostatic alveolar macrophages present in the normal lung

summary:
In Homo sapiens, profibrotic monocyte-derived alveolar macrophages are characterized by expression of SPP1, ILRN, MMP9, CHI3L1, and PLA2G7 and reduced expression of FABP4, INHBA, and PPARG.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:432a10b8e3b67fde96fb
claim_id: claim:432a10b8e3b67fde96fb
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
Human profibrotic monocyte-derived alveolar macrophages are characterized by expression of SPP1 , ILRN , MMP9 , CHI3L1, and PLA2G7 and reduced expression of FABP4 , INHBA , and PPARG, which mark tissue-resident homeostatic alveolar macrophages present in the normal lung

summary:
In Homo sapiens, tissue-resident homeostatic alveolar macrophages are marked by expression of FABP4, INHBA, and PPARG.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:773a46004f873e600939
claim_id: claim:773a46004f873e600939
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
Our analysis also identified a small group of cells in the lung samples from patient PMB1 and case 1 that expressed genes including AK5 , SIGLEC15 , CKB , and SLC9B2 , suggesting that these cells could have been osteoclasts in areas of lung necrosis and calcification

summary:
In Homo sapiens, osteoclasts in areas of lung necrosis and calcification express AK5, SIGLEC15, CKB, and SLC9B2.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:87892fe4ad0cd5043570
claim_id: claim:87892fe4ad0cd5043570
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
These macrophages expressed genes involved in iron ( SLC40A1 and CD163 ) and lipid ( MERTK , PLTP , and ABCA1 ) metabolism, and cell motility and immune signaling ( MARCKS , TLR2 , and CCL20 ), potentially reflecting ongoing inflammation

summary:
In Homo sapiens, a macrophage population (cluster 3) enriched in the lung explant expresses SLC40A1, CD163, MERTK, PLTP, ABCA1, MARCKS, TLR2, and CCL20, potentially reflecting ongoing inflammation.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:c2aff8a99604f8fd04aa
claim_id: claim:c2aff8a99604f8fd04aa
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
summary: In Homo sapiens, myofibroblast cluster 2 cells show increased expression of POSTN and COL1A1.
span_literal:
Cluster 2 cells showed increased expression of POSTN and COL1A1 and other extracellular matrix genes implicated in pulmonary fibrosis


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:5014f005ffd4b8685ad8
claim_id: claim:5014f005ffd4b8685ad8
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
Specifically, we observed the emergence of an abnormal population of basaloid-like epithelial cells expressing Keratin-17 that have been observed lining fibroblastic foci in patients with IPF, as well as profibrotic macrophages and myofibroblasts

summary:
In Homo sapiens, basaloid-like epithelial cells lining fibroblastic foci in patients with idiopathic pulmonary fibrosis express Keratin-17.


claim_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac:claim:4fe00f77adb0d8072ce8
claim_id: claim:4fe00f77adb0d8072ce8
paper_key: hca:0209_10.1126_scitranslmed.abe4282_13877fdeac
span_literal:
In normal healthy lung, expression of KRT17 is restricted to basal, club, ciliated, and alveolar type 1 cells

summary:
In Homo sapiens normal healthy lung, expression of KRT17 is restricted to basal cells, club cells, ciliated cells, and alveolar type 1 cells.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:e5f6a95f014deea9e3e8
claim_id: claim:e5f6a95f014deea9e3e8
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
an PDGFRA HI / F3 HI / DLL1 HI mesenchymal population lines the crypt-villus axis and is the source of the EGF family member NEUREGULIN1 ( NRG1 )

summary:
In Homo sapiens, a PDGFRA-high/F3-high/DLL1-high mesenchymal population expresses NEUREGULIN1 (NRG1) along the crypt-villus axis of the developing intestine.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:afa320170ebd17e68625
claim_id: claim:afa320170ebd17e68625
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
PDGFRA HI /F3 HI /DLL1 HI population, a GPX3 HI population, a TAGLN HI /RGS5 - smooth muscle population and a prominent clusters of cells defined as fibroblasts based on their expression COLLAGEN genes ( COL1A1, COL1A2) and DECORIN ( DCN ) ( Figure 1E , Figure S1D ) ( Kinchen et al., 2018 ). F3 was recently shown to be expressed in a population of mesenchymal cells that is adjacent to the human colonic epithelium ( Kinchen et al., 2018 ) and we identified that these cells were additionally characterized by their enrichment of NPY, DLL1, FRZB and SOX6 ( Figure 1E , Figure S1B – D ).
Mesenchymal cell lineages emerge across developmental time.
Force directed layouts following Harmony implementation suggested that different mesenchymal cell populations emerge across developmental time. For example, F3 HI /PDGFRA HI cells

summary:
In Homo sapiens developing intestine, a mesenchymal population is annotated by high expression of PDGFRA.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:404d0e03e72ffe2323ec
claim_id: claim:404d0e03e72ffe2323ec
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: an ACTA2 HI /TAGLN HI /RGS5 + population of vascular smooth muscle cells (VSMC)
summary:
In Homo sapiens developing intestine, vascular smooth muscle cells are marked by high ACTA2, high TAGLN, and RGS5 expression.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:de4323b8989fd4097c00
claim_id: claim:de4323b8989fd4097c00
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
a prominent clusters of cells defined as fibroblasts based on their expression COLLAGEN genes ( COL1A1, COL1A2) and DECORIN ( DCN )

summary:
In Homo sapiens developing intestine, fibroblasts are defined by expression of COL1A1, COL1A2, and DECORIN (DCN).


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:3f55ba41fa0e207c57f8
claim_id: claim:3f55ba41fa0e207c57f8
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
we identified that these cells were additionally characterized by their enrichment of NPY, DLL1, FRZB and SOX6

summary:
In Homo sapiens developing intestine, F3-high subepithelial mesenchymal cells are additionally characterized by enrichment of NPY, DLL1, FRZB, and SOX6.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:c6ffc88d1366a4cebe74
claim_id: claim:c6ffc88d1366a4cebe74
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
the WNT pathway members with the highest expression were RSPO2, RSPO3 and WNT2B, which are expressed in the TAGLN HI /RGS5 - smooth muscle cells and COL1A1 HI fibroblasts, but are not expressed by the F3 HI / PDGFRA HI subepithelial cells

summary:
In Homo sapiens developing intestine, RSPO2, RSPO3, and WNT2B are expressed in TAGLN-high/RGS5-negative smooth muscle cells and COL1A1-high fibroblasts, but are not expressed by F3-high/PDGFRA-high subepithelial cells.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:b4275011258b4e6f1284
claim_id: claim:b4275011258b4e6f1284
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
the WNT pathway members with the highest expression were RSPO2, RSPO3 and WNT2B, which are expressed in the TAGLN HI /RGS5 - smooth muscle cells and COL1A1 HI fibroblasts, but are not expressed by the F3 HI / PDGFRA HI subepithelial cells

summary:
In Homo sapiens developing intestine, RSPO2, RSPO3, and WNT2B are expressed in COL1A1-high fibroblasts but are not expressed by F3-high/PDGFRA-high subepithelial cells.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:a6fab5311ba9f9286068
claim_id: claim:a6fab5311ba9f9286068
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
the WNT pathway members with the highest expression were RSPO2, RSPO3 and WNT2B, which are expressed in the TAGLN HI /RGS5 - smooth muscle cells and COL1A1 HI fibroblasts, but are not expressed by the F3 HI / PDGFRA HI subepithelial cells

summary:
In Homo sapiens developing intestine, RSPO2, RSPO3, and WNT2B are not expressed by F3-high/PDGFRA-high subepithelial cells.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:2e998fe05e899df7ce11
claim_id: claim:2e998fe05e899df7ce11
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
EGF expression was not observed in the mesenchyme, whereas the EGF family member NRG1 was abundant in the F3 HI /PDGFRA HI cell population

summary:
In Homo sapiens developing intestine, NRG1 is abundantly expressed in the F3-high/PDGFRA-high mesenchymal cell population, whereas EGF expression was not observed in the mesenchyme.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:139d318b3bacdd4a48d6
claim_id: claim:139d318b3bacdd4a48d6
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: EGF is expressed in a small subset of differentiated epithelial FABP2 HI enterocytes
summary:
In Homo sapiens developing intestine, EGF is expressed in a small subset of differentiated FABP2-high enterocytes.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:c35d74870ca8cdb69a30
claim_id: claim:c35d74870ca8cdb69a30
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
summary: In Homo sapiens fetal intestine, intestinal stem cells are defined by expression of LGR5 and OLFM4.
span_literal:
We defined 9 epithelial cell types based on published data ( Table S3 ), including intestinal stem cells (ISCs, cluster 2 - LGR5, OLFM4 )


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:c172a63d40d973eb271e
claim_id: claim:c172a63d40d973eb271e
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: BEST4+ enterocytes (cluster 5 - BEST4, SPIB )
summary:
In Homo sapiens fetal intestine, BEST4-positive enterocytes are defined by expression of BEST4 and SPIB.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:04bbdde0523f9e265aa0
claim_id: claim:04bbdde0523f9e265aa0
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: goblet cells and goblet cell precursors (cluster 4 - MUC2, SPDEF, DLL1 )
summary:
In Homo sapiens fetal intestine, goblet cells and goblet cell precursors are defined by expression of MUC2, SPDEF, and DLL1.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:6f349aaab9dea8fc74c2
claim_id: claim:6f349aaab9dea8fc74c2
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: enteroendocrine cells (EECs, clusters 1 and 8 – CHGA, NEUROD1, PAX6, ARX, REG4 )
summary:
In Homo sapiens fetal intestine, enteroendocrine cells are defined by expression of CHGA, NEUROD1, PAX6, ARX, and REG4.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:97637838a56086389c3c
claim_id: claim:97637838a56086389c3c
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
Smooth muscle cells of the muscularis mucosa, proximal to proliferative crypts, are a source of WNT and RSPONDIN ligands, while EGF is expressed far from crypts in the villus epithelium.

summary:
In Homo sapiens developing intestine, smooth muscle cells of the muscularis mucosa are a source of WNT and RSPONDIN ligands.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:38e53ee119517dc66835
claim_id: claim:38e53ee119517dc66835
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
we observed that WNT2B, RSPO2 and RSPO3 are expressed in the muscularis mucosae in the human fetal intestine, as well as in cells more broadly defined as fibroblasts.

summary:
In Homo sapiens fetal intestine, WNT2B, RSPO2, and RSPO3 are expressed in the muscularis mucosae smooth muscle cells as well as in fibroblasts.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:96d2cbcf6b446aa0ccdd
claim_id: claim:96d2cbcf6b446aa0ccdd
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
we identify a subepithelial cell that lines the entire crypt-villus axis, marked by high levels of DLL1 , F3 and PDGFRA expression.

summary:
In Homo sapiens developing intestine, a subepithelial cell lining the crypt-villus axis is marked by high levels of DLL1, F3, and PDGFRA expression.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:b9d50f5ddc2128f89460
claim_id: claim:b9d50f5ddc2128f89460
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
These cells can be further sub-divided using the marker NPY , which is expressed in the villus ( NPY/DLL1/F3) but not the crypt.

summary:
In Homo sapiens developing intestine, villus subepithelial cells can be sub-divided using the marker NPY, which is expressed in the villus but not the crypt.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:ee289c3e49047e67fffd
claim_id: claim:ee289c3e49047e67fffd
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
Within the F3 transcriptional signature, we also observed robust expression of FRZB and SOX6 , which have previously been described in the human colon as a subepithelial cell population that expresses several WNT family members ( WNT5A, WNT5B ) and several BMP family members ( BMP2, BMP5 )

summary:
In Homo sapiens colon, a subepithelial cell population with the F3 transcriptional signature expresses FRZB, SOX6, WNT5A, WNT5B, BMP2, and BMP5.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:ecff64c47861e6b55243
claim_id: claim:ecff64c47861e6b55243
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal:
cluster 11 expressed genes associated with secretory and goblet cells ( MUC2 ), and cluster 12 expressed genes associated with enteroendocrine cells ( CHGA )

summary:
In Homo sapiens intestinal enteroids grown in NRG1, goblet cells express MUC2 and enteroendocrine cells express CHGA.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:ffb7bb7e31a07951c21d
claim_id: claim:ffb7bb7e31a07951c21d
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: ACTA2 + /TAGLN + smooth muscle cells of the muscularis mucosae
summary:
In Homo sapiens developing intestine, smooth muscle cells of the muscularis mucosae express ACTA2 and TAGLN.


claim_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4:claim:3189e77316104a4eba8e
claim_id: claim:3189e77316104a4eba8e
paper_key: hca:0210_10.1016_j.stem.2020.11.008_213dabcee4
span_literal: NRG1 ) is expressed by PGDFRA HI /F3+/DLL1 HI subepithelial mesenchyme
summary:
In Homo sapiens developing intestine, NRG1 is expressed by PDGFRA-high/F3-positive/DLL1-high subepithelial mesenchymal cells.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:875dee74c82aac8a8604
claim_id: claim:875dee74c82aac8a8604
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal: The HR+ cluster was enriched for the hormone receptors ESR1 and PGR
summary:
In Homo sapiens, the hormone-responsive luminal cell cluster is enriched for the hormone receptors ESR1 and PGR in the breast.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:e3615ccc1b056d5ee538
claim_id: claim:e3615ccc1b056d5ee538
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
The HR+ cluster was enriched for the hormone receptors ESR1 and PGR ( Figure S1G ), and other known markers such as ANKRD30A

summary:
In Homo sapiens, the hormone-responsive luminal cell cluster is enriched for ANKRD30A in the breast.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:c4d558c7488c387aaf6e
claim_id: claim:c4d558c7488c387aaf6e
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
Activity program 1 in HR+ luminal cells (“ER/PR signaling”) was associated with high expression of the essential PR target genes WNT4 and TNFSF11 (RANKL)

summary:
In Homo sapiens, the hormone-responsive luminal cell ER/PR signaling activity program is associated with high expression of WNT4 and TNFSF11 (receptor activator of nuclear factor kappa-B ligand).


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:ec0a68077bda8c54d64b
claim_id: claim:ec0a68077bda8c54d64b
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
We identified LRRC26 as a marker of the ER/PR signaling activity program HR+ 1 and P4HA1 as a marker of the hypoxia/pro-angiogenic activity program HR+ 18

summary:
In Homo sapiens, LRRC26 is a marker of the hormone-responsive luminal cell ER/PR signaling activity program, and P4HA1 is a marker of the hormone-responsive luminal cell hypoxia/pro-angiogenic activity program in the breast.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:97417d3939a2b623614f
claim_id: claim:97417d3939a2b623614f
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
We identified LRRC26 as a marker of the ER/PR signaling activity program HR+ 1 and P4HA1 as a marker of the hypoxia/pro-angiogenic activity program HR+ 18

summary:
In Homo sapiens, P4HA1 is a marker of the hormone-responsive luminal cell hypoxia/pro-angiogenic activity program in the breast.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:0d40899c5c9d9842c08c
claim_id: claim:0d40899c5c9d9842c08c
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
Activity programs in both modules were characterized by high expression of death receptor ligands such as TNFSF10 (TRAIL) and TNF

summary:
In Homo sapiens, secretory luminal cell activity programs in the involution-like and post-lactational involution modules are characterized by high expression of TNFSF10 (TNF-related apoptosis-inducing ligand) and TNF.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:c81753a5e25a694f542e
claim_id: claim:c81753a5e25a694f542e
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
secretory luminal cells was characterized by expression of major histocompatibility complex class II (MHC-II) molecules and the phagocytic receptor MARCO

summary:
In Homo sapiens, the involution-like secretory luminal cell subpopulation is characterized by expression of the phagocytic receptor MARCO in the breast.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:1aa32bd88fdf83449111
claim_id: claim:1aa32bd88fdf83449111
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal: identified keratin 23 (KRT23) as highly enriched in the secretory luminal cell cluster
summary:
In Homo sapiens, keratin 23 (KRT23) is highly enriched in the secretory luminal cell cluster in the breast.


claim_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6:claim:8a82c61dd5422e604bad
claim_id: claim:8a82c61dd5422e604bad
paper_key: hca:0211_10.1016_j.cels.2022.06.005_7669df70b6
span_literal:
Stromal cell types in this module were characterized by upregulation of ECM and matrix remodeling proteins including collagens (COL3A1, COL1A2), the crosslinking enzyme LOXL2, and the cytokine TGFB3

summary:
In Homo sapiens, stromal cells in the ER/PR response module are characterized by upregulation of COL3A1, COL1A2, LOXL2, and TGFB3 in the breast.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:71f5770010d6893185d5
claim_id: claim:71f5770010d6893185d5
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
We defined a six-gene signature RUNX1+HOXA9+MLLT3+MECOM+HLF+SPINK2+ that distinguishes human HSCs from lineage-restricted progenitors in all stages

summary:
In Homo sapiens, hematopoietic stem cells are distinguished from lineage-restricted progenitors by expression of RUNX1, HOXA9, MLLT3, MECOM, HLF, and SPINK2.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:1c65c6bff27e2334b8b9
claim_id: claim:1c65c6bff27e2334b8b9
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
HSC signature RUNX1+HOXA9+MLLT3+MECOM+HLF+SPINK2+ distinguishes HSCs from progenitors throughout gestation

summary:
In Homo sapiens, the hematopoietic stem cell signature of RUNX1, HOXA9, MLLT3, MECOM, HLF, and SPINK2 distinguishes hematopoietic stem cells from progenitors throughout gestation.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:0eaf4758c4d00d5e41da
claim_id: claim:0eaf4758c4d00d5e41da
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
HSC origin was tracked to ALDH1A1+KCNK17+ hemogenic endothelial (HE) cells, which arose from IL33+ALDH1A1+ arterial endothelial subset, termed pre-HE.

summary:
In Homo sapiens, hemogenic endothelial cells are marked by ALDH1A1 and KCNK17, and arise from an IL33-positive ALDH1A1-positive arterial endothelial subset termed pre-hemogenic endothelium.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:f20200c9da5161c1f074
claim_id: claim:f20200c9da5161c1f074
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
HSC origin was tracked to ALDH1A1+KCNK17+ hemogenic endothelial (HE) cells, which arose from IL33+ALDH1A1+ arterial endothelial subset, termed pre-HE.

summary:
In Homo sapiens, the pre-hemogenic endothelium is an IL33-positive ALDH1A1-positive arterial endothelial cell subset that gives rise to hemogenic endothelial cells.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:308c2b1a658a34e76f5b
claim_id: claim:308c2b1a658a34e76f5b
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
HSC transition to the liver marked a molecular shift evidenced by suppression of surface antigens, reflecting nascent HSC identity, and acquisition of HSC maturity markers PROM1/CD133 and HLA-DR.

summary:
In Homo sapiens, mature hematopoietic stem cells in the liver acquire expression of the maturity markers PROM1 and HLA-DR.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:51b1bac84d612f2084b1
claim_id: claim:51b1bac84d612f2084b1
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
co-expression of transcription factors regulating HSC specification (medial HOXA genes 32 , 33 ) and self-renewal (MLLT3 34 , MECOM 35 , HLF 36 ) and HSC surface markers CD34, THY1/CD90 and ACE 37

summary:
In Homo sapiens, hematopoietic stem cells co-express transcription factors MLLT3, MECOM, and HLF, and surface markers CD34, THY1, and ACE.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:4e5606156102eb07f9b1
claim_id: claim:4e5606156102eb07f9b1
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
The expression of the highly HSC-enriched gene HLF 16 , 34 , 38 , 39 was most specific to the HSC cluster.

summary:
In Homo sapiens, HLF is a highly enriched and specific marker of the hematopoietic stem cell cluster.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:393be335cf9c593e8afd
claim_id: claim:393be335cf9c593e8afd
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
The top 30 HSC-enriched genes identified from these two comparisons included known HSC regulators (GFI1, MYB) and potential new human AGM HSC markers (SPINK2, RAB27B)

summary:
In Homo sapiens, the top hematopoietic stem cell-enriched genes in the aorta-gonad-mesonephros region include GFI1, MYB, SPINK2, and RAB27B.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:4c1684fedd0ea1b7b8cb
claim_id: claim:4c1684fedd0ea1b7b8cb
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
SPINK2 40 , a serine protease inhibitor observed recently in HSPC datasets 16 , 38 , was the most significantly enriched gene in HSC cluster.

summary:
In Homo sapiens, SPINK2 is the most significantly enriched gene in the hematopoietic stem cell cluster.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:d834d3ea13dde6810e4f
claim_id: claim:d834d3ea13dde6810e4f
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal: AGM HSCs also posseesed distinct endothelial signature (PROCR, EMCN).
summary:
In Homo sapiens, aorta-gonad-mesonephros hematopoietic stem cells possess a distinct endothelial signature including PROCR and EMCN.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:f58976605a306f0925fd
claim_id: claim:f58976605a306f0925fd
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
Genes characteristic for AGM HSCs include endothelial and megakaryocytic surface antigens (CDH5, ITGA2B) and cytokine receptors (IL3RA, CSF1R) associated with myeloid progenitors and early HSC development

summary:
In Homo sapiens, aorta-gonad-mesonephros hematopoietic stem cells characteristically express CDH5, ITGA2B, IL3RA, and CSF1R.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:dab10422b60c463d68cd
claim_id: claim:dab10422b60c463d68cd
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
Genes linked to fetal properties (LIN28B, IGFBP2, HMGA2 43 ) and proliferative activity, oxidative phosphorylation, glucose and nucleotide metabolism were gradually suppressed in liver HSCs, reflecting transition to homeostatic state

summary:
In Homo sapiens, LIN28B, IGFBP2, and HMGA2 are gradually suppressed in liver hematopoietic stem cells during maturation.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:bdbfed0c3a998da729b8
claim_id: claim:bdbfed0c3a998da729b8
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal: The expression of MLLT3 and its targets (HLF, MSI2, PROM1/CD133) 34 also increased over time.
summary:
In Homo sapiens, MLLT3 and its targets HLF, MSI2, and PROM1 increase in expression during hematopoietic stem cell maturation over time.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:c17e54edb57526b6aa0a
claim_id: claim:c17e54edb57526b6aa0a
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
summary: In Homo sapiens, GJA5 marks arterial endothelial cells that give rise to hematopoietic stem cells.
span_literal:
A direct developmental trajectory was observed from GJA5+ arterial endothelial cells (ECs) to HSCs, but not other hematopoietic cells.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:9dcd33b64f072479ec75
claim_id: claim:9dcd33b64f072479ec75
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
Classical arterial genes (GJA5, CXCR4, SOX17) were expressed across arterial clusters and downregulated after HE

summary:
In Homo sapiens, classical arterial genes GJA5, CXCR4, and SOX17 are expressed in arterial endothelial cells and downregulated after hemogenic endothelium.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:4e31e30de4e712cd5f95
claim_id: claim:4e31e30de4e712cd5f95
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
These related populations could be distinguished by the expression of IL33 and SULF1 in arterial cluster 3, and KCNK17, RUNX1 and MYCN in HE.

summary:
In Homo sapiens, pre-hemogenic endothelium (arterial cluster 3) is distinguished by IL33 and SULF1 expression, while hemogenic endothelium is distinguished by KCNK17, RUNX1, and MYCN expression.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:3cbf9134350fb26ad2ac
claim_id: claim:3cbf9134350fb26ad2ac
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
These related populations could be distinguished by the expression of IL33 and SULF1 in arterial cluster 3, and KCNK17, RUNX1 and MYCN in HE.

summary:
In Homo sapiens, hemogenic endothelium is distinguished from pre-hemogenic endothelium by expression of KCNK17, RUNX1, and MYCN.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:767b2f7ab7fab0783979
claim_id: claim:767b2f7ab7fab0783979
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
ALDH1A1 (RA-signaling, essential for HSC fate 10 , 47 ) was expressed from arterial cluster 3 to HSCs.

summary:
In Homo sapiens, ALDH1A1 is expressed from pre-hemogenic endothelium through to hematopoietic stem cells.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:17f46348a8ad7b966925
claim_id: claim:17f46348a8ad7b966925
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
Many CS14 liver SPINK2+ cells co-expressed genes associated with progenitors (CD34, KIT), lymphoid differentiation (IL7R, IL2RG), and EMP/microglial development (MRC1, CX3CR1)

summary:
In Homo sapiens, CS14 liver SPINK2-positive lympho-myeloid progenitors co-express CD34, KIT, IL7R, IL2RG, MRC1, and CX3CR1.


claim_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904:claim:e9932b8ef3d7b4760f86
claim_id: claim:e9932b8ef3d7b4760f86
paper_key: hca:0212_10.1038_s41586-022-04571-x_30a05d7904
span_literal:
HSCs in the liver suppress fetal programs (LIN28B, IGFBP2) and transition towards homeostatic, post-natal HSC state, they acquire surface expression of PROM1

summary:
In Homo sapiens, hematopoietic stem cells in the liver suppress LIN28B and IGFBP2 and acquire surface expression of PROM1 and MHC class II molecules during maturation.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:013d542cac0f8c7b1ba8
claim_id: claim:013d542cac0f8c7b1ba8
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, tumor cells of renal cell carcinoma specifically express CA9.
span_literal:
Tumor cells were identified within clusters that specifically expressed CA9 and harbored extensive copy-number variations (CNVs) across their genomes, as inferred from scRNA-seq data


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:4abb3041dde0c00efd2e
claim_id: claim:4abb3041dde0c00efd2e
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, natural killer cells include subsets expressing NCAM1, FCGR3A, KRT81, and KRT86.
span_literal:
Subclustering of natural killer (NK) cells revealed well-known NCAM1- and FCGR3A- expressing subsets and an interesting keratin ( KRT81 and KRT86 )-expressing subset potentially enriched in tumor tissues


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:a7d944159521e9c3f0f8
claim_id: claim:a7d944159521e9c3f0f8
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
We identified resident memory T (TRM) cells highly expressing tissue-residency markers (i.e., ITGAE and CD69 ) and specifically expressing CXCL13 among all cell types

summary:
In Homo sapiens, resident memory T cells highly express the tissue-residency markers ITGAE and CD69 and specifically express CXCL13.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:e915928e38f837bdb8bd
claim_id: claim:e915928e38f837bdb8bd
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
We found cluster 6 highly expressed FGFBP2 and CX3CR1 , and was substantially enriched in peripheral blood

summary:
In Homo sapiens, CD8-positive effector memory T cells re-expressing CD45RA (cluster 6) highly express FGFBP2 and CX3CR1.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:c5be5bff892213a38582
claim_id: claim:c5be5bff892213a38582
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
Two exhausted T cell clusters (clusters 7 and 8) were identified on the basis of elevated expression of genes including LAG3 , TIGIT , PDCD1 , HAVCR2 , and CTLA4

summary:
In Homo sapiens, exhausted T cells are identified by elevated expression of LAG3, TIGIT, PDCD1, HAVCR2, and CTLA4.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:f4f0933db01f0e684945
claim_id: claim:f4f0933db01f0e684945
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
Interestingly, we found that cluster 8 had the highest expression of LAG3 and specifically expressed the immunosuppressive cytokine IL10

summary:
In Homo sapiens, exhausted T cell cluster 8 has the highest expression of LAG3 and specifically expresses IL10.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:9714ed3e34bd03199eaa
claim_id: claim:9714ed3e34bd03199eaa
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
Clusters 1, 2, 3, and 4 were predominantly present in the blood with high expression of CD14 but lack of FCGR3A expression, thus representing circulating classical monocytes.

summary:
In Homo sapiens, circulating classical monocytes show high expression of CD14 but lack FCGR3A expression.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:e1c7cbc183001e6970ea
claim_id: claim:e1c7cbc183001e6970ea
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
Cluster 5 represented circulating non-classical monocytes with high expression of FCGR3A but lack of CD14 expression

summary:
In Homo sapiens, circulating non-classical monocytes show high expression of FCGR3A but lack CD14 expression.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:3345edbe7ebd2ec46bd7
claim_id: claim:3345edbe7ebd2ec46bd7
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, plasmacytoid dendritic cells are characterized by specific expression of JCHAIN.
span_literal:
We identified three dendritic cell (DC) clusters: plasmacytoid DC (pDC) and types 1 and 2 conventional DC (cDC1 and cDC2), characterized by specific expression of JCHAIN , CLEC9A , and CD1C , respectively


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:c9292b7110bec9deda67
claim_id: claim:c9292b7110bec9deda67
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
We identified three dendritic cell (DC) clusters: plasmacytoid DC (pDC) and types 1 and 2 conventional DC (cDC1 and cDC2), characterized by specific expression of JCHAIN , CLEC9A , and CD1C , respectively

summary:
In Homo sapiens, type 1 conventional dendritic cells are characterized by specific expression of CLEC9A.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:881ce923781b2e687735
claim_id: claim:881ce923781b2e687735
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal:
We identified three dendritic cell (DC) clusters: plasmacytoid DC (pDC) and types 1 and 2 conventional DC (cDC1 and cDC2), characterized by specific expression of JCHAIN , CLEC9A , and CD1C , respectively

summary:
In Homo sapiens, type 2 conventional dendritic cells are characterized by specific expression of CD1C.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:6cf83490b17f7ad9e84a
claim_id: claim:6cf83490b17f7ad9e84a
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, mast cells are characterized by specific expression of TPSAB1.
span_literal:
We found mast cells, which were characterized by specific expression of TPSAB1 , potentially enriched in the tumor core


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:52001eb560c240ba592b
claim_id: claim:52001eb560c240ba592b
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, macrophages are identified based on high expression of CD163 and C1QC.
span_literal:
we identified nine macrophage clusters (clusters 6–8 and 11–16) based on the high expression of CD163 and C1QC


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:02c782c630b17e2120be
claim_id: claim:02c782c630b17e2120be
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, MHC-II tumor-associated macrophages highly express HLA-DRB5, APOE, and APOC1.
span_literal:
MHC-II TAM (cluster 14) highly expressed HLA-DRB5 , APOE , and APOC1 , and was more enriched in tumor core than in tumor-normal interface.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:4f384ecaf341d00d5c93
claim_id: claim:4f384ecaf341d00d5c93
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
span_literal: FN1 + TAM highly expressed fibronectin 1 ( FN1 ) and scavenger receptor MARCO
summary:
In Homo sapiens, FN1-positive tumor-associated macrophages highly express fibronectin 1 (FN1) and MARCO.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:9c27d0845f99037fdda7
claim_id: claim:9c27d0845f99037fdda7
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, SPP1-positive tumor-associated macrophages express GPNMB.
span_literal:
We identified an SPP1 + TAM cluster expressing GPNMB that showed a high similarity to the GPNMB + TAM identified by the previous study


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:6e683f9a90a407d54f6b
claim_id: claim:6e683f9a90a407d54f6b
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, SPP1-positive tumor-associated macrophages express SPP1 and APOC4-APOC2.
span_literal:
Besides expressing SPP1 , we found that SPP1 + TAM also expressed APOC4-APOC2 , a gene not reported by previous RCC studies


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:a0a492aafb43b2e7731d
claim_id: claim:a0a492aafb43b2e7731d
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, SPP1-positive tumor-associated macrophages express TREM2.
span_literal:
and TREM2 ( Figure 5 C), which has been reported in various biological and pathological processes such as obesity and cancer.


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:250102ab850ee5992661
claim_id: claim:250102ab850ee5992661
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, tissue-resident macrophage 2 highly expresses IL1B and AREG.
span_literal:
TR Mac.2 was enriched at the interface ( Figures 5 B and S5 D) and highly expressed interleukin IL1B and the epidermal growth factor receptor ligand AREG


claim_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4:claim:f9a15e9c2b0de24986bc
claim_id: claim:f9a15e9c2b0de24986bc
paper_key: hca:0213_10.1016_j.ccell.2022.11.001_63fadcc3b4
summary: In Homo sapiens, tissue-resident macrophage 3 shows high expression of SEPP1 and MRC1.
span_literal:
TR Mac.3 showed high expression of SEPP1 and MRC1 , and was extremely enriched in normal adrenal gland


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:10d1a3dfe9640c56e26f
claim_id: claim:10d1a3dfe9640c56e26f
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
Our cross-tissue analysis distinguished three distinct subsets of monocytes, characterized by a differential distribution between prenatal bone marrow and peripheral tissues and by the expression of CXCR4, CCR2, or IL1B

summary:
In Homo sapiens, three distinct subsets of monocytes are characterized by the expression of CXCR4, CCR2, or IL1B.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:7800c6e31fe2caa26654
claim_id: claim:7800c6e31fe2caa26654
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
LYVE1 hi ”, “iron-recycling”, “MHC class II hi ”, “Kupffer-like” (18), “microglia-like TREM2 hi ” ( 19 ), “osteoclasts” ( 11 , 20 ), and “proliferating” macrophages. Assigning proliferating cells to the other identified subsets, we observed a high fraction of proliferating macrophages in the yolk sac and within the LYVE1 hi

summary:
In Homo sapiens, LYVE1 hi macrophages are characterized by high expression of LYVE1, and microglia-like TREM2 hi macrophages are characterized by high expression of TREM2.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:5bb6b69a6471bef4ace1
claim_id: claim:5bb6b69a6471bef4ace1
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
Cross-tissue integration enabled the identification of cell populations that were too rare to be resolved through analysis of datasets from individual tissues, such as AXL and SIGLEC6- expressing dendritic cells (AS DC)

summary:
In Homo sapiens, AXL and SIGLEC6-expressing dendritic cells (AS DC) are marked by expression of AXL and SIGLEC6.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:823f7f5d41b372a2ba3d
claim_id: claim:823f7f5d41b372a2ba3d
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
These putative B1 cells had the highest expression of CD5, CD27 , and SPN (CD43), consistent with previously reported markers ( 39 – 41 ), as well as CCR10, a highly-specific marker that was expressed in a subset of B1 cells

summary:
In Homo sapiens, putative B1 cells have the highest expression of CD5, CD27, SPN (CD43), and CCR10 among non-progenitor B cells.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:fe4d9199ce8c97083609
claim_id: claim:fe4d9199ce8c97083609
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
RORC- and CCR6- expressing type 3 innate T cells; EOMES- and TBX21- expressing type 1 innate T cells; and PDCD1 - expressing and thymus-restricted CD8AA cells

summary:
In Homo sapiens, type 3 innate T cells express RORC and CCR6, type 1 innate T cells express EOMES and TBX21, and CD8AA cells express PDCD1.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:eafdc1cb289f5c12dcdd
claim_id: claim:eafdc1cb289f5c12dcdd
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
Cells simultaneously expressing VPREB1, RAG1 , and/or DNTT were present in the prenatal gut, spleen, and thymus ( Fig. 4B and fig. S21, A to C ), consistent with B cell progenitors.

summary:
In Homo sapiens, B cell progenitors are identified by simultaneous expression of VPREB1, RAG1, and/or DNTT in prenatal gut, spleen, and thymus.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:458568a97c7cbeeca1b0
claim_id: claim:458568a97c7cbeeca1b0
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal: B1 cells expressed lower levels of IGHD and higher levels of IGHM compared to mature B cells
summary:
In Homo sapiens, B1 cells express lower levels of IGHD and higher levels of IGHM compared to mature B cells.


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:ea64fbe35c5ac8d52de3
claim_id: claim:ea64fbe35c5ac8d52de3
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
summary: In Homo sapiens, cycling cells are indicated by non-zero MKI67 expression among B cell subsets.
span_literal:
we calculated the percentage of cycling cells (as indicated by non-zero MKI67 expression) within immature B, mature B, B1, and plasma B cells, respectively


claim_key: hca:0214_10.1126_science.abo0510_808a3cb920:claim:7a4fc4ad378f5c049f95
claim_id: claim:7a4fc4ad378f5c049f95
paper_key: hca:0214_10.1126_science.abo0510_808a3cb920
span_literal:
Specifically, early mast cells in yolk sac, liver, and skin displayed a similar proinflammatory phenotype characterized by expression of TNF and NF-κB subunits, as well as chemokines associated with endothelial cell recruitment ( CXCL3 , CXCL2 , and CXCL8 )

summary:
In Homo sapiens, early mast cells in yolk sac, liver, and skin express TNF, CXCL3, CXCL2, and CXCL8.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:75cbaca6d99bcf9e05c2
claim_id: claim:75cbaca6d99bcf9e05c2
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
summary: In Homo sapiens, T cells are identified by expression of CD3E, CD8A, CD4, and IL7R (CD127).
span_literal:
expressions of canonical markers for T cells ( CD3E , CD8A , CD4 , and IL7R or CD127), B cells ( CD19 and MS4A1 ), myeloid cells ( CD14 and FCGR3A or CD16), and natural killer (NK) cells ( KLRD1 and NKG7 )


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:c24aa1de8b7207da9a3c
claim_id: claim:c24aa1de8b7207da9a3c
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal: The first pattern was the discovery of a naïve CCR7 + SELL + TCF7 + being seen in CD8_4
summary:
In Homo sapiens, the naive CD8+ T-cell subcluster CD8_4 is marked by expression of CCR7, SELL, and TCF7.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:cb548a6adc881e79590a
claim_id: claim:cb548a6adc881e79590a
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
summary: In Homo sapiens, effector CD8+ T-cell subclusters CD8_1 and CD8_0 express IFNG and PRF1.
span_literal:
Looking for effector CD8 + T cells, we next observed two populations of IFNG + PRF1 + T cells, principally in CD8_1 and CD8_0


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:d0b96a22aee7d228bc2c
claim_id: claim:d0b96a22aee7d228bc2c
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal: The latter also expressed immune checkpoints, such as CTLA4 , HAVCR2 , PDCD1 , and TIGIT
summary:
In Homo sapiens, the CD8+ T-cell subcluster CD8_0 expresses immune checkpoint genes CTLA4, HAVCR2, PDCD1, and TIGIT.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:016bd6fb7dca8c0642b2
claim_id: claim:016bd6fb7dca8c0642b2
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
CD8_6 exclusively expressed a number of proliferation markers, such as CDK1 , MKI67 , STMN1 , and TOP2A

summary:
In Homo sapiens, the proliferative CD8+ T-cell subcluster CD8_6 exclusively expresses proliferation markers CDK1, MKI67, STMN1, and TOP2A.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:b118c4e0a1f5116dc95d
claim_id: claim:b118c4e0a1f5116dc95d
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal: The first pattern that emerged was a naive CCR7 + SELL + TCF7 + being seen in CD4_1 and CD4_3
summary:
In Homo sapiens, naive CD4+ T-cell subclusters CD4_1 and CD4_3 are marked by expression of CCR7, SELL, and TCF7.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:f99980ce213f64d98550
claim_id: claim:f99980ce213f64d98550
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal: The first pattern that emerged was a naive CCR7 + SELL + TCF7 + being seen in CD4_1 and CD4_3
summary:
In Homo sapiens, naive CD4+ T-cell subclusters CD4_3 and CD4_1 are marked by expression of CCR7, SELL, and TCF7.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:c0a2a5f4b8a8e6e32abb
claim_id: claim:c0a2a5f4b8a8e6e32abb
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
Within the tumor-infiltrating CD4_4 cluster, we observed increased expression of the Th1 driver TBX21 (T-bet), activation marker LAG3 and NR4A2 and cytokine expression

summary:
In Homo sapiens, the tumor-infiltrating CD4+ T-cell subcluster CD4_4 shows increased expression of TBX21, LAG3, and NR4A2.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:79454f6c3508db79b95e
claim_id: claim:79454f6c3508db79b95e
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
Both CD4_5 and CD4_7 had expression of regulatory T (Tregs) cell markers (Fig. 4c ), with higher levels of FOXP3 , IL2RA (CD25), CTLA4 , and TNFRSF18 (GITR) in the tumor-predominant CD4_5

summary:
In Homo sapiens, the tumor-predominant regulatory T-cell subcluster CD4_5 has higher levels of FOXP3, IL2RA (CD25), CTLA4, and TNFRSF18 (GITR).


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:470f78dcd80ed643a4a7
claim_id: claim:470f78dcd80ed643a4a7
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
Both CD4_5 and CD4_7 had expression of regulatory T (Tregs) cell markers (Fig. 4c ), with higher levels of FOXP3 , IL2RA (CD25), CTLA4 , and TNFRSF18 (GITR) in the tumor-predominant CD4_5

summary:
In Homo sapiens, the regulatory T-cell subcluster CD4_7 expresses regulatory T-cell markers FOXP3, IL2RA (CD25), CTLA4, and TNFRSF18 (GITR).


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:531e82213855c83c7b1d
claim_id: claim:531e82213855c83c7b1d
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal: The tumor-infiltrating Tregs, CD4_5, had high levels of CTLA4 , GITR ( TNFRSF18 ) and TIGIT
summary:
In Homo sapiens, the tumor-infiltrating regulatory T-cell subcluster CD4_5 has high levels of CTLA4, TNFRSF18 (GITR), and TIGIT.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:f41a6333749239621c32
claim_id: claim:f41a6333749239621c32
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
In addition, CD4_5 had the highly-specific expression CCR8 and LAYN , corresponding to previous reports

summary:
In Homo sapiens, the tumor-infiltrating regulatory T-cell subcluster CD4_5 has highly specific expression of CCR8 and LAYN.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:d03f2cd28f0a31394c2a
claim_id: claim:d03f2cd28f0a31394c2a
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
summary: In Homo sapiens, the CD4+ T-cell subcluster CD4_6 has increased expression of OSM, AREG, and SOCS3.
span_literal:
The CD4_6 cluster had increased expression of the IL-6 cytokine, OSM6 , and AREG and SOCS3 , downstream of interleukin signaling


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:820bcea12a70eb58fa6b
claim_id: claim:820bcea12a70eb58fa6b
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
macrophage subclusters (0, 3, 7, 13, and 14) identified using markers such as CD1C , CLEC10A (CD301), FCER1A , and MSR1

summary:
In Homo sapiens, macrophage subclusters are identified using markers CD1C, CLEC10A (CD301), FCER1A, and MSR1.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:cd79f9eea85be106a1ba
claim_id: claim:cd79f9eea85be106a1ba
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
the CD88 high ( C5AR1 ) CD54 + ( ICAM1 ) TAM_1 expressed increased levels of chemokines and cytokines, like CCL3 , CCL4 , CXCL2 , and IL10

summary:
In Homo sapiens, tumor-associated macrophage 1 (TAM_1) expresses C5AR1 (CD88), ICAM1 (CD54), CCL3, CCL4, CXCL2, and IL10.


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:9a76cb5441da643f3661
claim_id: claim:9a76cb5441da643f3661
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
CD64 high ( FCGR1A ) CD16 high ( FCGR3A ) TAM_2 subcluster expressed the apolipoprotein gene APOE , lysosomal lipase ( LIPA ), and ferroportin ( SLC40A1 )

summary:
In Homo sapiens, tumor-associated macrophage 2 (TAM_2) expresses FCGR1A (CD64), FCGR3A (CD16), APOE, LIPA, and SLC40A1 (ferroportin).


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:c721b59d31c6b5c6cb70
claim_id: claim:c721b59d31c6b5c6cb70
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
CD1C high CD86 + TAM_3 had high levels of IL1R2 and Langerhin ( CD207 ), a marker of the skin-resident Langerhans cells

summary:
In Homo sapiens, tumor-associated macrophage 3 (TAM_3) expresses high levels of CD1C, CD86, IL1R2, and CD207 (Langerin).


claim_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea:claim:916c86bd9ae5530f15ea
claim_id: claim:916c86bd9ae5530f15ea
paper_key: hca:0215_10.1038_s42003-020-01625-6_cc9e14f4ea
span_literal:
The pM subcluster had the highest level of the cell adhesion molecules CLEC10A , SELL (CD62L), and ITGB7 , which can dimerize with ITGA4 (CD49d) or ITGAE (CD103)

summary:
In Homo sapiens, the peripheral macrophage subcluster has the highest levels of CLEC10A, SELL (CD62L), and ITGB7.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:6a76ed63f575daff258c
claim_id: claim:6a76ed63f575daff258c
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
Epithelial cells are classified into four main groups based on their marker expression: (1) SOX9 populations, enriched in the proliferative phase and expressing genes characteristic of rising estrogen levels ( MMP7 , ESR1 ); (2) ciliated cells ( PIFO , TPPP3 ); (3) lumenal cells ( LGR5 ); and (4) glandular cells ( SCGB2A2 )

summary:
In Homo sapiens endometrium, SOX9-positive epithelial cells express MMP7 and ESR1, ciliated cells express PIFO and TPPP3, lumenal epithelial cells express LGR5, and glandular epithelial cells express SCGB2A2.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:21591f24804c500c018c
claim_id: claim:21591f24804c500c018c
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
A fraction of the glandular epithelial cells express molecules characteristic of uterine milk in the secretory stage ( PAEP , CXCL8 ).

summary:
In Homo sapiens endometrium, a fraction of glandular epithelial cells express PAEP and CXCL8 during the secretory stage.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:3c04456fabf3a47c0625
claim_id: claim:3c04456fabf3a47c0625
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
summary: In Homo sapiens endometrium, SOX9-positive LGR5-positive epithelial cells express KRT17 and WNT7A.
span_literal:
we can now resolve three clusters within the SOX9 population: (1) SOX9 + LGR5 + cells, expressing KRT17 and WNT7A ; (2) SOX9 + LGR5 − cells, expressing IHH ; and (3) proliferative SOX9 + cells, including both LGR5 + and LGR5 − cycling cells (that is, cells in G2M/S phase).


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:667f6503e46c92cf4a68
claim_id: claim:667f6503e46c92cf4a68
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
in addition to the FOXJ1 , PIFO , TP73 ciliated population, we define a distinct subset of preciliated cells that express MUC12 , HES6 and cell cycle genes ( CDC20B , CCNO )

summary:
In Homo sapiens endometrium, ciliated cells express FOXJ1, PIFO and TP73, while preciliated cells express MUC12, HES6, CDC20B and CCNO.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:214f8fabc5903cae0c73
claim_id: claim:214f8fabc5903cae0c73
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
There is enriched expression of both COX1 (encoded by PTGS1 ) and KRT5 in the lumenal epithelium and SCGB2A2 in the glandular epithelium.

summary:
In Homo sapiens endometrium, lumenal epithelial cells show enriched expression of PTGS1 and KRT5, while glandular epithelial cells show enriched expression of SCGB2A2.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:0d71f3fda6bb649bd2be
claim_id: claim:0d71f3fda6bb649bd2be
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
There is enriched expression of both COX1 (encoded by PTGS1 ) and KRT5 in the lumenal epithelium and SCGB2A2 in the glandular epithelium.

summary:
In Homo sapiens endometrium, glandular epithelial cells show enriched expression of SCGB2A2 compared to lumenal epithelial cells.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:206d1d8239cc79c6e7da
claim_id: claim:206d1d8239cc79c6e7da
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
Validation of KRT5, COX1 (marker of lumenal cells) and SCGB2A2 (marker of glandular population) with IHC in endometrial tissue (proliferative and secretory phases).

summary:
In Homo sapiens endometrium, KRT5 and COX1 are markers of lumenal epithelial cells and SCGB2A2 is a marker of the glandular epithelial cell population.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:f58c21d3548b9a3b1c02
claim_id: claim:f58c21d3548b9a3b1c02
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
summary: In Homo sapiens endometrial organoids, proliferative cells express TOP2A, PCNA and ESR1.
span_literal:
Before hormonal treatment, the majority of cells within the organoids are proliferative (expressing TOP2A , PCNA ) and all express the estrogen receptor ESR1


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:ec1cea91e5f67119df8c
claim_id: claim:ec1cea91e5f67119df8c
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal:
an estrogen-induced population expressing the progesterone receptor ( PGR ), a target gene of estrogen

summary:
In Homo sapiens endometrial organoids, the estrogen-induced cell population expresses the progesterone receptor PGR.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:a4661cca9d5daa39155a
claim_id: claim:a4661cca9d5daa39155a
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
span_literal: Markers of secreted products ( PAEP , DEFB1 ) and glands ( SCGB2A2 ) are both seen.
summary:
In Homo sapiens endometrial organoids, secretory cells express PAEP and DEFB1, and glandular markers include SCGB2A2.


claim_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c:claim:4cf428ae682d1d5e0441
claim_id: claim:4cf428ae682d1d5e0441
paper_key: hca:0216_10.1038_s41588-021-00972-2_b07f96cf7c
summary: In Homo sapiens endometrial organoids, ciliated cells express the typical markers FOXJ1 and TP73.
span_literal:
Ciliated cells express typical markers ( FOXJ1 , TP73 ) and closely match their in vivo counterparts.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:76d715fc713168141693
claim_id: claim:76d715fc713168141693
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
summary: In Homo sapiens, excitatory neurons are marked by SNAP25 and SLC17A7.
span_literal:
excitatory neurons (as marked by SNAP25, SLC17A7 ), inhibitory neurons ( SNAP25, GAD1 ), REELIN-positive neurons ( SNAP25, RELN ), astrocytes ( GJA1, GFAP ), microglia and macrophages ( CD74, P2RY12 ), endothelial cells and pericytes ( CLDN5, NOTCH3 ), oligodendrocytes ( PLP1, CNP ), their precursor cells ( PDGFRA, PTPRZ1 ) and immune cells ( HLA-A, PTPRC )


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:59e2afa02306f03d1da7
claim_id: claim:59e2afa02306f03d1da7
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
summary: In Homo sapiens, oligodendrocyte clusters are positive for myelin genes such as PLP1, MBP, and MAG.
span_literal:
The cluster analysis revealed six oligodendrocyte clusters (positive for myelin genes such as PLP1, MBP, MAG ), two OPC clusters (positive for PDGFRA, CSPG4 and BCAN ) and three committed oligodendrocyte precursor (COP) cell clusters (positive for GPR17, GPC5 or GAP43 ), confirming that oligodendroglia are heterogeneous in the healthy adult human CNS


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:a40af575ad2044981549
claim_id: claim:a40af575ad2044981549
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
The cluster analysis revealed six oligodendrocyte clusters (positive for myelin genes such as PLP1, MBP, MAG ), two OPC clusters (positive for PDGFRA, CSPG4 and BCAN ) and three committed oligodendrocyte precursor (COP) cell clusters (positive for GPR17, GPC5 or GAP43 ), confirming that oligodendroglia are heterogeneous in the healthy adult human CNS

summary:
In Homo sapiens, committed oligodendrocyte precursor cell clusters are positive for GPR17, GPC5, or GAP43.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:4e85f7a4761a4d3f6e31
claim_id: claim:4e85f7a4761a4d3f6e31
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal: They almost mutually exclusively express the markers OPALIN , RBFOX1 and SPARC respectively
summary:
In Homo sapiens, the oligodendrocyte cluster Oligo_A expresses the marker OPALIN, Oligo_B-E expresses RBFOX1, and Oligo_F expresses SPARC.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:79527abf878945752e86
claim_id: claim:79527abf878945752e86
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Oligo_B-E ( RBFOX1 +) are subclustered based on the expression of additional genes: Oligo_B: AFF3 + LGALS1 - FMN1 -; Oligo_C: FMN1 ; Oligo_D: LGALS1 + FMN1 - SPARC -; Oligo_E: HHIP + OPALIN - AFF3 -

summary:
In Homo sapiens, oligodendrocyte Oligo_B is positive for RBFOX1 and AFF3 but negative for LGALS1 and FMN1.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:0133b9f462ac683b6678
claim_id: claim:0133b9f462ac683b6678
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Oligo_B-E ( RBFOX1 +) are subclustered based on the expression of additional genes: Oligo_B: AFF3 + LGALS1 - FMN1 -; Oligo_C: FMN1 ; Oligo_D: LGALS1 + FMN1 - SPARC -; Oligo_E: HHIP + OPALIN - AFF3 -

summary:
In Homo sapiens, oligodendrocyte Oligo_D is positive for RBFOX1 and LGALS1 but negative for FMN1 and SPARC.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:d2b8947d0f7f4da2b71d
claim_id: claim:d2b8947d0f7f4da2b71d
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
summary:
In Homo sapiens, oligodendrocyte Oligo_E is positive for RBFOX1 and HHIP but negative for OPALIN and AFF3.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:82d8ccf8809ef2a03556
claim_id: claim:82d8ccf8809ef2a03556
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Oligo_A and F are RBFOX1 -negative and strikingly different; Oligo_A expresses OPALIN, PLXDC2, LAMA2 and PALM2 , and Oligo_F expresses SPARC, DHCR24, TUBA1A, TUBB2B, PMP2 and HCN2

summary:
In Homo sapiens, oligodendrocyte Oligo_A is RBFOX1-negative and expresses OPALIN, PLXDC2, LAMA2, and PALM2.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:7bdf5a43479fbf82372e
claim_id: claim:7bdf5a43479fbf82372e
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Oligo_A and F are RBFOX1 -negative and strikingly different; Oligo_A expresses OPALIN, PLXDC2, LAMA2 and PALM2 , and Oligo_F expresses SPARC, DHCR24, TUBA1A, TUBB2B, PMP2 and HCN2

summary:
In Homo sapiens, oligodendrocyte Oligo_F is RBFOX1-negative and expresses SPARC, DHCR24, TUBA1A, TUBB2B, PMP2, and HCN2.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:d33155b619cea3e5375d
claim_id: claim:d33155b619cea3e5375d
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal: OPC_A expresses the Paired Box 3 gene PAX3 and the cation transporter gene SLC22A3
summary:
In Homo sapiens, oligodendrocyte precursor cell OPC_A expresses the Paired Box 3 gene PAX3 and the cation transporter gene SLC22A3.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:d32e070e7ae7c0661be1
claim_id: claim:d32e070e7ae7c0661be1
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal: Oligo_F expresses the novel oligodendrocyte marker SPARC and is mostly found in CSC
summary:
In Homo sapiens, oligodendrocyte Oligo_F expresses the novel oligodendrocyte marker SPARC and is mostly found in the cervical spinal cord.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:d13975f09aa5fbf37cf3
claim_id: claim:d13975f09aa5fbf37cf3
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
summary: In Homo sapiens, ependymal cells (AS_9_ep) express motile cilia genes CFAP43, SPAG17, and DNAH6.
span_literal:
Ependymal cells (AS_9_ep) express motile cilia genes ( CFAP43, SPAG17, DNAH6 ) in keeping with their function in promoting cerebrospinal fluid flow


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:98b7fb7ccba5edee37a6
claim_id: claim:98b7fb7ccba5edee37a6
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Microglia_1 ( RASGEF1C, AC008691.1 , TLN2 ) express markers for a homeostatic phenotype ( P2RY13 and CX3CR1 )

summary:
In Homo sapiens, Microglia_1 expresses RASGEF1C, AC008691.1, TLN2, and homeostatic markers P2RY13 and CX3CR1.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:4c415117b141985915ed
claim_id: claim:4c415117b141985915ed
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Conversely, Microglia_2 (GPNMB) and Microglia_4 ( ACSL1 , CXCR4 ) appear more activated, expressing the phagocytotic markers CD68 and TREM2

summary:
In Homo sapiens, Microglia_2 is marked by GPNMB and expresses the phagocytic markers CD68 and TREM2.


claim_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163:claim:24510ffeff5cb88b0f89
claim_id: claim:24510ffeff5cb88b0f89
paper_key: hca:0217_10.1186_s40478-023-01568-z_30cfefc163
span_literal:
Conversely, Microglia_2 (GPNMB) and Microglia_4 ( ACSL1 , CXCR4 ) appear more activated, expressing the phagocytotic markers CD68 and TREM2

summary:
In Homo sapiens, Microglia_4 is marked by ACSL1 and CXCR4 and expresses the phagocytic markers CD68 and TREM2.


claim_key: hca:0219_10.1016_j.cell.2020.06.026_35457f0d2b:claim:b352383c1217a2f01014
claim_id: claim:b352383c1217a2f01014
paper_key: hca:0219_10.1016_j.cell.2020.06.026_35457f0d2b
span_literal:
Brain CD4 + T cells exhibited elevated expression of residency markers such as CD69 and chemotactic receptors, and pathway analysis consistent with adaption to the tissue environment

summary:
In Homo sapiens, brain-resident CD4 T cells exhibit elevated expression of the residency marker CD69 compared to circulating CD4 T cells.


claim_key: hca:0219_10.1016_j.cell.2020.06.026_35457f0d2b:claim:5920422dfee78f67b2a0
claim_id: claim:5920422dfee78f67b2a0
paper_key: hca:0219_10.1016_j.cell.2020.06.026_35457f0d2b
span_literal:
Conventional brain CD4 T cells separated from their blood and meningeal counterparts ( Figures 2 E and 2F), with elevated expression of activation markers and the CD69 residency marker

summary:
In Homo sapiens, conventional brain CD4 T cells show elevated expression of the CD69 residency marker compared to blood and meningeal counterparts.


claim_key: hca:0219_10.1016_j.cell.2020.06.026_35457f0d2b:claim:ce3cabf2563f47198d5d
claim_id: claim:ce3cabf2563f47198d5d
paper_key: hca:0219_10.1016_j.cell.2020.06.026_35457f0d2b
span_literal:
tSNE dimensionality reduction is used for cluster display, with lineage marker expression indicated by color for CD3D , CD4 , IL7R , IL2RA , FOXP3 , CD44 , SELL , AREG , CD69 , KLRG1 and NR4A1 .

summary:
In Homo sapiens, CD4 T cell clusters from brain and peripheral blood mononuclear cells are characterized by lineage markers CD3D, CD4, IL7R, IL2RA, FOXP3, CD44, SELL, AREG, CD69, KLRG1, and NR4A1.


claim_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85:claim:3ded3d862e8f63574911
claim_id: claim:3ded3d862e8f63574911
paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
summary: In Homo sapiens hepatoblastoma, CYP3A4, ALB, APOC3, and HPGD are canonical markers for hepatocytes.
span_literal:
eleven distinct cell types were classified (Fig. 3a ) with enriched pathways and canonical markers, such as CYP3A4 , ALB , APOC3 , and HPGD for hepatocytes, FLT1 for endothelial cells, COL3A1 and COL6A3 for hepatic stellate cells, CD68 and CD163 for Kupffer cells, and PTPRC for immune cells


claim_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85:claim:93db2b9d722f8289b322
claim_id: claim:93db2b9d722f8289b322
paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
summary: In Homo sapiens hepatoblastoma, HPGD identifies hepatocytes.
span_literal:
DLK1 shows tumor, HPGD identifies hepatocytes, FLT1 indicates epithelial cells, COL6A3 represents hepatic stellate cells, CD163 marks Kupffer cells, and PTPRC indicates immune cells.


claim_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85:claim:1ad22adaa0d336f6affe
claim_id: claim:1ad22adaa0d336f6affe
paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
span_literal: GPC3 and HMGA2 are upregulated in all tumor clusters compared with background liver.
summary:
In Homo sapiens hepatoblastoma, GPC3 and HMGA2 are upregulated in all tumor cell clusters compared with background liver.


claim_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85:claim:a201a36c3ce553d186f3
claim_id: claim:a201a36c3ce553d186f3
paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
span_literal:
Tr2 has high expression of FANCD2 , RBL1 , EZH2 , and numerous WNT pathway genes, Tr4/1 has elevated FLT1 , CALCRL , VIM , and VCAN 30 , Tr5 has high PTCH1 , LEF1 , and CD44 expression, and Tr3 has elevated EGFR , CYP3A5 , and IGFBP2 among many other defining expression patterns

summary:
In Homo sapiens hepatoblastoma, tumor cell cluster Tr2 has high expression of FANCD2, RBL1, and EZH2.


claim_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85:claim:697d1f85d6e890dcc103
claim_id: claim:697d1f85d6e890dcc103
paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
span_literal:
increased expression of GPC3 , DLK1 , and HMGA2 are genes that define the driving pathways of HB, and these genes have also been previously reported as cancer stem cell markers in HB

summary:
In Homo sapiens hepatoblastoma, GPC3, DLK1, and HMGA2 have been reported as cancer stem cell markers.


claim_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85:claim:d4d3663b0d648f24eed6
claim_id: claim:d4d3663b0d648f24eed6
paper_key: hca:0220_10.1038_s42003-021-02562-8_904d08be85
span_literal:
The gene signature of this cell cluster includes HMGA2 , EZH2 , and FANCD2 , as well as robust increase in cell cycle.

summary:
In Homo sapiens hepatoblastoma, the gene signature of tumor cell cluster Tr2 includes HMGA2, EZH2, and FANCD2.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:2c04e81c6214dd002408
claim_id: claim:2c04e81c6214dd002408
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
The glandular component of undifferentiated assembloids harboured actively dividing EpC (EpS1; n = 198) as well as EpC-expressing marker genes of E2-responsive proliferative phase endometrium (EpS2; n = 692), including PGR and CPM

summary:
In Homo sapiens, estradiol-responsive proliferative phase epithelial cells (epithelial subpopulation 2) express progesterone receptor (PGR) and carboxypeptidase M (CPM) as marker genes.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:7716e1c46e9f55fb708b
claim_id: claim:7716e1c46e9f55fb708b
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
EpS3 (n = 29) consisted of ciliated EpC, expressing an abundance of genes involved in cilium assembly and organization, including DNAI1 and TUBA4B

summary:
In Homo sapiens, ciliated epithelial cells (epithelial subpopulation 3) express DNAI1 and TUBA4B as marker genes involved in cilium assembly and organization.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:af4f8025750f7d62629f
claim_id: claim:af4f8025750f7d62629f
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
However, while expression of EpS4 marker genes, including SOD2 , MAOA, and PTGS1 , generally peaks during the midluteal window of implantation, EpS5 genes tend to persist or peak during the late-luteal phase

summary:
In Homo sapiens, differentiated epithelial cells (epithelial subpopulation 4) express SOD2, MAOA, and PTGS1 as marker genes peaking during the midluteal window of implantation.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:64ca3d7e9fe3a23c2b48
claim_id: claim:64ca3d7e9fe3a23c2b48
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
Notably, several canonical implantation factors secreted by this subpopulation are also well-characterized SASP components, including dipeptidyl peptidase 4 ( DPP4; Kim et al., 2017 ), growth differentiation factor 15 ( GDF15; Basisty et al., 2020 ), and insulin-like growth factor binding protein 3 ( IGFBP3; Elzi et al., 2012 ).

summary:
In Homo sapiens, senescent epithelial cells (epithelial subpopulation 5) secrete dipeptidyl peptidase 4 (DPP4), growth differentiation factor 15 (GDF15), and insulin-like growth factor binding protein 3 (IGFBP3) as senescence-associated secretory phenotype components.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:582a44c6eddfc4cc3054
claim_id: claim:582a44c6eddfc4cc3054
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
A hallmark of this subset, termed ‘transitional population’ (TP; n = 472), is the induction of long non-coding RNAs involved in mesenchymal-epithelial and epithelial-mesenchymal transition (MET/EMT), such as NEAT1 (nuclear paraspeckle assembly transcript 1) and KCNQ1OT1 (KCNQ1 opposite strand/antisense transcript 1)

summary:
In Homo sapiens, the transitional population is marked by induction of NEAT1 (nuclear paraspeckle assembly transcript 1) and KCNQ1OT1 (KCNQ1 opposite strand/antisense transcript 1), long non-coding RNAs involved in mesenchymal-epithelial and epithelial-mesenchymal transition.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:9225da47ea666e0e0907
claim_id: claim:9225da47ea666e0e0907
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
The stromal fraction of undifferentiated assembloids consisted of actively dividing EnSC (stromal subpopulation 1 [SS1]; n = 434) and E2-responsive EnSC (SS2; n = 874) expressing proliferative phase marker genes, such as PGR , MMP11 , and CRABP2

summary:
In Homo sapiens, estradiol-responsive endometrial stromal cells (stromal subpopulation 2) express PGR, MMP11, and CRABP2 as proliferative phase marker genes.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:59dd9552996eebff6879
claim_id: claim:59dd9552996eebff6879
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
Pre-decidual cells in SS3 express HAND2 , a key decidual transcription factor ( Marinić et al., 2021 ), as well as previously identified genes encoding secreted factors, including VEGFA (vascular endothelial growth factor A), CRISPLD2 (a progesterone-dependent anti-inflammatory response gene coding cysteine-rich secretory protein LCCL domain containing 2) , IL15 (interleukin 15), and TIMP3 (TIMP metallopeptidase inhibitor 3)

summary:
In Homo sapiens, pre-decidual cells (stromal subpopulation 3) express HAND2, VEGFA (vascular endothelial growth factor A), CRISPLD2 (cysteine-rich secretory protein LCCL domain containing 2), IL15 (interleukin 15), and TIMP3 (TIMP metallopeptidase inhibitor 3) as marker genes.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:9d10e0c3bb2783ff994d
claim_id: claim:9d10e0c3bb2783ff994d
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
Novel candidate pre-decidual genes were also identified, such as DDIT4 (DNA damage-inducible transcript 4), encoding a stress response protein intimately involved in autophagy, stemness, and antioxidative defences

summary:
In Homo sapiens, pre-decidual cells express DDIT4 (DNA damage-inducible transcript 4) as a novel candidate marker gene.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:f0838aad6df2abfb2215
claim_id: claim:f0838aad6df2abfb2215
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
senescent decidual cells (SS5) express a multitude of SASP-related genes ( Figure 3—figure supplement 3 ), including matrix metallopeptidases (e.g. MMP3 , 7 , 9 , 10 , 11, and 14 ), insulin-like growth factor binding proteins (e.g. IGFBP1 , 3 , 6, and 7 ), growth factors (e.g. AREG , FGF2 , FGF7 , HGF , and VEGFA ) and growth factor receptors ( PDGFRA and PDGFRB ), cytokines (e.g. LIF , IL6 , IL1A , and IL11 ), chemokines (e.g. CXCL8 and CXCL1 ), and members of the TGF-β superfamily of proteins (e.g. GDF15 , INHBA , and BMP2 ).

summary:
In Homo sapiens, senescent decidual cells (stromal subpopulation 5) express senescence-associated secretory phenotype-related genes including MMP3, IGFBP1, AREG, FGF2, FGF7, HGF, VEGFA, PDGFRA, PDGFRB, LIF, IL6, IL1A, IL11, CXCL8, CXCL1, GDF15, INHBA, and BMP2.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:2511abb1fd6f31872beb
claim_id: claim:2511abb1fd6f31872beb
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
By contrast, decidual cells are characterized by expression of a unique network of secretory genes, some encoding ECM proteins (e.g. COL1A1 , COL3A1 , and LAMA4 ) and other known decidual markers (e.g. PRL , PROK1, and WNT4 ) as well as factors involved in uNK cell chemotaxis and activation (e.g. CCL2 , CXCL14 , and IL15 )

summary:
In Homo sapiens, decidual cells are characterized by expression of COL1A1, COL3A1, LAMA4, PRL, PROK1, WNT4, CCL2, CXCL14, and IL15.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:e2d6685c14ce667557dd
claim_id: claim:e2d6685c14ce667557dd
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
Importantly, we demonstrate that acute senescence in glandular EpC (EpS5) underpins production of an implantation-specific SASP, comprising canonical implantation factors and growth factors, such as amphiregulin ( AREG ) and epiregulin ( EREG ), implicated in transforming cytotrophoblasts into extravillous trophoblasts

summary:
In Homo sapiens, senescent glandular epithelial cells (epithelial subpopulation 5) produce amphiregulin (AREG) and epiregulin (EREG) as part of an implantation-specific senescence-associated secretory phenotype.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:cb662faa488bfbe9d28b
claim_id: claim:cb662faa488bfbe9d28b
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal: Further, differentiated EpC highly express SLC2A1 , encoding the major glucose transporter GLUT1.
summary:
In Homo sapiens, differentiated epithelial cells (epithelial subpopulation 4) highly express SLC2A1, encoding the major glucose transporter GLUT1.


claim_key: hca:0221_10.7554_elife.69603_ab573a325d:claim:30a9515b7c655a601c74
claim_id: claim:30a9515b7c655a601c74
paper_key: hca:0221_10.7554_elife.69603_ab573a325d
span_literal:
Activation of tumour suppressor pathways and upregulation of cyclin-dependent kinase inhibitors p16 INK4a (encoded by CDKN2A ) and p21 CIP1 ( CDKN1A ) lead to permanent cell cycle arrest, induction of survival genes, and production of a bioactive secretome, referred to as the senescence-associated secretory phenotype (SASP).

summary:
In Homo sapiens, senescent cells are marked by upregulation of cyclin-dependent kinase inhibitors p16INK4a (encoded by CDKN2A) and p21CIP1 (encoded by CDKN1A), leading to permanent cell cycle arrest.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:1dfe743c0c1bcb4ec7a6
claim_id: claim:1dfe743c0c1bcb4ec7a6
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
summary: In Homo sapiens, cycling CD8 T cells are marked by positive expression of MKI67 in colon tissue.
span_literal:
clusters 7 (cytotoxic effectors) and 8 (cycling T cells, MKI67 +) were nearly exclusive to +CPI colitis patients


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:181beab223cc225b7921
claim_id: claim:181beab223cc225b7921
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
CD8+ T cells from both clusters 7 and 8 showed high expression of cytotoxicity genes including GZMB ( Figure 2F ) and characteristic IFNγ response genes ( HLA-DRA and CD74 )

summary:
In Homo sapiens, colitis-associated CD8 T cells show high expression of the interferon-gamma response genes HLA-DRA and CD74.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:621a60cab344c26640f8
claim_id: claim:621a60cab344c26640f8
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
summary: In Homo sapiens, T helper 1 effector cells highly express GBP1, GBP5, STAT1, and CD74.
span_literal:
Cells in cluster 9 were Th1 effector cells that highly expressed a number of IFNγ inducible genes, including GBP1/5 , STAT1 and CD74


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:4aa8122486917a4b8d71
claim_id: claim:4aa8122486917a4b8d71
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
summary: In Homo sapiens, cycling conventional and regulatory T cells express MKI67.
span_literal:
Cluster 10 was comprised of MKI67 + cycling conventional and regulatory T cells, which we corroborated at the protein level


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:8995128247d68138c54a
claim_id: claim:8995128247d68138c54a
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
summary: In Homo sapiens, cytotoxic CD4-positive T cells are identified by expression of GZMA and GZMH.
span_literal:
A population of cytotoxic CD4+ T cells (cluster 8) was identified based on expression of GZMA and GZMH


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:692de3cfbdbad49f7de6
claim_id: claim:692de3cfbdbad49f7de6
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
Treg cluster 1 cells expressed several genes characteristic of Th1 cells, such as IL12RB2 (IL-12 receptor), CXCR3 and STAT1 , and this population was enriched in +CPI colitis patients

summary:
In Homo sapiens, regulatory T cell cluster 1 expresses IL12RB2 (interleukin-12 receptor beta 2), CXCR3, and STAT1.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:31616ffdca6f5eee2fbc
claim_id: claim:31616ffdca6f5eee2fbc
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
Cytotoxicity genes GZMB and GNLY (CD8+ T cells) and GZMA (CD4+ T cells) were the top differentially expressed genes in colitis-associated clusters

summary:
In Homo sapiens, colitis-associated CD8-positive T cells are marked by GZMB and GNLY as top differentially expressed cytotoxicity genes.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:2156b006421c782d5119
claim_id: claim:2156b006421c782d5119
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
Cytotoxicity genes GZMB and GNLY (CD8+ T cells) and GZMA (CD4+ T cells) were the top differentially expressed genes in colitis-associated clusters

summary:
In Homo sapiens, colitis-associated CD4-positive T cells are marked by GZMA as a top differentially expressed cytotoxicity gene.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:fe9f4d945fa32bf86723
claim_id: claim:fe9f4d945fa32bf86723
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
IFNγ and TNFα induced signatures were significantly upregulated in myeloid cells (cluster 5) compared to all other immune cell populations

summary:
In Homo sapiens colon, myeloid cells show significantly upregulated interferon-gamma and tumor necrosis factor alpha induced gene signatures compared to all other immune cell populations.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:3cf5e57479731a72490c
claim_id: claim:3cf5e57479731a72490c
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
The top differentially expressed genes in myeloid cells from +CPI colitis compared to control patients were IFNγ response genes including CXCL9 and CXCL10 , which encode chemokines that recruit CXCR3+ effector T cells to sites of inflammation

summary:
In Homo sapiens, myeloid cells in checkpoint inhibitor-induced colitis express CXCL9 and CXCL10 as top differentially expressed genes.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:a0e14ee176a5ce2d52d8
claim_id: claim:a0e14ee176a5ce2d52d8
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
The chemokine receptor genes CXCR3 and CXCR6 were upregulated in T cells from +CPI colitis patients compared to control subjects

summary:
In Homo sapiens, T cells in checkpoint inhibitor-induced colitis show upregulated expression of CXCR3 and CXCR6.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:530d7893069291936e59
claim_id: claim:530d7893069291936e59
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
The ITGAE chain was highly expressed by CD8+ T cells in colitis-associated clusters (#7, 8 and 5) and Trm clusters

summary:
In Homo sapiens, CD8-positive T cells in colitis-associated and tissue-resident memory clusters highly express ITGAE.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:80fc623f20e254ca81fd
claim_id: claim:80fc623f20e254ca81fd
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
the ITGA4 gene was elevated in CD4+ colitis-associated clusters (9 and 10) and Tregs (cluster 7), as well as a fraction of CD8+ cytotoxic effector cells (cluster 7)

summary:
In Homo sapiens, ITGA4 is elevated in colitis-associated CD4-positive T cells, regulatory T cells, and CD8-positive cytotoxic effector cells.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:8a6bf9639b7489915ad7
claim_id: claim:8a6bf9639b7489915ad7
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
Myeloid cells from +CPI colitis compared to healthy controls subjects overexpressed several cytokine genes related to intestinal homeostasis, including TNF , IL1B and OSM

summary:
In Homo sapiens, myeloid cells in checkpoint inhibitor-induced colitis overexpress TNF, IL1B, and OSM.


claim_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df:claim:2c48a01630e96833d996
claim_id: claim:2c48a01630e96833d996
paper_key: hca:0222_10.1016_j.cell.2020.06.001_353fb6b4df
span_literal:
CXCR6 was one of the top differentially expressed genes in colitis-associated CD4+ T cell populations

summary:
In Homo sapiens, CXCR6 is one of the top differentially expressed genes in colitis-associated CD4-positive T cell populations.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:d7459380ef491a395b73
claim_id: claim:d7459380ef491a395b73
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The intratelencephalic subclass that accounted for more than 80% of the excitatory neurons was predicted to span layers L2 to L6 and was marked by layer-specific markers (L2–3: PCDH8 ; L3–5: RORB ; L6: OPRK1 ; Fig. 1B ).

summary:
In Homo sapiens, layer 2-3 intratelencephalic excitatory neurons are marked by PCDH8 in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:2a0599d427a73442d0e1
claim_id: claim:2a0599d427a73442d0e1
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The intratelencephalic subclass that accounted for more than 80% of the excitatory neurons was predicted to span layers L2 to L6 and was marked by layer-specific markers (L2–3: PCDH8 ; L3–5: RORB ; L6: OPRK1 ; Fig. 1B ).

summary:
In Homo sapiens, layer 3-5 intratelencephalic excitatory neurons are marked by RORB in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:dc687d008a92b0e9ccd8
claim_id: claim:dc687d008a92b0e9ccd8
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The intratelencephalic subclass that accounted for more than 80% of the excitatory neurons was predicted to span layers L2 to L6 and was marked by layer-specific markers (L2–3: PCDH8 ; L3–5: RORB ; L6: OPRK1 ; Fig. 1B ).

summary:
In Homo sapiens, layer 6 intratelencephalic excitatory neurons are marked by OPRK1 in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:09fb7e90595bfe89a283
claim_id: claim:09fb7e90595bfe89a283
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The extratelencephalic, corticothalamic and other subclasses were predicted to be localized in deep layers and were transcriptomically distinct (L5 extratelencephalic: FEZF2 , BCL11B and POU3F1 ; L6 corticothalamic: SYT6 ; L5–6 near-projecting: HTR2C ; L6B: CTGF ; Fig. 1B ).

summary:
In Homo sapiens, layer 5 extratelencephalic excitatory neurons are marked by FEZF2, BCL11B, and POU3F1 in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:1cf64baa44339fa782d5
claim_id: claim:1cf64baa44339fa782d5
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The extratelencephalic, corticothalamic and other subclasses were predicted to be localized in deep layers and were transcriptomically distinct (L5 extratelencephalic: FEZF2 , BCL11B and POU3F1 ; L6 corticothalamic: SYT6 ; L5–6 near-projecting: HTR2C ; L6B: CTGF ; Fig. 1B ).

summary:
In Homo sapiens, layer 6 corticothalamic excitatory neurons are marked by SYT6 in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:c9edd0586712094d58c6
claim_id: claim:c9edd0586712094d58c6
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The extratelencephalic, corticothalamic and other subclasses were predicted to be localized in deep layers and were transcriptomically distinct (L5 extratelencephalic: FEZF2 , BCL11B and POU3F1 ; L6 corticothalamic: SYT6 ; L5–6 near-projecting: HTR2C ; L6B: CTGF ; Fig. 1B ).

summary:
In Homo sapiens, layer 5-6 near-projecting excitatory neurons are marked by HTR2C in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:b3fae2aed334725bed39
claim_id: claim:b3fae2aed334725bed39
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
summary:
In Homo sapiens, layer 6B excitatory neurons are marked by CTGF in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:82530ac65af31a966009
claim_id: claim:82530ac65af31a966009
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
This analysis also highlighted human L3–5 intratelencephalic subclass enrichment of PKD2L1 , which encodes a calcium-regulated cation channel.

summary:
In Homo sapiens, layer 3-5 intratelencephalic excitatory neurons show enrichment of PKD2L1, which encodes a calcium-regulated cation channel.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:1744b34d3c8773dde110
claim_id: claim:1744b34d3c8773dde110
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The 29 genes detected in the human lineage included genes encoding transcription factors ( TWIST2 and ELK3 ), genes associated with autism spectrum disorder (ASD) in SFARI gene list ( https://gene.sfari.org/ ; CCDC88C , MET , ANXA1 ) as well as genes encoding critical retinoic acid signaling components ( ALDH1A1 ; Fig. 3D and fig. S12C – D ), which have recently been shown to regulate gene expression, spinogenesis and connectivity in PFC ( 29 ).

summary:
In Homo sapiens, excitatory neurons in the dorsolateral prefrontal cortex show human-lineage enrichment of TWIST2, ELK3, CCDC88C, MET, ANXA1, and ALDH1A1.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:5178c9f96dd132426bd6
claim_id: claim:5178c9f96dd132426bd6
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
MELTF , which encodes melanotransferrin and is involved in cellular iron uptake, was specifically upregulated in PVALB chandelier subtypes in humans ( fig. S14H ), suggesting novel roles of iron homeostasis in fast-spiking inhibitory neurons.

summary:
In Homo sapiens, MELTF is specifically upregulated in parvalbumin chandelier cell subtypes in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:09f5c53452fda852c264
claim_id: claim:09f5c53452fda852c264
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
We found that many genes orchestrating key dopamine signaling pathway processes, including dopamine synthesis ( TH, GCH1 ), transport ( SLC18A2 ), and binding to presynaptic receptors ( DRD2 ) ( 7 ), were expressed in the human subtype InN SST HGF GABRQ.

summary:
In Homo sapiens, the inhibitory neuron subtype InN SST HGF GABRQ expresses TH, GCH1, SLC18A2, and DRD2, which are key dopamine signaling pathway genes.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:b259649a9036c9cbe2dd
claim_id: claim:b259649a9036c9cbe2dd
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
Although expression of SLC6A3 was not detected in either our dlPFC or published MTG single cell dataset, SLC47A1 , which encodes a non-canonical dopamine transporter ( 35 ), was uniquely expressed in both TH -expressing inhibitory neuron subtypes in humans ( fig. S15A ).

summary:
In Homo sapiens, SLC47A1, which encodes a non-canonical dopamine transporter, is uniquely expressed in tyrosine hydroxylase-expressing inhibitory neuron subtypes, while SLC6A3 is not detected.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:5e3097de61230e61fa29
claim_id: claim:5e3097de61230e61fa29
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The human-specific microglial subtype expressed signatures of preactivation ( FOS, CD83 ), chemokine secretion ( CCL3, CCL4 ), anti-viral defense ( CH25H ), co-stimulation ( CD86 ) and proliferation ( BTG2, CDKN1A ; Fig. 5E ) and was very similar to a previously reported pre-active immune-sensing subpopulation, which emerges as early as the 10 th gestational weeks and expands to mid-gestation in the absence of inflammation ( 38 ).

summary:
In Homo sapiens, the human-specific microglial subtype expresses FOS, CD83, CCL3, CCL4, CH25H, CD86, BTG2, and CDKN1A as markers of preactivation, chemokine secretion, anti-viral defense, co-stimulation, and proliferation.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:306ec5625449d1730e3b
claim_id: claim:306ec5625449d1730e3b
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
The Hominini-specific microglial type showed high expression of GLDN , MYO1E , PADI2 and PPARG ( Fig. 5E ).

summary:
In Homo sapiens, the Hominini-specific microglial subtype shows high expression of GLDN, MYO1E, PADI2, and PPARG.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:0080d8d056dfe97fbec9
claim_id: claim:0080d8d056dfe97fbec9
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
Module 1 included many genes encoding the major effectors for astrocyte-mediated clearance of glutamate and GABA from the extracellular space, such as glutamate transporters ( SLC1A2 and SLC1A3 ) and GABA transporters ( SLC6A11 and SLC6A1 ; Fig. 5D ).

summary:
In Homo sapiens, a subset of interlaminar astrocytes expresses SLC1A2, SLC1A3, SLC6A11, and SLC6A1, encoding glutamate and GABA transporters involved in neurotransmitter clearance.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:dc6abe1a0a856842e331
claim_id: claim:dc6abe1a0a856842e331
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
Among the three genes encoding its signaling molecules, VEGFA was sparsely expressed in pericytes of all species while VEGFB and PGF were enriched in human pericytes ( Fig. 5F ), suggesting the presence of human-specific signaling shaping vascular cell identity and communication.

summary:
In Homo sapiens, VEGFB and PGF are enriched in pericytes of the dorsolateral prefrontal cortex, while VEGFA is sparsely expressed in pericytes across species.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:71cab6fbf28a57adfab7
claim_id: claim:71cab6fbf28a57adfab7
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
we also observed a previously unknown enrichment of FOXP2 expression in L3–5 intratelencephalic excitatory neurons across primates, that was not detected in mice ( Fig. 6A ).

summary:
In Homo sapiens, FOXP2 expression is enriched in layer 3-5 intratelencephalic excitatory neurons in the dorsolateral prefrontal cortex.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:3e1d1cb17a369d5e9e16
claim_id: claim:3e1d1cb17a369d5e9e16
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
we independently validated human specificity of FOXP2 expression in microglia and found that it was a common feature shared by multiple brain regions ( fig. S18B – E ).

summary:
In Homo sapiens, FOXP2 expression in microglia is human-specific and shared across multiple brain regions.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:e303707ebad84491ae55
claim_id: claim:e303707ebad84491ae55
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
MERTK showed conserved expression in microglia, consistent with its known function in myelination equilibrium regulation by modulating microglia activities ( fig. S23F ).

summary:
In Homo sapiens, MERTK shows conserved expression in microglia, consistent with its role in myelination equilibrium regulation.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:329b4a87670c3609b253
claim_id: claim:329b4a87670c3609b253
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
Similarly, the ASD risk gene, NR4A2 , which encodes a transcription factor, exhibited human-specific expression in smooth muscle cells ( fig. S23E – F ), suggesting possible reorganization of transcriptional regulation in anthropoids.

summary:
In Homo sapiens, the autism spectrum disorder risk gene NR4A2, which encodes a transcription factor, exhibits human-specific expression in smooth muscle cells.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:a973d529ad059cbc8b49
claim_id: claim:a973d529ad059cbc8b49
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
Furthermore, DSCAM implicated in Down syndrome, was predicted to be positively regulated by FOXP2 in microglia and exhibited human-specific expression in microglia as well ( fig. S22C – D ).

summary:
In Homo sapiens, DSCAM, implicated in Down syndrome, exhibits human-specific expression in microglia and is predicted to be positively regulated by FOXP2.


claim_key: hca:0223_10.1126_science.abo7257_14645ac97f:claim:edc80f0fa4560ee272c4
claim_id: claim:edc80f0fa4560ee272c4
paper_key: hca:0223_10.1126_science.abo7257_14645ac97f
span_literal:
This is exemplified by FLT1 , encoding the vascular endothelial growth factor receptor, with conserved expression marking the capillary endothelial subtype.

summary:
In Homo sapiens, FLT1, encoding the vascular endothelial growth factor receptor, marks the capillary endothelial cell subtype with conserved expression.


claim_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6:claim:0ddabdd42d83e64dd354
claim_id: claim:0ddabdd42d83e64dd354
paper_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6
span_literal: PD-1, LAG-3, TIGIT, TIM-3, CD49b, and CCR5 in IL-10-producing CD25 low CD4 + T cells
summary:
In Homo sapiens, co-inhibitory receptor rich IL-10-producing CD25 low CD4-positive T cells are identified by expression of PD-1, LAG-3, TIGIT, TIM-3, CD49b, and CCR5.


claim_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6:claim:ea234c53f9aa463f75e7
claim_id: claim:ea234c53f9aa463f75e7
paper_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6
span_literal:
we confirmed that co-expression of only IL-10, CD49b, and LAG-3 showed the highest sensitivity to enrich for these human CIR rich cells

summary:
In Homo sapiens, co-expression of IL-10, CD49b, and LAG-3 identifies co-inhibitory receptor rich CD4-positive T cells with the highest sensitivity.


claim_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6:claim:9c875143149ab68ddb4a
claim_id: claim:9c875143149ab68ddb4a
paper_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6
span_literal:
we observed that IL-10-producing CD4 + T cells are very distinct from CD25 high CD127 low CD4 + T cells.

summary:
In Homo sapiens, CD25 high CD127 low CD4-positive T cells are distinct from IL-10-producing CD4-positive T cells, being characterized by high CD25 and low CD127 expression.


claim_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6:claim:fb271c7f9f852c768d9e
claim_id: claim:fb271c7f9f852c768d9e
paper_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6
span_literal:
we compared IL-10-producing CD4 + T cells with the clusters C4, C5, and C6, which are rich in FOXP3 high IL2R high CD127 low cells and have previously been proved to be the bona-fide FOXP3 + Treg cells

summary:
In Homo sapiens, bona-fide FOXP3-positive regulatory T cells are characterized by high FOXP3, high IL2R, and low CD127 expression.


claim_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6:claim:907ae15218c332e36dbf
claim_id: claim:907ae15218c332e36dbf
paper_key: hca:0224_10.1038_s41467-018-07581-4_ec3b4906f6
span_literal: Finally CIR rich cells also express a higher level of LXRα compared to CIR poor cells
summary:
In Homo sapiens, co-inhibitory receptor rich IL-10-producing CD4-positive T cells express a higher level of liver X receptor alpha compared to co-inhibitory receptor poor cells.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:9d3900b355721e5fdd8d
claim_id: claim:9d3900b355721e5fdd8d
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
span_literal:
Clusters 1–2 were interpreted as being derived from rod photoreceptor cells, with high expression of the rod-specific opsin rhodopsin ( RHO ) as well as the rod-specific phosphodiesterase PDE6A.

summary:
In Homo sapiens retina, rod photoreceptor cells are marked by high expression of rhodopsin (RHO) and phosphodiesterase PDE6A.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:dbc8f327fabf76ef964f
claim_id: claim:dbc8f327fabf76ef964f
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
span_literal:
Clusters 3-4 were proposed to consist of cone photoreceptor cells, which were enriched for the cone-specific phosphodiesterase PDE6H and arrestin ARR3.

summary:
In Homo sapiens retina, cone photoreceptor cells are enriched for the cone-specific phosphodiesterase PDE6H and arrestin ARR3.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:561d5cd2c56f3e9a0e87
claim_id: claim:561d5cd2c56f3e9a0e87
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
span_literal:
Clusters 5-6 were interpreted as being derived from bipolar cells, with strong expression of TRPM1, a cation channel involved in bipolar cell depolarization.

summary:
In Homo sapiens retina, bipolar cells show strong expression of TRPM1, a cation channel involved in bipolar cell depolarization.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:23c0b8545a3f46404c3e
claim_id: claim:23c0b8545a3f46404c3e
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
summary: In Homo sapiens retina, retinal ganglion cells show high expression of THY1 and NRN1.
span_literal:
Cluster 7 was interpreted as retinal ganglion cells, with high expression of THY1 and NRN1, which regulate axonal architecture and neurofilament integrity.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:e260092f4507e280e070
claim_id: claim:e260092f4507e280e070
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
summary: In Homo sapiens retina, horizontal cells express ONECUT2.
span_literal:
Interestingly, Cluster 8 demonstrated transcriptomic evidence of two populations of interneurons, horizontal cells, which expresses ONECUT2, and amacrine cells, which express NRXN2 ( SI Figure 3 ).


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:c02f1545d55263aa80f2
claim_id: claim:c02f1545d55263aa80f2
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
summary: In Homo sapiens retina, retinal endothelial cells express ICAM2.
span_literal:
Pericytes and smooth muscle cells, proposed Cluster 10, regulate blood flow through ICAM2 expressing retinal endothelial cells, which are interpreted as Cluster 11.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:277fb0d5a5474419bc8a
claim_id: claim:277fb0d5a5474419bc8a
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
summary: In Homo sapiens retina, microglia are noted for strong expression of complement component C1QA.
span_literal:
Microglia, resident immune cells of the retina, were restricted to Cluster 12 and are noted for strong expression of complement component C1QA.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:1ce0a105f21d8f724e35
claim_id: claim:1ce0a105f21d8f724e35
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
summary: In Homo sapiens retina, Müller cells show high expression of RLBP1.
span_literal:
All five glial clusters also showed elevated expression of RLBP1, a gene with high expression in Müller cells.


claim_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea:claim:25ba819a88bc9b9d7bda
claim_id: claim:25ba819a88bc9b9d7bda
paper_key: hca:0225_10.1016_j.exer.2019.05.001_df51932aea
summary: In Homo sapiens retina, ALDH1L1 and GFAP are reported markers specific for astrocytes.
span_literal:
Expression of ALDH1L1 and GFAP, both reported markers specific for retinal astrocytes ( Yang et al., 2011 ), were low in all clusters ( SI Figure 8 ).


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:2ab1e5695b1cb072590e
claim_id: claim:2ab1e5695b1cb072590e
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
We identified RORB as a marker of selectively vulnerable excitatory neurons in the entorhinal cortex, and subsequently validated their depletion and selective susceptibility to neurofibrillary inclusions during disease progression using quantitative neuropathological methods.

summary:
In Homo sapiens, RORB is a marker of selectively vulnerable excitatory neurons in the entorhinal cortex.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:3c16cbd31e65acbc637d
claim_id: claim:3c16cbd31e65acbc637d
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
We found that EC:Exc.s2 and EC:Exc.s4 specifically expressed RORB , CTC-340A15.2 and CTC-535M15.2 ( Fig. 2c ).

summary:
In Homo sapiens entorhinal cortex, selectively vulnerable excitatory neuron subpopulations EC:Exc.s2 and EC:Exc.s4 specifically expressed RORB, CTC-340A15.2, and CTC-535M15.2.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:59a4d6ddd95ec9319917
claim_id: claim:59a4d6ddd95ec9319917
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
We also found that EC:Exc.s1 was marked by high expression of CDH9 ( Fig. 2c ), which encodes a cadherin with neuron-specific expression.

summary:
In Homo sapiens entorhinal cortex, excitatory neuron subpopulation EC:Exc.s1 is marked by high expression of CDH9.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:85bc0bdc9914984e9269
claim_id: claim:85bc0bdc9914984e9269
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
summary: In Homo sapiens brain, SLC17A7 and CAMK2A are markers of excitatory neurons.
span_literal:
To assign clusters identified in the aligned subspace generated by scAlign to major brain cell types, the following marker genes were used: SLC17A7 and CAMK2A for excitatory neurons, GAD1 and GAD2 for inhibitory neurons, SLC1A2 and AQP4 for astrocytes, MBP and MOG for oligodendrocytes, PDGFRA and SOX10 for oligodendrocyte precursor cells (OPCs), CD74 and CX3CR1 for microglia/myeloid cells, and CLDN5 and FLT1 for endothelial cells.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:5b3895e4962187a5cc13
claim_id: claim:5b3895e4962187a5cc13
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
In the EC, GFAP high astrocytes also expressed CD44 and HSPB1 , markers of pan-reactive astrocytes 37 ; TNC , which is upregulated in stab-wound reactive astrocytes 38 ; and HSP90AA1 , which is upregulated in reactive astrocytes associated with middle cerebral artery occlusion 39 ( Fig. 5c , d ).

summary:
In Homo sapiens entorhinal cortex, GFAP-high astrocytes expressed CD44, HSPB1, TNC, and HSP90AA1, which are markers of reactive astrocytes.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:504b0c34c79a80233875
claim_id: claim:504b0c34c79a80233875
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
In terms of downregulated genes, GFAP high astrocytes consistently expressed lower levels of genes associated with glutamate/GABA homeostasis ( SLC1A2 , SLC1A3 , GLUL , SLC6A11 ) and synaptic adhesion/maintenance ( NRXN1 , CADM2 , PTN , GPC5 ), suggesting a loss of homeostatic function.

summary:
In Homo sapiens, GFAP-high astrocytes expressed lower levels of SLC1A2, SLC1A3, GLUL, SLC6A11, NRXN1, CADM2, PTN, and GPC5, suggesting a loss of homeostatic function.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:2365511ccca1dc3f6939
claim_id: claim:2365511ccca1dc3f6939
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
In each brain region, there was at least one subpopulation (EC:Astro.3, SFG:Astro.s4 and SFG:Astro.s5) that expressed dramatically higher levels of GFAP , which we will refer to as GFAP high astrocytes ( Fig. 5c , d ).

summary:
In Homo sapiens, astrocyte subpopulations EC:Astro.3, SFG:Astro.s4, and SFG:Astro.s5 expressed dramatically higher levels of GFAP and are referred to as GFAP-high astrocytes.


claim_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691:claim:34e2f088d1d81958677b
claim_id: claim:34e2f088d1d81958677b
paper_key: hca:0226_10.1038_s41593-020-00764-7_dc0bba5691
span_literal:
TBR1, or T-box, brain, 1 is a transcription factor protein that has a role in differentiation of glutamatergic neurons and is a marker for excitatory neurons, including EC excitatory neurons 85 , 86 .

summary:
In Homo sapiens, TBR1 (T-box, brain, 1) is a marker for excitatory neurons, including entorhinal cortex excitatory neurons.


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:e6fb5c73a1ac6474d603
claim_id: claim:e6fb5c73a1ac6474d603
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
summary: In Homo sapiens, naive B cells are identified by positive expression of MME (CD10) and CD52.
span_literal:
By subclustering the B-cell population, we identified naive B cells (MME/CD10 + CD52 ++ ), memory B cells (MS4A1/CD20 ++ CD22 ++ ), plasmablasts (CD27 ++ TNFRSF17/CD269 + ), and plasma cells (CD27 ++ IGTA4 + SDC1/CD138 + ) based on their specific markers as previously described


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:a5c77aaff53c19af9c17
claim_id: claim:a5c77aaff53c19af9c17
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
summary:
In Homo sapiens, plasma cells are identified by positive expression of CD27, IGTA4, and SDC1 (CD138).


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:b6940183f19249ae48a9
claim_id: claim:b6940183f19249ae48a9
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
summary: In Homo sapiens, macrophages are defined by expression of CD163 and SIGLEC1.
span_literal:
Macrophage and dendritic cell types were defined by picking monocytes with the expression of CD163 plus SIGLEC1 and FCER1A plus CST3, respectively.


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:2c0fb1027a60c30f20ef
claim_id: claim:2c0fb1027a60c30f20ef
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
summary: In Homo sapiens, memory B cells are distinguished by positive expression of CD19, CD20, and CD27.
span_literal:
we used surface markers to distinguish memory B cells (CD19 + CD20 + CD27 + ), plasmablasts (CD19 + CD20 − CD38 + ), and plasma cells (CD19 + CD20 − CD38 + CD138 + ) as previously described


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:e04a2039ef9ba68de825
claim_id: claim:e04a2039ef9ba68de825
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
span_literal:
we used surface markers to distinguish memory B cells (CD19 + CD20 + CD27 + ), plasmablasts (CD19 + CD20 − CD38 + ), and plasma cells (CD19 + CD20 − CD38 + CD138 + ) as previously described

summary:
In Homo sapiens, plasmablasts are distinguished by positive expression of CD19 and CD38 and negative expression of CD20.


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:c23113917671024b770f
claim_id: claim:c23113917671024b770f
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
span_literal:
we used surface markers to distinguish memory B cells (CD19 + CD20 + CD27 + ), plasmablasts (CD19 + CD20 − CD38 + ), and plasma cells (CD19 + CD20 − CD38 + CD138 + ) as previously described

summary:
In Homo sapiens, plasma cells are distinguished by positive expression of CD19, CD38, and CD138 and negative expression of CD20.


claim_key: hca:0228_10.1128_mbio.02583-20_5085db2792:claim:a367f49341464d69a80f
claim_id: claim:a367f49341464d69a80f
paper_key: hca:0228_10.1128_mbio.02583-20_5085db2792
summary: In Homo sapiens, T cells are identified by CD3, B cells by CD19, and natural killer cells by CD56.
span_literal:
Lineage-specific antibodies against T cells (CD3 + ), B cells (CD19 + ), and NK cells (CD56 + ) were used to identify specific PBMC subsets.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:873c05c0281f4eca7ad8
claim_id: claim:873c05c0281f4eca7ad8
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal: cluster 3 (C3) was characterized by erythroid fate regulators and markers GATA1 , CD36 , and KLF1
summary:
In Homo sapiens, megakaryocyte-erythroid progenitor is characterized by the erythroid fate regulators and markers GATA1, CD36, and KLF1.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:91f8ce2fc8e3b971b15a
claim_id: claim:91f8ce2fc8e3b971b15a
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
gene expression of C2 was similar to our MEP subgroup, but contained unique upregulation of genes whose expression has been previously associated with the development of mast cells ( TPSAB1 , a mast cell specific protease), basophils ( LMO4; Paul et al , 2015 ), and eosinophils (MS4A2, FCER1A; Eon Kuek et al , 2016 )

summary:
In Homo sapiens, basophil/eosinophil/mast cell progenitor is marked by upregulation of TPSAB1, LMO4, MS4A2, and FCER1A.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:e37caa26bc0ad02f631c
claim_id: claim:e37caa26bc0ad02f631c
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
in contrast to our GMP‐like cluster (C9), C2 cells did not express neutrophil or monocytic genes, such as MPO , ELANE , LYZ , or CSF3R

summary:
In Homo sapiens, basophil/eosinophil/mast cell progenitor does not express the neutrophil or monocytic genes MPO, ELANE, LYZ, or CSF3R, in contrast to granulocyte-macrophage progenitor.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:2c179a395766ccf69791
claim_id: claim:2c179a395766ccf69791
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
Cluster 1 was uniquely marked by high expression of clear megakaryocytic (Mk) markers including PF4 , ITGA2B , and CLEC1A, suggesting a putative Mk progenitor identity for C1 cells.

summary:
In Homo sapiens, megakaryocyte progenitor is uniquely marked by high expression of PF4, ITGA2B, and CLEC1A.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:8b37154ae9294c7adc1e
claim_id: claim:8b37154ae9294c7adc1e
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
summary: In Homo sapiens, early erythroid progenitor expresses high levels of GATA2 and KIT.
span_literal:
C4 cells lacked the expression of mature erythroblast markers, but expressed high levels of GATA2 and KIT , likely representing a transitioning population along the early stages of erythroid commitment.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:b3a075d38065b3c458e3
claim_id: claim:b3a075d38065b3c458e3
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
clusters 7 and 8 were marked by elevated expression of FLT3 and CSF3R with gradually reduced levels of stem cell markers, likely representing populations similar to the lymphoid‐primed multipotent progenitor (LMPP) that have previously been described in mouse

summary:
In Homo sapiens, lymphoid-primed multipotent progenitor is marked by elevated expression of FLT3 and CSF3R.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:967554163a444716e67e
claim_id: claim:967554163a444716e67e
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
These populations also exhibited high expression of L‐selectin ( SELL ; CD62L ), consistent with a recent study which identified CD62L as an early marker of lympho‐myeloid fate commitment in human bone marrow

summary:
In Homo sapiens, lymphoid-primed multipotent progenitor exhibits high expression of SELL, an early marker of lympho-myeloid fate commitment.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:38c6693ba681f846ea2b
claim_id: claim:38c6693ba681f846ea2b
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
the initial transition out of multipotency is marked by a reduction in HSC markers, and concomitant upregulation of CDK6 , which has been shown to control the exit from quiescence in cord blood hematopoiesis

summary:
In Homo sapiens, hematopoietic stem cell undergoing exit from quiescence shows upregulation of CDK6 in cord blood.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:62e46b4752efabd1be92
claim_id: claim:62e46b4752efabd1be92
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
One path was characterized by the upregulation of transcription factors and cell surface proteins that are commonly associated with the LMPP in both mouse and human, namely, FLT3 , CSF3R , and SELL

summary:
In Homo sapiens, lymphoid-primed multipotent progenitor is characterized by upregulation of FLT3, CSF3R, and SELL.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:e8d4e7c95b7c260912cf
claim_id: claim:e8d4e7c95b7c260912cf
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
LMPP cells subsequently subdivided into MPO ‐expressing neutrophil/monocyte progenitors, or MME (CD10) ‐expressing lymphoid progenitors

summary:
In Homo sapiens, neutrophil/monocyte progenitor expresses MPO, while lymphoid progenitor expresses MME.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:214cef807f6de9a754f0
claim_id: claim:214cef807f6de9a754f0
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
LMPP cells subsequently subdivided into MPO ‐expressing neutrophil/monocyte progenitors, or MME (CD10) ‐expressing lymphoid progenitors

summary:
In Homo sapiens, lymphoid progenitor expresses MME, distinguishing it from neutrophil/monocyte progenitor.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:a3e2fcd9d47994e0bf64
claim_id: claim:a3e2fcd9d47994e0bf64
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
genes that were induced during the transition from HSC to LMPP— FLT3, CSF3R, SELL, CD99 —were absent from the GATA2 ‐dependent trajectory, including the Ba/Eo/Ma progenitors, but maintained high levels of expression in Neu/Mo progenitors.

summary:
In Homo sapiens, neutrophil/monocyte progenitor maintains high expression of FLT3, CSF3R, SELL, and CD99, while basophil/eosinophil/mast cell progenitor lacks expression of these genes.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:cfafd4ba57963744c86f
claim_id: claim:cfafd4ba57963744c86f
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
genes that were induced during the transition from HSC to LMPP— FLT3, CSF3R, SELL, CD99 —were absent from the GATA2 ‐dependent trajectory, including the Ba/Eo/Ma progenitors, but maintained high levels of expression in Neu/Mo progenitors.

summary:
In Homo sapiens, basophil/eosinophil/mast cell progenitor lacks expression of FLT3, CSF3R, SELL, and CD99, in contrast to neutrophil/monocyte progenitor.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:adf8569f33679c18a598
claim_id: claim:adf8569f33679c18a598
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
In Neu/Mo progenitors, we identified “ de novo ” activation of specific markers and regulators ( MPO , CEBPA ), but also observed “primed” expression of canonical myeloid receptors ( CSF3R , IL17RA )

summary:
In Homo sapiens, neutrophil/monocyte progenitor shows de novo activation of MPO and CEBPA, and primed expression of CSF3R and IL17RA.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:4de5c8281de4a57c816e
claim_id: claim:4de5c8281de4a57c816e
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
span_literal:
CD52 (Rodig et al , 2006 ) was detected as early as the HSC and maintained its expression throughout lymphoid differentiation

summary:
In Homo sapiens, CD52 is a primed lymphoid marker expressed in hematopoietic stem cell and maintained throughout lymphoid progenitor differentiation.


claim_key: hca:0229_10.15252_msb.20178041_0277072a61:claim:c9d0b0104778b92555ea
claim_id: claim:c9d0b0104778b92555ea
paper_key: hca:0229_10.15252_msb.20178041_0277072a61
summary: In Homo sapiens, B cell is enriched for MS4A1, CD83, CD22, and CD79A, while lacking MME expression.
span_literal:
Cluster 11 was enriched in genes unique for B cells— MS4A1 , CD83 , CD22, and CD79A , while lacking MME (CD10) expression


claim_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546:claim:793f90fe82fb69665b85
claim_id: claim:793f90fe82fb69665b85
paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
span_literal:
on the basis of marker expression (including high expression of ACAN and COL2A1), we identified these as extra-articular chondrocytes

summary:
In Homo sapiens skin, extra-articular chondrocytes are identified by high expression of ACAN and COL2A1.


claim_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546:claim:7cd414ad5e0c4b6f61f2
claim_id: claim:7cd414ad5e0c4b6f61f2
paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
span_literal:
there were two major pericyte populations, which we denoted RGS5+ and TAGLN+ based on high expression of those genes

summary:
In Homo sapiens skin, RGS5-positive pericytes are marked by high expression of RGS5, and TAGLN-positive pericytes are marked by high expression of TAGLN.


claim_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546:claim:0c0c509585c16fb92d48
claim_id: claim:0c0c509585c16fb92d48
paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
span_literal:
Unbiased clustering of our integrated scRNAseq dataset identified 4 main populations of fibroblasts which we designated APOD+, SFRP2+, PTGDS+ and POSTN+ fibroblasts based on specific gene expression

summary:
In Homo sapiens skin, four main fibroblast subpopulations are designated APOD-positive fibroblast, SFRP2-positive fibroblast, PTGDS-positive fibroblast, and POSTN-positive fibroblast based on specific gene expression of APOD, SFRP2, PTGDS, and POSTN respectively.


claim_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546:claim:5316d3733e67a59b5402
claim_id: claim:5316d3733e67a59b5402
paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
span_literal:
KRT14, POSTN, DLL1 represented the IFE basal K; Dividing K co-expressed CDK1 and PCNA; KRT17 in the inner bulb cluster.

summary:
In Homo sapiens skin, interfollicular epidermis basal keratinocytes are represented by KRT14, POSTN, and DLL1; dividing keratinocytes co-express CDK1 and PCNA; and inner bulb keratinocytes express KRT17.


claim_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546:claim:0ebc26d091fc18eb6c30
claim_id: claim:0ebc26d091fc18eb6c30
paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
span_literal:
KRT1, KRT10 and LY6D marked spinous IFE keratinocytes; KRT19 and DCD marked sweat glands; MGST1 marked sebaceous glands.

summary:
In Homo sapiens skin, spinous interfollicular epidermis keratinocytes are marked by KRT1, KRT10, and LY6D.


claim_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546:claim:774f1faf0f4e6f48669f
claim_id: claim:774f1faf0f4e6f48669f
paper_key: hca:0231_10.1101_2023.08.08.551504_0d646c9546
span_literal:
Immunostaining of RGS5 in papillary and reticular dermis showed RGS5+ cells to be in close contact with NCAM+ cells, a pan vascular marker, in healthy skin and BCC

summary:
In Homo sapiens skin, vascular cells are marked by NCAM as a pan vascular marker, and RGS5-positive pericytes express RGS5.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:32570a55dee59b2ce10f
claim_id: claim:32570a55dee59b2ce10f
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
We identified two populations of effector CD8 + T cells (T eff ), expressing PRF1 and GZMB ; a population of likely memory (mem)/ precursor effector (pec) CD8 + T cells (T mem/pec ) expressing CCR6 [ 35 ]; and two populations of exhausted CD8 + T cells (T ex ) expressing EOMES , GZMK , and TIGIT

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, effector CD8-positive T cells express PRF1 and GZMB.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:c8f927563dda5b745f5e
claim_id: claim:c8f927563dda5b745f5e
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
We identified two populations of effector CD8 + T cells (T eff ), expressing PRF1 and GZMB ; a population of likely memory (mem)/ precursor effector (pec) CD8 + T cells (T mem/pec ) expressing CCR6 [ 35 ]; and two populations of exhausted CD8 + T cells (T ex ) expressing EOMES , GZMK , and TIGIT

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, memory/precursor effector CD8-positive T cells express CCR6.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:a9e2f230857dffeaa0aa
claim_id: claim:a9e2f230857dffeaa0aa
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
We identified two populations of effector CD8 + T cells (T eff ), expressing PRF1 and GZMB ; a population of likely memory (mem)/ precursor effector (pec) CD8 + T cells (T mem/pec ) expressing CCR6 [ 35 ]; and two populations of exhausted CD8 + T cells (T ex ) expressing EOMES , GZMK , and TIGIT

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, exhausted CD8-positive T cells express EOMES, GZMK, and TIGIT.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:3dd9afa37770823b1e3a
claim_id: claim:3dd9afa37770823b1e3a
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal: We observed an abundant granulocyte population expressing CXCR1 and CXCR2, FCGR3B and S100A8
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, granulocytes express CXCR1, CXCR2, FCGR3B, and S100A8.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:39376aae11708ba161c4
claim_id: claim:39376aae11708ba161c4
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal: we detected resident macrophages and alternatively activated macrophages ( MARCO + )
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, alternatively activated macrophages express MARCO.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:3bc1c65c0c48af528020
claim_id: claim:3bc1c65c0c48af528020
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
We also observed an additional myeloid population, denoted as alternatively activated macrophages 2, that resembled alternatively activated macrophages and was uniquely defined by abundant expression of CHIT1 and multiple immune checkpoint ligands

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, alternatively activated macrophages 2 are uniquely defined by abundant expression of CHIT1.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:1777d8e2e9aee6bf9d4b
claim_id: claim:1777d8e2e9aee6bf9d4b
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
We found two populations of plasmacytoid DCs ( IRF8, GZMB ) and two populations of Langerhans-like DCs ( CD207 , CD1A ) as previously described

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, plasmacytoid dendritic cells express IRF8 and GZMB.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:545ddf904167087018b1
claim_id: claim:545ddf904167087018b1
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
We found two populations of plasmacytoid DCs ( IRF8, GZMB ) and two populations of Langerhans-like DCs ( CD207 , CD1A ) as previously described

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, Langerhans-like dendritic cells express CD207 and CD1A.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:20ba8a94102b819b4530
claim_id: claim:20ba8a94102b819b4530
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
Langerhans-like DC2 had robust expression of IL22RA2 , also known as IL22BP, and the IL-22-IL22BP axis is known to be a crucial mediator of tumorigenesis in the colon

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, Langerhans-like dendritic cell 2 has robust expression of IL22RA2 (also known as IL22BP).


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:fcb3094800e9b8c03fae
claim_id: claim:fcb3094800e9b8c03fae
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal: We also detected a population of conventional DC1s ( CLEC9A, IRF8 )
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, conventional dendritic cell 1 expresses CLEC9A and IRF8.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:d3016ab40b50362eaf3b
claim_id: claim:d3016ab40b50362eaf3b
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
summary: In Homo sapiens pancreatic ductal adenocarcinoma, conventional dendritic cell 2 expresses SIRPA.
span_literal:
two additional populations of potential conventional DC2s that expressed immune checkpoint ligand SIRPA


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:1e64f77f1bbd658cfddb
claim_id: claim:1e64f77f1bbd658cfddb
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal: We also detected two unique populations of activated DCs ( LAMP3 , CCL22 )
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, activated dendritic cells express LAMP3 and CCL22.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:684be73eeff31af6593d
claim_id: claim:684be73eeff31af6593d
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
A highly enriched gene analysis of CD4 + subsets revealed expression of naïve T cell markers CCR7 and SELL [ 43 ] in cluster 0 and expression of regulatory T cell marker FOXP3 in cluster 3

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, naïve CD4-positive T cells express CCR7 and SELL, while regulatory T cells express FOXP3.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:b3ce8ee5bcdeaec85a92
claim_id: claim:b3ce8ee5bcdeaec85a92
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal: TIGIT appeared as a top expressed gene in Tregs
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, TIGIT appeared as a top expressed gene in regulatory T cells.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:e0f69426395b0fbc245e
claim_id: claim:e0f69426395b0fbc245e
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal: As expected, based on previous studies, CTLA4 was highly expressed within Tregs
summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CTLA4 is highly expressed within regulatory T cells.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:311b0162a6fe0d4d1019
claim_id: claim:311b0162a6fe0d4d1019
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
The only immune checkpoint receptor identified as differentially overexpressed in tumor-infiltrating CD8 + T cells, compared to CD8 + T cells in adjacent/normal tissue, was TIGIT , a gene encoding a receptor belonging to the Ig superfamily

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, TIGIT is differentially overexpressed in tumor-infiltrating CD8-positive T cells compared to CD8-positive T cells in adjacent/normal tissue.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:4de938889295594fb8e6
claim_id: claim:4de938889295594fb8e6
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
Further, TIGIT was the sole immune checkpoint receptor that specifically defined exhausted CD8 + T cells.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, TIGIT is the sole immune checkpoint receptor that specifically defines exhausted CD8-positive T cells.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:d7ef79e7f8d27a1031bc
claim_id: claim:d7ef79e7f8d27a1031bc
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
NK cluster 1 was enriched for immune checkpoint HAVCR2 , while NK cluster 3 expressed high levels of immune checkpoint TNFRSF4

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, natural killer cell cluster 1 is enriched for HAVCR2, while natural killer cell cluster 3 expresses high levels of TNFRSF4.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:6de2ec0059bda5056f55
claim_id: claim:6de2ec0059bda5056f55
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
NK cluster 1 was enriched for immune checkpoint HAVCR2 , while NK cluster 3 expressed high levels of immune checkpoint TNFRSF4

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, natural killer cell cluster 3 expresses high levels of TNFRSF4.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:70bf8362798e69265850
claim_id: claim:70bf8362798e69265850
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
LGALS9 , the ligand for HAVCR2 (encoding for TIM3), was significantly increased within alternatively activated macrophages, while SIRPA , the ligand for CD47 , was higher in PDA granulocytes compared to granulocytes in adjacent/normal tissue

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, LGALS9 is significantly increased within alternatively activated macrophages.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:82dbf199f0e8bb06dad7
claim_id: claim:82dbf199f0e8bb06dad7
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
LGALS9 , the ligand for HAVCR2 (encoding for TIM3), was significantly increased within alternatively activated macrophages, while SIRPA , the ligand for CD47 , was higher in PDA granulocytes compared to granulocytes in adjacent/normal tissue

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, SIRPA is higher in granulocytes compared to granulocytes in adjacent/normal tissue.


claim_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276:claim:5ecc498043f844f085c5
claim_id: claim:5ecc498043f844f085c5
paper_key: hca:0232_10.1038_s43018-020-00121-4_6badfd3276
span_literal:
TIGIT expression was enriched specifically within EOMES high CD8 + T cells, or exhausted T cells, similar to recent findings in human prostate, bladder, and kidney cancer

summary:
In Homo sapiens, TIGIT expression is enriched specifically within EOMES-high exhausted CD8-positive T cells.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:3193bde0ab4fd0a4d16b
claim_id: claim:3193bde0ab4fd0a4d16b
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
Innate lymphocytes (130,414 cells) were predominantly mature CD56 dim CD16 + NK cells expressing cytolytic markers ( KLRF1 , GZMB ) and enriched in blood, BM and lungs

summary:
In Homo sapiens, mature CD56 dim CD16 positive natural killer cells express the cytolytic markers KLRF1 and GZMB.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:543f7ac3468f83688cc4
claim_id: claim:543f7ac3468f83688cc4
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
We detected low frequencies of ILCs consisting largely of CD16 − NCR2 + IL7R − ILC1s with high expression of tissue residency markers (CD69, CD49a, CD103) enriched in JEJ, and IL7R + KIT + RORC + ILC3 (ref. 8 ) found in LN, spleen and JEJ

summary:
In Homo sapiens, innate lymphoid cell type 1 is characterized by negative CD16, positive NCR2, and negative IL7R expression.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:f6d02717e1284ae660e9
claim_id: claim:f6d02717e1284ae660e9
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
We detected low frequencies of ILCs consisting largely of CD16 − NCR2 + IL7R − ILC1s with high expression of tissue residency markers (CD69, CD49a, CD103) enriched in JEJ, and IL7R + KIT + RORC + ILC3 (ref. 8 ) found in LN, spleen and JEJ

summary:
In Homo sapiens, innate lymphoid cell type 3 is characterized by positive IL7R, positive KIT, and positive RORC expression.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:6c06398e55bc7b677f9e
claim_id: claim:6c06398e55bc7b677f9e
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
summary: In Homo sapiens, naive B cells are marked by positive IgD expression.
span_literal:
B cells (272,162 cells) were classified into 6 subsets largely confined to lymphoid organs (Fig. 2e,f ), including IgD + naive B cells, CD27 + memory B cells, germinal center B cells expressing AICDA (encoding activation-induced adenosine deaminase, which mediates somatic mutation and class switch recombination 19 ), plasma cells expressing immunoglobulin genes and SDC1 (CD138) and plasmablasts expressing proliferation markers ( MKI67 , TOP2A )


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:4f368456d5132520caaa
claim_id: claim:4f368456d5132520caaa
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
CD11c + memory B cells expressing TBX21 (encoding the transcription factor T-BET) resembled ‘atypical B cells’ 20 and were found at low frequencies in spleen and BM

summary:
In Homo sapiens, atypical B cells (CD11c positive memory B cells) express TBX21 (encoding the transcription factor T-BET).


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:d2ac2e001c91118ebae2
claim_id: claim:d2ac2e001c91118ebae2
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
summary: In Homo sapiens, macrophages are marked by positive C1QA and MS4A7 expression.
span_literal:
Myeloid lineage cells (225,268 cells) comprised C1QA + MS4A7 + macrophages, FCN1 + CD14 + classical and FCN1 + FCGR3A + non-classical monocytes and DC subsets, including CLEC9A + DC1, CLEC10A + DC2, CCR7 + migratory DCs and CD123 + LILRA4 + plasmacytoid DCs (pDCs)


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:fabe4c6caaa269c26342
claim_id: claim:fabe4c6caaa269c26342
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
summary: In Homo sapiens, lung macrophages express ITGAX, MRC1, MARCO, PPARG, TREM2, and FABP4.
span_literal:
lung macrophages had higher expression of CD11c ( ITGAX ), markers of efferocytosis ( MRC1 , MARCO ) and lipid metabolism ( PPARG , TREM2 , FABP4 )


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:84522e1b9a1fac331347
claim_id: claim:84522e1b9a1fac331347
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
C5 genes encoding stem-like transcription factors and markers ( TCF7 , LEF1 , ITGA6 ) 25 , 26 and LN homing receptors ( CCR7 , SELL ) were enriched in CD4 + and CD8 + T RM cells and T EM cells in LN

summary:
In Homo sapiens, CD4 positive and CD8 positive tissue resident memory T cells and effector memory T cells in lymph node are enriched for TCF7, LEF1, ITGA6, CCR7, and SELL.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:773c517618dfde359011
claim_id: claim:773c517618dfde359011
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
C6 genes encoding molecules for mucosal residency ( ITGA1 , CXCR6 , ITGAE ) 6 and gut homing ( CCR9 ) were enriched in CD4 + and CD8 + T RM cells, γδ T cells, MAIT cells and NK cells in the JEJ

summary:
In Homo sapiens, tissue resident memory T cells, gamma delta T cells, mucosal-associated invariant T cells, and natural killer cells in the jejunum are enriched for ITGA1, CXCR6, ITGAE, and CCR9.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:9e1af981cbb5abc19f29
claim_id: claim:9e1af981cbb5abc19f29
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
C6 genes encoding molecules for mucosal residency ( ITGA1 , CXCR6 , ITGAE ) 6 and gut homing ( CCR9 ) were enriched in CD4 + and CD8 + T RM cells, γδ T cells, MAIT cells and NK cells in the JEJ

summary:
In Homo sapiens, mucosal-associated invariant T cells in the jejunum are enriched for ITGA1, CXCR6, ITGAE, and CCR9.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:92ef8aef25ba8f58c71c
claim_id: claim:92ef8aef25ba8f58c71c
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
summary:
In Homo sapiens, natural killer cells in the jejunum are enriched for ITGA1, CXCR6, ITGAE, and CCR9.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:913e7730d7c26330f4e9
claim_id: claim:913e7730d7c26330f4e9
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
summary: In Homo sapiens, plasma cells in the jejunum express IGHA2, CD1d, RUNX2, ID3, and CD69.
span_literal:
For plasma cells, we found several JEJ-enriched genes, including IGHA2 (consistent with predominant IgA + plasma cells in the gut), the non-classical HLA molecule CD1d, plasma cell transcription factors ( RUNX2 , ID3 ) 34 , 35 and the tissue residency marker CD69


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:bdba6a8f162c40fb9271
claim_id: claim:bdba6a8f162c40fb9271
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
JEJ macrophages had increased expression of integrins ( ICAM1 , ITGA4 ), chemokines ( CCL24 , CCL3L1 ) and regulators of macrophage activation (for example, SLAMF7 ) 36

summary:
In Homo sapiens, jejunum macrophages have increased expression of ICAM1, ITGA4, CCL24, CCL3L1, and SLAMF7.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:53ec17e7e96b4b7614c6
claim_id: claim:53ec17e7e96b4b7614c6
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal: MAIT) cells, distinguished by TRAV1.2 expression, CD161 and other markers 16
summary:
In Homo sapiens, mucosal-associated invariant T cells are distinguished by TRAV1.2 and CD161 expression.


claim_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba:claim:82cb08bb4738702aaab0
claim_id: claim:82cb08bb4738702aaab0
paper_key: hca:0233_10.1038_s41590-025-02241-4_110ace5bba
span_literal:
Putative CD127 + CD62L + TCF7 + NK/ILC precursors, resembling CD56 bright CD16 − NK and ILC3s 18 , were enriched in blood but present in all tissues

summary:
In Homo sapiens, natural killer cell/innate lymphoid cell precursors are marked by positive CD127, CD62L, and TCF7 expression.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:5ea296781d7e561b5fa0
claim_id: claim:5ea296781d7e561b5fa0
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
PT_VCAM1 can be distinguished from PCT by expression of VCAM1 and HAVCR1 (KIM-1), which is a marker of kidney injury (Supplementary Fig. 3 ).

summary:
In Homo sapiens, VCAM1-positive proximal tubule cells can be distinguished from proximal convoluted tubule cells by expression of VCAM1 and HAVCR1 (kidney injury molecule 1), which is a marker of kidney injury.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:415ba7da9b7929207427
claim_id: claim:415ba7da9b7929207427
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
The PT_PROM1 cluster was PROM1 high VCAM1- in contrast to PT_VCAM1, which was PROM1 low VCAM1+ (Supplementary Fig. 3 ).

summary:
In Homo sapiens, the PROM1-positive proximal tubule cluster is characterized by high PROM1 and negative VCAM1, in contrast to VCAM1-positive proximal tubule cells.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:555b9bc6de62bc819b56
claim_id: claim:555b9bc6de62bc819b56
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
The PT_PROM1 cluster was PROM1 high VCAM1- in contrast to PT_VCAM1, which was PROM1 low VCAM1+ (Supplementary Fig. 3 ).

summary:
In Homo sapiens, VCAM1-positive proximal tubule cells are characterized by low PROM1 and positive VCAM1, in contrast to PROM1-positive proximal tubule cells.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:36c05d4204bb987a7c71
claim_id: claim:36c05d4204bb987a7c71
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
For example, there was a cell-specific tCRE in podocytes in the promoter region of NPHS1 and a cell-specific tCRE in the proximal tubule in the promoter region of CUBN (Supplementary Dataset 8 ).

summary:
In Homo sapiens, podocytes have a cell-specific transcribed cis-regulatory element in the promoter region of NPHS1.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:a39ef1159e75781c0352
claim_id: claim:a39ef1159e75781c0352
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
For example, there was a cell-specific tCRE in podocytes in the promoter region of NPHS1 and a cell-specific tCRE in the proximal tubule in the promoter region of CUBN (Supplementary Dataset 8 ).

summary:
In Homo sapiens, proximal tubule cells have a cell-specific transcribed cis-regulatory element in the promoter region of CUBN.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:dfd53645f6c396598326
claim_id: claim:dfd53645f6c396598326
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
Cell-specific ATAC peaks were enriched for established transcription factors that drive cell type differentiation like HNF4A in the proximal tubule and TFAP2B in the distal nephron (Supplementary Dataset 12 ).

summary:
In Homo sapiens, proximal tubule cells are enriched for HNF4A motifs in cell-specific ATAC peaks, indicating HNF4A as a marker of proximal tubule cell differentiation.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:d1abd47d7fc41ac62638
claim_id: claim:d1abd47d7fc41ac62638
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
Cell-specific ATAC peaks were enriched for established transcription factors that drive cell type differentiation like HNF4A in the proximal tubule and TFAP2B in the distal nephron (Supplementary Dataset 12 ).

summary:
In Homo sapiens, distal nephron cells are enriched for TFAP2B motifs in cell-specific ATAC peaks, indicating TFAP2B as a marker of distal nephron cell differentiation.


claim_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f:claim:f0c11b215b4eff834d0c
claim_id: claim:f0c11b215b4eff834d0c
paper_key: hca:0234_10.1038_s41467-022-32972-z_b918df798f
span_literal:
PT_PROM1 is characterized by a PROM1 high VCAM1- chromatin accessibility profile that differentiates it from PT_VCAM1, which is PROM1 low VCAM1 +.

summary:
In Homo sapiens, PROM1-positive proximal tubule cells are characterized by high PROM1 and negative VCAM1 chromatin accessibility, differentiating them from VCAM1-positive proximal tubule cells.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:ae4539dbe8581a22af08
claim_id: claim:ae4539dbe8581a22af08
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
summary: In Homo sapiens, AQP4 is a marker gene for astrocytes in the cerebral cortex.
span_literal:
AQP4 (astrocytes), SLC17A7 (EN), GAD2 (IN), PLP1 (oligodendrocytes), CD86 (microglia), and GPR17 (OPC) were marker genes with concordant expression and chromatin accessibility in their corresponding cell types.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:61a80b78d550f43e1e2f
claim_id: claim:61a80b78d550f43e1e2f
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
summary:
In Homo sapiens, GPR17 is a marker gene for oligodendrocyte progenitor cells in the cerebral cortex.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:96ba283461fd4c28f873
claim_id: claim:96ba283461fd4c28f873
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
CD74 + microglia expressed marker genes related to antigen processing and presentation/major histocompatibility complex (MHC) class II genes ( HLA-DRA , HLA-DPA1 , HLA-DPB1 , HLA-DRB1 , and HLA-DQA1 ), adaptive immune system response and microglial cell activation ( CD74 , SC1N , C1QA , C1QB , and C1QC ), and interferon signaling ( IFNGR1 , JAK2 , and B2M ).

summary:
In Homo sapiens, CD74-positive microglia express marker genes HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQA1, CD74, SC1N, C1QA, C1QB, C1QC, IFNGR1, JAK2, and B2M.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:23abe3afb857791e06bc
claim_id: claim:23abe3afb857791e06bc
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
CD83 + microglia expressed high levels of pro-inflammatory cytokines including IL1B , CCL2 , CCL3 , CCL4 , and TNFSF18 .

summary:
In Homo sapiens, CD83-positive microglia express high levels of pro-inflammatory cytokines IL1B, CCL2, CCL3, CCL4, and TNFSF18.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:3638259d4f988b2c52ef
claim_id: claim:3638259d4f988b2c52ef
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
Interestingly, CD83 and CD74 expression are largely non-overlapping, indicating that these surface markers can be effectively used to distinguish microglia states in FCD ( Figure 4 C).

summary:
In Homo sapiens, CD83 and CD74 expression are largely non-overlapping and can be used to distinguish microglia states, with CD83 marking CD83-positive microglia and CD74 marking CD74-positive microglia.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:a31021089fd3234788a9
claim_id: claim:a31021089fd3234788a9
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
Feature plots depicting normalized gene expression of immature astrocyte markers CD44 , TNC , VCAN , and GFAP (top), and differentiated astrocyte markers SLC1A2 , SLC1A3 , and GPC5 (bottom).

summary:
In Homo sapiens, CD44, TNC, VCAN, and GFAP are markers of immature astrocytes in the cerebral cortex.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:5e30951a111212f703d1
claim_id: claim:5e30951a111212f703d1
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
Feature plots depicting normalized gene expression of immature astrocyte markers CD44 , TNC , VCAN , and GFAP (top), and differentiated astrocyte markers SLC1A2 , SLC1A3 , and GPC5 (bottom).

summary:
In Homo sapiens, SLC1A2, SLC1A3, and GPC5 are markers of differentiated astrocytes in the cerebral cortex.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:596ecd8542bd402b4277
claim_id: claim:596ecd8542bd402b4277
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
In particular, we found two neurofilament subunits NEFL and NEFM overexpressed in the DS cluster ( Figure 3 C).

summary:
In Homo sapiens, neurofilament subunits NEFL and NEFM are overexpressed in the disease-specific cluster containing dysmorphic neurons.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:40ce5ca14b68d878d4ca
claim_id: claim:40ce5ca14b68d878d4ca
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
NEFM was exclusively expressed in the DS cluster and not detected in any other cell type in either lesions or non-lesion tissues ( Figure 3 D).

summary:
In Homo sapiens, NEFM is exclusively expressed in the disease-specific cluster containing dysmorphic neurons and not detected in any other cell type.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:b0e6e72d7e3d9090b30c
claim_id: claim:b0e6e72d7e3d9090b30c
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
Genes associated with balloon cells and reactive astrocytes including CHI3L1 , HSPB1 , SERPINA3 , GFAP , and VIM were upregulated in FCD IIb astrocytes compared to FCD IIa or internal controls ( Figure 6 E).

summary:
In Homo sapiens, CHI3L1, HSPB1, SERPINA3, GFAP, and VIM are upregulated in balloon cells in focal cortical dysplasia type IIb.


claim_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6:claim:a891eebf518bd38f780a
claim_id: claim:a891eebf518bd38f780a
paper_key: hca:0235_10.1016_j.isci.2024.111337_a37d387ae6
span_literal:
Genes associated with balloon cells and reactive astrocytes including CHI3L1 , HSPB1 , SERPINA3 , GFAP , and VIM were upregulated in FCD IIb astrocytes compared to FCD IIa or internal controls ( Figure 6 E).

summary:
In Homo sapiens, CHI3L1, HSPB1, SERPINA3, GFAP, and VIM are upregulated in reactive astrocytes in focal cortical dysplasia type IIb.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:a03fd09cbe1548497981
claim_id: claim:a03fd09cbe1548497981
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Cluster #9 was identified as myeloid cells, showing specific LIN(CD3D/CD79A/NKG7) − HLA-DQ + and expression of myeloid-specific genes (ITGAM, ITGAX, CD14, CSF1R, CD68 and CD209); and verified by expression of MS4A4A, CD1C and CLEC9A, markers for macrophage, cDC2 and cDC1, respectively

summary:
In Homo sapiens skin, MS4A4A is a marker for macrophages, CD1C is a marker for conventional dendritic cell type 2, and CLEC9A is a marker for conventional dendritic cell type 1.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:531970b0182f93c4367c
claim_id: claim:531970b0182f93c4367c
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Subclusters #1 and #3 highly expressed CD1C and represented two cDC2 populations, highly expressing either markers MCOLN2 or CXorf21 (MCOLN2 + DC and CXorf21 + DC)

summary:
In Homo sapiens skin, conventional dendritic cell type 2 populations highly express CD1C, with one subset marked by MCOLN2 and another by CXorf21.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:7bfe598c50e75441b09f
claim_id: claim:7bfe598c50e75441b09f
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
summary: In Homo sapiens skin, conventional dendritic cell type 1 highly expresses CLEC9A.
span_literal:
Subcluster #6 highly expressed CLEC9A and other cDC1 markers, and was identified as cDC1 cells, corresponding to closely to circulating DC1 cells


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:2b26633deb21a167d0dc
claim_id: claim:2b26633deb21a167d0dc
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
The cells in myeloid cluster #7, highly expressing CD1C and proliferation genes, such as MKI67, KIAA0101, TYMS, PTTG1, were identified as proliferating cDC2.

summary:
In Homo sapiens skin, proliferating conventional dendritic cell type 2 highly expresses CD1C, MKI67, KIAA0101, TYMS, and PTTG1.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:ec10667152e3ad0917a5
claim_id: claim:ec10667152e3ad0917a5
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Cells in subcluster #8 highly expressing LAMP3, CCL17, BIRC3 were identified as a mature subpopulation of cDC (LAMP3 + DC)

summary:
In Homo sapiens skin, LAMP3-positive mature conventional dendritic cell highly expresses LAMP3, CCL17, and BIRC3.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:7cf56e5d28c0d9bd9800
claim_id: claim:7cf56e5d28c0d9bd9800
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
summary: In Homo sapiens skin, Langerhans cells highly express CD207, FCGBP, and HLA-DQB2.
span_literal:
cells in subcluster #9 highly expressing CD207, FCGBP and HLA-DQB2 were identified as Langerhans cells


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:431640f995e85bfa34b4
claim_id: claim:431640f995e85bfa34b4
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
summary: In Homo sapiens healthy skin, three macrophage clusters selectively express CCR1, MARCO, or TREM2.
span_literal:
Three previously described macrophage clusters in healthy skin, selectively expressing CCR1, MARCO or TREM2, were also detected


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:78e86ca9927d200ab416
claim_id: claim:78e86ca9927d200ab416
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
HMOX1, MMP9, MMP19, CCL2, CEBPB, CTSL, CREM, THBD, EIF4E still highly expressed by cells in subcluster #0 (CCR1 + macrophages)

summary:
In Homo sapiens skin, CCR1-positive macrophages highly express HMOX1, MMP9, MMP19, CCL2, CEBPB, CTSL, CREM, THBD, and EIF4E.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:d8e2968f76fd06962538
claim_id: claim:d8e2968f76fd06962538
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
A distinct third macrophage population seen in both HC and SSc was distinguished by high expression of TREM2, FABP4 and FABP5, paralleled to the TREM2 + macrophages, which we previously identified in healthy skin

summary:
In Homo sapiens skin, TREM2-positive macrophages are distinguished by high expression of TREM2, FABP4, and FABP5.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:e92d05c591ee6dfa0449
claim_id: claim:e92d05c591ee6dfa0449
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Cells in subcluster #4 (FCG3A + macrophages) highly expressed macrophage markers, including MS4A4A and FCGR3A encoding CD16A

summary:
In Homo sapiens skin, FCGR3A-positive macrophages highly express macrophage markers MS4A4A and FCGR3A.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:c0f09e654f770c58a0e9
claim_id: claim:c0f09e654f770c58a0e9
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
These cells also selectively expressed SLC40A1, IFI27, MSR1 (macrophage scavenger receptor 1), RCAN1 and OLR1 suggesting specialized functions of FCGR3A + macrophages

summary:
In Homo sapiens skin, FCGR3A-positive macrophages selectively express SLC40A1, IFI27, MSR1 (macrophage scavenger receptor 1), RCAN1, and OLR1.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:f46be383ab631c3e7108
claim_id: claim:f46be383ab631c3e7108
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Genes, encoding chemokines: CCL18, CXCL1, CCL8, CCL3, CCL4, CCL2, CCL13, and CXCL2 were highly expressed in this cluster.

summary:
In Homo sapiens skin, FCGR3A-positive macrophages highly express chemokines CCL18, CXCL1, CCL8, CCL3, CCL4, CCL2, CCL13, and CXCL2.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:05547f9a19fbae13f7c9
claim_id: claim:05547f9a19fbae13f7c9
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Cells in this cluster (cluster #5, FCN1 + mo-DC) selectively showed upregulated expression of FCN1, EREG, S100A8, AQP9, VCAN and THBS1, and expressed macrophage markers: CD163, F13A1, and MS4A4A at only moderate levels

summary:
In Homo sapiens skin, FCN1-positive monocyte-derived dendritic cells selectively express FCN1, EREG, S100A8, AQP9, VCAN, and THBS1, while expressing CD163, F13A1, and MS4A4A at only moderate levels.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:46382f6e65b891fe9330
claim_id: claim:46382f6e65b891fe9330
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Among the FCN1 + myeloid cell, 50 top differentially expressed genes: FCN1, S100A8, AQP9, VCAN, CD300E, S100A9, FPR1, SOD2 and C5AR1, are markers for classical monocytes

summary:
In Homo sapiens, FCN1, S100A8, AQP9, VCAN, CD300E, S100A9, FPR1, SOD2, and C5AR1 are markers for classical monocytes.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:c2ee2aaa5b0d26a5f590
claim_id: claim:c2ee2aaa5b0d26a5f590
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
Re-clustering these cells detected two clusters, one prominently expressing B cell markers (MS4A1A, CD79A and immunoglobulin genes) and the other markers of pDC (LILRA4, IL3RA, CLEC4C), described previously as circulating DC6

summary:
In Homo sapiens skin, B cells prominently express MS4A1A and CD79A, while plasmacytoid dendritic cells express LILRA4, IL3RA, and CLEC4C.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:73de59ba2fd56ab2a6d1
claim_id: claim:73de59ba2fd56ab2a6d1
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
We detected upregulated expression of transcription factors important in pDC differentiation: IRF4, IRF7, IRF8 and ZEB2 compared to other skin cells or B cells, but not expression of IFNA1-11 or CXCL4

summary:
In Homo sapiens skin, plasmacytoid dendritic cells show upregulated expression of IRF4, IRF7, IRF8, and ZEB2 compared to other skin cells or B cells.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:ef1930773da9149c1fb7
claim_id: claim:ef1930773da9149c1fb7
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
FCGR3A + macrophages expressed most other macrophage markers, failed to express monocyte markers and trajectory analysis suggested that CCR1 + macrophages and/or MARCO + macrophages are the progenitors of these cells.

summary:
In Homo sapiens skin, FCGR3A-positive macrophages fail to express monocyte markers, distinguishing them from monocytes.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:a132ebb253a541b1a306
claim_id: claim:a132ebb253a541b1a306
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
A second SSc-associated myeloid population, highly expressed monocyte markers: FCN1, EREG, S100A8 and S100A9, but was closely related to cDC2 on pseudotime analysis and identified as Mo-DC.

summary:
In Homo sapiens skin, monocyte-derived dendritic cells highly express monocyte markers FCN1, EREG, S100A8, and S100A9.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:2eccef5f9179c744ea3f
claim_id: claim:2eccef5f9179c744ea3f
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
summary: In Homo sapiens skin, an SSc-associated macrophage cluster highly expresses FCGR3A.
span_literal:
One SSc-associated macrophage cluster, highly expressing FCGR3A, on pseudotime analysis was suggested to derive from normal CCR1 + and MARCO + macrophages.


claim_key: hca:0238_10.1002_art.41813_55de40d8f6:claim:802aefe8209305a414fb
claim_id: claim:802aefe8209305a414fb
paper_key: hca:0238_10.1002_art.41813_55de40d8f6
span_literal:
In SSc skin FCN1 + cells maintained expression of CD14, CD13/ANPEP, CD172a/SIRPA, as well as S100A8 and S100A9, all described as markers of mo-DC

summary:
In Homo sapiens systemic sclerosis skin, FCN1-positive monocyte-derived dendritic cells express CD14, ANPEP, SIRPA, S100A8, and S100A9, all described as markers of monocyte-derived dendritic cells.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:de28cd6f8e5e63b22dd6
claim_id: claim:de28cd6f8e5e63b22dd6
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal: COL11A1 / ACTA2 -expressing dermal sheath cells
summary:
In Homo sapiens, dermal sheath cells express COL11A1. In Homo sapiens, dermal sheath cells express COL11A1 and ACTA2.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:387331700f643c962388
claim_id: claim:387331700f643c962388
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal: papillary ( COL6A5 , APCDD1 , HSPB3 , WIF1 , and CD39 ) and reticular
summary:
In Homo sapiens, papillary dermal fibroblasts are distinguished from reticular dermal fibroblasts by COL6A5, APCDD1, HSPB3, WIF1, and CD39.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:daf7b0f0cb52b9dce5b6
claim_id: claim:daf7b0f0cb52b9dce5b6
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal: papillary ( COL6A5 , APCDD1 , HSPB3 , WIF1 , and CD39 ) and reticular ( CD36
summary:
In Homo sapiens, reticular dermal fibroblasts are distinguished from papillary dermal fibroblasts by CD36.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:0bba78b2827d5419d23a
claim_id: claim:0bba78b2827d5419d23a
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal: DES ) and smoothelin ( SMTN ) for SMCs
summary:
In Homo sapiens, smooth muscle cells are marked by expression of desmin (DES) and smoothelin (SMTN).


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:36ec0614f81711a7cc8e
claim_id: claim:36ec0614f81711a7cc8e
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
regulator of G protein signaling 5 ( RGS5 ), chondroitin sulfate proteoglycan 4 CSPG4/NG2 , platelet-derived growth factor receptor beta ( PDGFRB ) for pericytes

summary:
In Homo sapiens, pericytes are marked by regulator of G protein signaling 5 (RGS5), chondroitin sulfate proteoglycan 4 (CSPG4), and platelet-derived growth factor receptor beta (PDGFRB).


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:eed4b497969017217595
claim_id: claim:eed4b497969017217595
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal: CRABP1 / COCH -expressing dermal papilla
summary:
In Homo sapiens, dermal papilla cells express CRABP1 and COCH, while dermal sheath cells express COL11A1 and ACTA2.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:12fea5dce988627fade1
claim_id: claim:12fea5dce988627fade1
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
two small discrete populations of fibroblasts expressed SFRP4 / ANGPTL7 (cluster 8) and SFRP4 / LINC01133 (subset of cluster 3).

summary:
In Homo sapiens, a discrete fibroblast population expresses SFRP4 and ANGPTL7, and another expresses SFRP4 and LINC01133.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:a550b9a793b2405cf977
claim_id: claim:a550b9a793b2405cf977
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
summary: In Homo sapiens, fibroblasts are marked by expression of COL1A1, COL1A2, and PDGFRA.
span_literal:
We selected the cell clusters of fibroblasts based on expression of COL1A1 , COL1A2 , and PDGFRA (clusters 3, 8, 10, 12, 17, and 26 from Fig. 1a ), as we described previously these genes to be robust fibroblast cluster markers


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:031ccae7b6ad9e92534c
claim_id: claim:031ccae7b6ad9e92534c
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal: CRABP1 -expressing cells likely represent dermal papilla fibroblasts
summary:
In Homo sapiens, dermal papilla fibroblasts express CRABP1, and dermal sheath fibroblasts express ACTA2 and SOX2.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:74fff7713d0bce1d2246
claim_id: claim:74fff7713d0bce1d2246
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
summary: In Homo sapiens, a population of papillary fibroblasts expresses ANGPTL7, C2orf40, and SFRP4.
span_literal:
Thus, ANGPTL7 / C2orf40 / SFRP4 -expressing cells (subcluster 7, Figs. 2a and 3a ) represent a population of papillary fibroblasts


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:517b2b44703d936c241b
claim_id: claim:517b2b44703d936c241b
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
Here, we show that SSc dermal myofibroblasts arise in two steps from an SFRP2 hi /DPP4 -expressing progenitor fibroblast population.

summary:
In Homo sapiens, systemic sclerosis dermal myofibroblasts arise from an SFRP2-high/DPP4-expressing progenitor fibroblast population.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:8cc3a68eb12c4d800c1c
claim_id: claim:8cc3a68eb12c4d800c1c
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
summary: In Homo sapiens, systemic sclerosis fibroblasts show upregulated expression of PRSS23 and THBS1.
span_literal:
SSc fibroblasts show globally upregulated expression of transcriptome markers, such as PRSS23 and THBS1


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:f98ac1c7ae309e301c92
claim_id: claim:f98ac1c7ae309e301c92
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
PRSS23 , THBS1 , and TNC , or they were expressed by a subset of cells in this cluster, such as SFRP4 , ADAM12 , TNFSF18 , CTGF , FNDC1 , COL10A1 , and MATN3

summary:
In Homo sapiens, systemic sclerosis SFRP2-high PRSS23-positive fibroblasts express PRSS23, THBS1, and TNC broadly, while a subset (myofibroblasts) expresses SFRP4, ADAM12, TNFSF18, CTGF, FNDC1, COL10A1, and MATN3.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:5970d0344d9eb9e8020f
claim_id: claim:5970d0344d9eb9e8020f
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
Violin plots indicate gene expression by proliferating cells (subcluster 9), showing markers of dermal sheath cells ( DPEP1 and COL11A1 ) by healthy control cells (2 cells) and markers of SFRP2 hi PRSS23 + WIF1 − cells ( SFRP2 , PRSS23 , TNC , COMP , and TNFSF18 ) by SSc fibroblasts (37 cells).

summary:
In Homo sapiens, dermal sheath cells are marked by DPEP1 and COL11A1, while SFRP2-high PRSS23-positive WIF1-negative fibroblasts are marked by SFRP2, PRSS23, TNC, COMP, and TNFSF18.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:957575e2fc42f5b32944
claim_id: claim:957575e2fc42f5b32944
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
Violin plots indicate gene expression by proliferating cells (subcluster 9), showing markers of dermal sheath cells ( DPEP1 and COL11A1 ) by healthy control cells (2 cells) and markers of SFRP2 hi PRSS23 + WIF1 − cells ( SFRP2 , PRSS23 , TNC , COMP , and TNFSF18 ) by SSc fibroblasts (37 cells).

summary:
In Homo sapiens, SFRP2-high PRSS23-positive WIF1-negative fibroblasts are marked by SFRP2, PRSS23, TNC, COMP, and TNFSF18.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:eaab3f1ad8a23551ea1d
claim_id: claim:eaab3f1ad8a23551ea1d
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
span_literal:
we show that SSc dermal myofibroblasts arise in two steps from an SFRP2 hi /DPP4 -expressing progenitor fibroblast population.

summary:
In Homo sapiens, systemic sclerosis dermal myofibroblasts arise from an SFRP2-high/DPP4-expressing progenitor fibroblast population.


claim_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5:claim:d6178d3d2ad91c029433
claim_id: claim:d6178d3d2ad91c029433
paper_key: hca:0239_10.1038_s41467-021-24607-6_2a0350c2e5
summary: In Homo sapiens, systemic sclerosis myofibroblasts are marked by SFRP4.
span_literal:
we identify the transcriptome of SSc myofibroblasts and show that SFRP4 is an immunohistochemical marker for these cells.


claim_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a:claim:c8a46cbd8f207ca1940b
claim_id: claim:c8a46cbd8f207ca1940b
paper_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a
span_literal:
Clustering of cells using t–distributed stochastic neighbor embedding ( tSNE ) revealed a separation of STMN2 expressing neurons, from progenitors and mitotically active cells expressing VIM and TOP2A

summary:
In Homo sapiens human cortical spheroid-derived cells, STMN2 is a positive marker of neurons, distinguishing them from progenitor cells.


claim_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a:claim:4e6e659592ea8c55c5cd
claim_id: claim:4e6e659592ea8c55c5cd
paper_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a
span_literal:
Clustering of cells using t–distributed stochastic neighbor embedding ( tSNE ) revealed a separation of STMN2 expressing neurons, from progenitors and mitotically active cells expressing VIM and TOP2A

summary:
In Homo sapiens human cortical spheroid-derived cells, VIM is a positive marker of progenitor cells. In Homo sapiens human cortical spheroid-derived cells, TOP2A is a positive marker of progenitor cells.


claim_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a:claim:6800b630796c179222bd
claim_id: claim:6800b630796c179222bd
paper_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a
span_literal:
We also identified a group of glutamatergic neurons ( VGLUT1 + ) expressing the cortical layer markers TBR1 ; a group of intermediate progenitors expressing EOMES ; a group of dorsal progenitors expressing PAX6 ; a group of astroglia ( CLU + ); a small group of cells that resemble the choroid plexus ( TTR + , SLC13A4 + ) and a very small number of GAD1 + cells.

summary:
In Homo sapiens human cortical spheroids, VGLUT1 is a positive marker of glutamatergic neurons. In Homo sapiens human cortical spheroids, TBR1 is a positive marker of glutamatergic neurons.


claim_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a:claim:222f8c464bc9365e0767
claim_id: claim:222f8c464bc9365e0767
paper_key: hca:0240_10.1038_s41591-020-1043-9_9c3b0c098a
summary:
In Homo sapiens human cortical spheroids, TTR and SLC13A4 are positive markers of choroid plexus cells.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:e012778d3981f5582c2b
claim_id: claim:e012778d3981f5582c2b
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal: we examined the metabolic phenotype of CD25 + CD127 lo/– Tregs in the presence of LCFAs.
summary:
In Homo sapiens, regulatory T cells are identified by positive expression of CD25 (IL2RA) and low/negative expression of CD127 (IL7R).


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:c05eb4831db0188802f7
claim_id: claim:c05eb4831db0188802f7
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
both fatty acids were negated by the addition of etomoxir. Unlike Tregs, the maximum OCR and spare respiratory capacity of Teffs increased with oleic acid, also in a CPT1A-dependent manner

summary:
In Homo sapiens, effector T cells showed CPT1A-dependent metabolic responses, indicating CPT1A is expressed in effector T cells.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:a4cefaa1645aac75e10f
claim_id: claim:a4cefaa1645aac75e10f
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal: CPT1A , CPT2 , ACADVL , ECHS1 , and PDSS1
summary:
In Homo sapiens, regulatory T cells upregulate CPT1A, CPT2, ACADVL, ECHS1, and PDSS1 in the presence of oleic acid.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:4009af31cda3d3caedd8
claim_id: claim:4009af31cda3d3caedd8
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal: Enrichment of CD69 and CD9 indicates that arachidonic acid–treated Tregs are more activated
summary:
In Homo sapiens, CD69 and CD9 are markers of activation in regulatory T cells treated with arachidonic acid.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:6888861ed8d889ed1fc2
claim_id: claim:6888861ed8d889ed1fc2
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
Notably, we detected genes that promote proinflammatory T cells, such as CKS2, LDHA, and LDHB, which promote Th17 ( 72 , 73 ) and Th1 ( 74 ) differentiation, respectively.

summary:
In Homo sapiens, CKS2 promotes T helper 17 cell differentiation, while LDHA and LDHB promote T helper 1 cell differentiation.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:0e2c61719483368659c4
claim_id: claim:0e2c61719483368659c4
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
Oleic acid–driven FAO and OXPHOS in Tregs drive the expression of FOXP3, CD25, and p-STAT5, all of which act to reinforce the Treg lineage by inducing and reinforcing demethylation of the FOXP3 Treg-specific demethylated region (TSDR), even under inflammatory conditions

summary:
In Homo sapiens, regulatory T cells express FOXP3, CD25, and phosphorylated STAT5, which reinforce the regulatory T cell lineage.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:806376992e3e63235e9c
claim_id: claim:806376992e3e63235e9c
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal: For example, ACBD7, ACOT11, and ACSL6 bind and convert LCFAs to acyl-CoA for degradation by FAO
summary:
In Homo sapiens, the oleic acid module in regulatory T cells includes ACBD7, ACOT11, and ACSL6, which are involved in long-chain fatty acid metabolism.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:28833ab479779876a2f0
claim_id: claim:28833ab479779876a2f0
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
LPIN3 has a general role in regulating fatty acid metabolism ( 60 ), and LETM1 regulates mitochondrial dynamics and maintains normal mitochondrial morphology

summary:
In Homo sapiens, the oleic acid module in regulatory T cells includes LPIN3 and LETM1, which regulate fatty acid metabolism and mitochondrial dynamics respectively.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:9916d88a1be074d377ed
claim_id: claim:9916d88a1be074d377ed
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal: PGK1 and PGM1 catalyze the breakdown of glucose ( 62 – 64 ), and SLC2A7 is a glucose transporter
summary:
In Homo sapiens, the arachidonic acid module in regulatory T cells includes PGK1, PGM1, and SLC2A7, which are involved in glucose metabolism.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:b7af83eb6459a6141f93
claim_id: claim:b7af83eb6459a6141f93
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
SIRT4 regulates FAO via inhibition of PPARα transcription ( 66 ) and FABP5, an intracellular lipid chaperone

summary:
In Homo sapiens, the arachidonic acid module in regulatory T cells includes SIRT4 and FABP5, which are involved in fatty acid oxidation regulation and intracellular lipid chaperoning.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:51ec23020b276348a673
claim_id: claim:51ec23020b276348a673
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
We also observed upregulation of C5AR2, which has been shown to promote peripherally induced Tregs in human and murine models.

summary:
In Homo sapiens, C5AR2 is upregulated in the oleic acid module and promotes peripherally induced regulatory T cells.


claim_key: hca:0242_10.1172_jci138519_8b328cd6bc:claim:f0b6d10fe71d4fe4b9f0
claim_id: claim:f0b6d10fe71d4fe4b9f0
paper_key: hca:0242_10.1172_jci138519_8b328cd6bc
span_literal:
Forced expression of FOXP3 in T cells suppresses glycolysis-related genes, while inducing lipid and oxidative metabolism–related genes that are required for maximum suppression

summary:
In Homo sapiens, FOXP3 expression in regulatory T cells induces lipid and oxidative metabolism-related genes required for suppressive function.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:6fc0406e907b5b007693
claim_id: claim:6fc0406e907b5b007693
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, interstitial cells of Cajal are marked by KIT and ANO.
span_literal:
we annotated eight fibroblast subtypes—interstitial cells of Cajal ( KIT , ANO ), glial cells ( SOX10 , CDH19 , PLP1 ), neurons ( SYP , SYT1 , RBFOX1 ), pericytes ( NOTCH3 , MCAM1 , RGS5 ), adipocytes ( PLIN1 , LPL ) and three endothelial cell clusters


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:8cd51067e4c7fdf24921
claim_id: claim:8cd51067e4c7fdf24921
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal: Cells with high expression of MYH11 and ACTA2 were classified as smooth muscle/myofibroblasts.
summary:
In Homo sapiens intestine, smooth muscle/myofibroblasts are marked by high expression of MYH11 and ACTA2.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:a8940e12bfca824620c2
claim_id: claim:a8940e12bfca824620c2
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, a smooth muscle cluster labelled DES high has high expression of DES.
span_literal:
One of these clusters had high expression of DES , which we labelled DES high and may represent smooth muscle.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:f122f275554ebb133034
claim_id: claim:f122f275554ebb133034
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, crypt fibroblasts are marked by high expression of RSPO3 and GREM1.
span_literal:
We also identified fibroblasts with high levels of WNT agonists, such as RSPO3 , and the BMP antagonist GREM1 , which are probably present at the crypts


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:8c74a0267b62dd52aef6
claim_id: claim:8c74a0267b62dd52aef6
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, BEST4-positive enterocytes are marked by BEST4.
span_literal:
Consistent with recent reports of BEST4 + enterocytes in the small and large intestine 6 , 32 , we observed populations of BEST4 + enterocytes in all eight intestinal regions assayed.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:fc316d30c0ef15974c93
claim_id: claim:fc316d30c0ef15974c93
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
We identified many known subtypes of enteroendocrine cells, including D cells ( SST high ), I cells ( CCK high ), K cells ( GIP high ), Mo cells ( MLN high ), S cells ( SCT high ), L cells ( GCG high and PYY high ) and enterochromaffin cells ( TPH1 high ).

summary:
In Homo sapiens intestine, D cells are marked by high SST expression, I cells by high CCK expression, K cells by high GIP expression, Mo cells by high MLN expression, S cells by high SCT expression, L cells by high GCG and PYY expression, and enterochromaffin cells by high TPH1 expression.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:51132f2ca28dae4f84e4
claim_id: claim:51132f2ca28dae4f84e4
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens colon, a subset of L cells is marked by INSL5 expression.
span_literal:
L cells can be further divided on the basis of expression of INSL5 + , which is primarily expressed by L cells in the colon.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:022e6fc77e46ce56ad81
claim_id: claim:022e6fc77e46ce56ad81
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
We found that RXFP4 is primarily expressed by colon enterochromaffin cells and, to a lesser extent, I cells, suggesting that these are the most likely cell types that the INSL5 + L cells are signalling

summary:
In Homo sapiens colon, enterochromaffin cells primarily express RXFP4, and I cells express it to a lesser extent.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:898d3ba8b5386c59c12d
claim_id: claim:898d3ba8b5386c59c12d
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal: MUC6 and TFF2
summary:
In Homo sapiens duodenum, a specialized secretory cell cluster is marked by high MUC6 and TFF2 expression.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:204284fc74d8db602ec4
claim_id: claim:204284fc74d8db602ec4
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
For example, ASCL2, a master regulator of intestinal stem cells 44 , exhibited high expression and motif accessibility in stem cells.

summary:
In Homo sapiens intestine, ASCL2, a master regulator of intestinal stem cells, exhibits high expression and motif accessibility in stem cells.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:5a2a68a751f610123229
claim_id: claim:5a2a68a751f610123229
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal: Other TFs with high expression and motif activity in stem cells include NFIX, NFIC and HNF1B.
summary:
In Homo sapiens intestine, stem cells show high expression and motif activity of NFIX, NFIC, and HNF1B.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:9cee2d2e6b1468d9f62b
claim_id: claim:9cee2d2e6b1468d9f62b
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, POU2F3 is highly expressed and has high motif activity in tuft cells.
span_literal:
POU2F3, a regulator necessary for the development of tuft cells in mice 45 , was highly expressed and had high motif activity in tuft cells throughout the human intestine.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:66009d01889bec8ba7ce
claim_id: claim:66009d01889bec8ba7ce
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
Along with POU2F3, RUNX1 and RUNX2 also exhibited high expression and accessibility in tuft cells throughout the intestine, indicating that they may also have a role in tuft cell differentiation or maintenance.

summary:
In Homo sapiens intestine, RUNX1 and RUNX2 exhibit high expression and chromatin accessibility in tuft cells.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:e1ffae563ac2035cf3df
claim_id: claim:e1ffae563ac2035cf3df
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, goblet cells exhibit high gene expression and motif activity of KLF4.
span_literal:
Among goblet cells, KLF4, which is required for terminal differentiation into colonic goblet cells in mice 46 , exhibited high gene expression and motif activity.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:6b6dd0ccec1f951d35cf
claim_id: claim:6b6dd0ccec1f951d35cf
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal: Several regulatory TFs were nominated in goblet cells, including ATOH1 and FOXA3.
summary:
In Homo sapiens intestine, goblet cells are associated with the regulatory transcription factors ATOH1 and FOXA3.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:0058ca30f70b001aab8b
claim_id: claim:0058ca30f70b001aab8b
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
Within enteroendocrine/enterochromaffin cells, RFX2, RFX3 and RFX6 exhibited high expression and accessibility.

summary:
In Homo sapiens intestine, enteroendocrine/enterochromaffin cells exhibit high expression and chromatin accessibility of RFX2, RFX3, and RFX6.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:7d7ad669290b59e4b7e6
claim_id: claim:7d7ad669290b59e4b7e6
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
Within the immune compartment, this analysis highlighted many TFs that are known to be important for cell type differentiation and maintenance, including GATA2 in mast cells 53 and PAX5 in B cells 54

summary:
In Homo sapiens intestine, GATA2 is an important transcription factor in mast cells and PAX5 in B cells.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:3822a2bf1fb1b505cd92
claim_id: claim:3822a2bf1fb1b505cd92
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
Among stromal cells, we identified TFs associated within specific lineages, including EBF1 in pericytes—which was recently suggested to contribute to pericyte cell commitment 55 —PPARG in adipocytes 56 and SOX10 in glia 57

summary:
In Homo sapiens intestine, EBF1 is a transcription factor associated with pericytes, PPARG with adipocytes, and SOX10 with glia.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:be8152990366f3c6663c
claim_id: claim:be8152990366f3c6663c
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
We also nominate potential regulatory TFs in interstitial cells of Cajal, including HAND1, HOXD11 and MEIS1

summary:
In Homo sapiens intestine, interstitial cells of Cajal are associated with the potential regulatory transcription factors HAND1, HOXD11, and MEIS1.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:d2e74d7406b68f216308
claim_id: claim:d2e74d7406b68f216308
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, intestinal stem cells are marked by RGMB, SOX9, SMOC2, and LGR5.
span_literal:
This cluster includes general markers of intestinal stem cells, including RGMB, SOX9, SMOC2 and LGR5.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:899b05e066363f34f12d
claim_id: claim:899b05e066363f34f12d
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, BEST4-positive enterocytes are marked by BEST4 and OTOP2.
span_literal:
Marker genes were used for initial annotation of cell types including BEST4 + enterocytes (BEST4, OTOP2), goblet cells (MUC2, TFF1, SYTL2), immature goblet cells (KLK1, RETNLB, CLCA1), stem cells (RGMB, SMOC2, LGR5, ASCL2), tuft cells (SH2D6, TRPM5, BMX, LRMP, HCK), enteroendocrine cells (SCGN, FEV, CHGA, PYY, GCG), cycling transit-amplifying cells (TICRR, CDC25C) and Paneth cells (LYZ, DEFA5).


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:3a43e11b1c0b7223905e
claim_id: claim:3a43e11b1c0b7223905e
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
summary: In Homo sapiens intestine, T cells are marked by CD2, CD3E, IL7R, CD4, and CD8.
span_literal:
we identified clusters of CD4 + and CD8 + T cells (CD2, CD3E, IL7R, CD4, CD8), B cells (PAX5, MS4A1, CD19), plasma cells (IGLL5, AMPD1), natural killer cells (SH2D1B), macrophages/monocytes (CD14) and mast cells (HDC, GATA2, TPSAB1)


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:74bf575caa919181e2f9
claim_id: claim:74bf575caa919181e2f9
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal: Smooth muscle/myofibroblast clusters exhibited high expression of ACTA2, MTH11 and TAGLN.
summary:
In Homo sapiens intestine, smooth muscle/myofibroblast clusters exhibit high expression of ACTA2, MTH11, and TAGLN.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:aab65b403106dd46d12b
claim_id: claim:aab65b403106dd46d12b
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
Villus fibroblasts exhibited high expression of WNT5B and some crypt fibroblasts exhibited high expression of RSPO3.

summary:
In Homo sapiens intestine, villus fibroblasts exhibit high expression of WNT5B and crypt fibroblasts exhibit high expression of RSPO3.


claim_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2:claim:fe1fc8c9c9019ded1d44
claim_id: claim:fe1fc8c9c9019ded1d44
paper_key: hca:0243_10.1038_s41586-023-05915-x_2f4aafa6a2
span_literal:
Exocrine cells were annotated on the basis of expression of CELA3B and CPB1, and MUC5B + and MUC6 + cells were annotated on the basis of expression of MUC5B and MUC6

summary:
In Homo sapiens intestine, exocrine cells are annotated on the basis of expression of CELA3B and CPB1, and MUC5B-positive and MUC6-positive cells on the basis of MUC5B and MUC6 expression.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:3b348ffe8b16d137014a
claim_id: claim:3b348ffe8b16d137014a
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
Examples of human-specific differentially expressed genes in adult cell classes (Fig. 4h ) include differentially expressed genes detected in developing neurons, such as COL6A1 , which has been shown to have a protective role in ageing neurons

summary:
In Homo sapiens, COL6A1 is a human-specific differentially expressed gene detected in developing neurons.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:61b419e7f3c40509b0e3
claim_id: claim:61b419e7f3c40509b0e3
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
Immunohistochemical staining for PAX6 (green) and BCL11B (also known as CTIP2 ) (pink) of a 63-day human organoid from iPSC line 409b2 (left) and a 63-day chimpanzee organoid from iPSC line SandraA (right), with a magnified view into a cortical-like region

summary:
In Homo sapiens cerebral organoids, PAX6 marks progenitor cells and BCL11B marks deep-layer neurons in cortical-like regions.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:640eacd8d7a885af3daf
claim_id: claim:640eacd8d7a885af3daf
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
Staining for deep-layer ( BCL11B ) and upper-layer ( SATB2 ) neuron markers for human (top right, Sc102a1, 45-day) and chimpanzee (bottom right, SandraA, 63-day) organoids.

summary:
In Homo sapiens, BCL11B is a marker of deep-layer neurons and SATB2 is a marker of upper-layer neurons. In Homo sapiens, BCL11B is a marker of deep-layer neurons distinguished from upper-layer neurons.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:6ff6ffd12360c69ab7f6
claim_id: claim:6ff6ffd12360c69ab7f6
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
Immunohistochemical staining of human (top left, Sc102a1, 50-day; top middle, 409b2, 63-day, the same organoid as the human organoid in b ) and chimpanzee (bottom left, SandraA, 50-day; bottom middle, SandraA, 63-day) organoids (scale bars, 200 μm) for progenitor ( PAX6 ) intermediate progenitor ( TBR2 ) and deep-layer neurons ( BCL11B ) in whole organoids.

summary:
In Homo sapiens organoids, PAX6 marks progenitor cells, TBR2 marks intermediate progenitor cells, and BCL11B marks deep-layer neurons.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:54063d8b3ba72d3cc3bc
claim_id: claim:54063d8b3ba72d3cc3bc
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
BCL11B and SATB2 become anti-correlated in their pseudotemporal expression profile in both human and chimpanzee (right), while the onset of anti-correlation happens earlier in chimpanzee than in human.

summary:
In Homo sapiens, BCL11B and SATB2 become anti-correlated along the cortical neuron pseudotemporal expression profile, marking deep-layer and upper-layer cortical neurons respectively.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:3c2cdc701f7cc1a56b7f
claim_id: claim:3c2cdc701f7cc1a56b7f
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
Expression of layer markers ( RASGRF2 , RORB , ETV1 and TLE4 ) in excitatory neurons and inhibitory neuron subtype markers ( PVALB and SST ) in inhibitory neurons, along the predicted laminar origin of the pseudonuclei in human, chimpanzee and bonobo, and macaque.

summary:
In Homo sapiens, RASGRF2, RORB, ETV1 and TLE4 are layer markers expressed in excitatory neurons, while PVALB and SST are subtype markers of inhibitory neurons in the adult prefrontal cortex.


claim_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190:claim:f9a3ee2340b153301058
claim_id: claim:f9a3ee2340b153301058
paper_key: hca:0244_10.1038_s41586-019-1654-9_7c485e5190
span_literal:
Expression of layer markers ( RASGRF2 , RORB , ETV1 and TLE4 ) in excitatory neurons and inhibitory neuron subtype markers ( PVALB and SST ) in inhibitory neurons, along the predicted laminar origin of the pseudonuclei in human, chimpanzee and bonobo, and macaque.

summary:
In Homo sapiens, PVALB and SST are subtype markers of inhibitory neurons in the adult prefrontal cortex.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:814374f64b06d8ea8b1c
claim_id: claim:814374f64b06d8ea8b1c
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
summary: In Homo sapiens, epithelial cell rests of Malassez are marked by cytokeratin 14 and cytokeratin 5.
span_literal:
In further analogy, the ERM markers cytokeratin (CK) 14 and CK5 [ 27 ] were detected in the organoids, as they are observed in compartments of the original DF tissue (Fig. 1 c).


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:9ce451a74cbf5c30a6df
claim_id: claim:9ce451a74cbf5c30a6df
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Importantly, the mesenchymal (fibroblast) marker CD90 (Thy-1 cell surface antigen, THY1), which is observed in compartments of the original DF tissue was not detected in the organoids (Supplementary Fig. 1i), indicating the absence of pure mesenchymal cells in the (epithelial) organoids.

summary:
In Homo sapiens, CD90 (Thy-1 cell surface antigen, THY1) is a marker of mesenchymal fibroblast cells and is not detected in epithelial organoids.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:029dc3a154033ef62f8e
claim_id: claim:029dc3a154033ef62f8e
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Previous studies proposed that the ERM contains DESCs, among others marked by CD44 and P63 [ 12 , 27 , 28 ].

summary:
In Homo sapiens, dental epithelial stem cells in the epithelial cell rests of Malassez are marked by CD44 and P63.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:8c7a47e3b01a05df044b
claim_id: claim:8c7a47e3b01a05df044b
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Moreover, the organoids and the native DF tissue expressed SOX2 (Fig. 1 d), a well-known marker of DESCs in mouse [ 29 – 32 ] and detected in epithelium of developing teeth in humans [ 4 ].

summary:
In Homo sapiens, SOX2 is detected in the epithelium of developing teeth, consistent with its role as a marker of dental epithelial stem cells.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:8c124fd813844eda3a0a
claim_id: claim:8c124fd813844eda3a0a
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Finally, the organoids showed prominent gene expression of the proposed ERM stem cell marker integrin-α6 ( ITGα6 ) [ 8 , 28 ], as well as of factors playing an important role in embryonic development of the dental epithelium (i.e. paired like homeodomain 2 ( PITX2 ) [ 33 ] and bone-morphogenetic protein 4 ( BMP4 )) [ 34 ], all markers also detected in the original DF tissue (Supplementary Fig. 1j).

summary:
In Homo sapiens, integrin-alpha 6 (ITGα6) is a proposed marker of epithelial cell rests of Malassez stem cells, and paired like homeodomain 2 (PITX2) and bone morphogenetic protein 4 (BMP4) are markers of dental epithelium.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:4969ef735c29eb9adf6f
claim_id: claim:4969ef735c29eb9adf6f
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Of note, mesenchymal markers such as fibroblast activation protein alpha ( FAP ) and collagen type I alpha 1 chain ( COL1A1 ), being present in the DF mesenchymal (fibroblast) cluster, were not detected in the organoid clusters, thereby again demonstrating the absence of pure mesenchymal cells in the (epithelial) organoids (Supplementary Fig. 2d).

summary:
In Homo sapiens, fibroblast activation protein alpha (FAP) and collagen type I alpha 1 chain (COL1A1) are mesenchymal markers present in the dental follicle mesenchymal fibroblast cluster.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:dc865c81c32c384342f0
claim_id: claim:dc865c81c32c384342f0
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Interestingly, the newly proposed mouse incisor epithelial (stem) cell markers KRT15 and dentin sialoprotein (DSP) [ 46 ] were among the top 10 DEGs in the organoid as well as ERM clusters (Fig. 2 b,c; Supplementary Fig. 2e).

summary:
In Homo sapiens, KRT15 and dentin sialoprotein (DSP) are among the top differentially expressed genes in the epithelial cell rests of Malassez and organoid clusters, mirroring their role as epithelial stem cell markers.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:f675ad05b5620b5d0b0d
claim_id: claim:f675ad05b5620b5d0b0d
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal: For instance, the cell cycle inhibitor CDKN1C is among the top DEGs in the ERM cluster (Fig. 2 b).
summary:
In Homo sapiens, the cell cycle inhibitor CDKN1C is among the top differentially expressed genes in the epithelial cell rests of Malassez cluster.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:9d8ca159fa49349cb267
claim_id: claim:9d8ca159fa49349cb267
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Also, other proliferation markers such as topoisomerase II alpha ( TOP2A ) and centromere protein F ( CENPF ) were found almost exclusively expressed in the organoid clusters (Supplementary Fig. 2g).

summary:
In Homo sapiens, topoisomerase II alpha (TOP2A) and centromere protein F (CENPF) are proliferation markers almost exclusively expressed in the tooth organoid clusters.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:6a67ee8a6c74507dd8f7
claim_id: claim:6a67ee8a6c74507dd8f7
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Intriguingly, we also detected gene expression of the mesenchymal marker vimentin ( VIM ) in ERM cells (Fig. 2 c; Supplementary Fig. 2a,e).

summary:
In Homo sapiens, the mesenchymal marker vimentin (VIM) is expressed in epithelial cell rests of Malassez cells.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:f8bc7cb1ab20c92f6e5b
claim_id: claim:f8bc7cb1ab20c92f6e5b
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
scRNA-seq mining exposed that the EGF receptor (EGFR) ligands amphiregulin ( AREG ) and heparin-binding EGF ( HB-EGF ), together with EGFR , are highly expressed in the organoids (Supplementary Fig. 3a) which may substitute for EGF.

summary:
In Homo sapiens, amphiregulin (AREG), heparin-binding epidermal growth factor (HB-EGF), and epidermal growth factor receptor (EGFR) are highly expressed in tooth organoid cells.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:ddfd2d7d7a53d9d17bef
claim_id: claim:ddfd2d7d7a53d9d17bef
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
summary: In Homo sapiens, ornithine decarboxylase 1 (ODC1) is a proposed marker of dental epithelial cells.
span_literal:
Among others, ornithine decarboxylase 1 ( ODC1 ), a gene involved in cell cycle regulation [ 58 ] and proposed as a marker of dental epithelium (moreover aberrantly expressed in specific odontogenic tumors [ 58 ]), is higher expressed in P4 versus P4-switch organoids (Fig. 5 c).


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:d326056bf084d93a57d3
claim_id: claim:d326056bf084d93a57d3
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
On the other hand, in addition to AMTN and ODAM surfacing in the top 10 DEGs of P4-switch as compared to P4 organoids (Fig. 5 c; Supplementary Dataset 6), laminin subunit gamma 2 ( LAMC2 ) and laminin subunit alpha 3 ( LAMA3 ), both expressed in mature ameloblasts in mouse incisor [ 46 ] and essential for amelogenesis in humans (with mutations linked to amelogenesis imperfecta [ 60 , 61 ]), are highly upregulated in P4-switch organoids (Fig. 5 c), further validated by RT-qPCR (Supplementary Fig. 5b).

summary:
In Homo sapiens, amelotin (AMTN), odontogenic ameloblast-associated protein (ODAM), laminin subunit gamma 2 (LAMC2), and laminin subunit alpha 3 (LAMA3) are markers of ameloblast differentiation, highly upregulated in differentiated tooth organoids.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:cd495f0cd8b3d44cf875
claim_id: claim:cd495f0cd8b3d44cf875
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Follicular dendritic cell secreted peptide ( FDCSP ), reported to bind to hydroxyapatite [ 62 ], is also distinctly expressed in the P4-switch organoids (Fig. 5 c).

summary:
In Homo sapiens, follicular dendritic cell secreted peptide (FDCSP) is distinctly expressed in differentiated tooth organoid cells undergoing ameloblast differentiation.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:c8dd759a6c6fb578d515
claim_id: claim:c8dd759a6c6fb578d515
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
In addition to KRT15 and ATF3 belonging to the top 10 upregulated DEGs in P4 organoids (Fig. 5 c), other undifferentiated epithelial cell markers are also distinctly expressed in P4 versus P4-switch organoids, including death-associated protein-like 1 ( DAPL1 ) and tissue inhibitor of metalloproteinases 1 ( TIMP1 ) (Fig. 5 c), both recently discovered markers of mouse dental epithelium [ 46 , 59 ].

summary:
In Homo sapiens, KRT15, activating transcription factor 3 (ATF3), death-associated protein-like 1 (DAPL1), and tissue inhibitor of metalloproteinases 1 (TIMP1) are markers of undifferentiated dental epithelial cells in tooth organoids.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:50284f92552cccda8daf
claim_id: claim:50284f92552cccda8daf
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Interestingly, CK19 expression emerged in MIM-switched organoids (Fig. 4 c), in accordance with the known gradual replacement of CK14 by CK19 in differentiating ameloblasts [ 57 ].

summary:
In Homo sapiens, cytokeratin 19 (CK19) expression emerges in differentiating ameloblasts, replacing cytokeratin 14 (CK14).


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:d05c670e2b728b1b11e7
claim_id: claim:d05c670e2b728b1b11e7
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Ameloblast differentiation encompasses a secretory stage with production of the EMPs AMELX and ameloblastin (AMBN), and a maturation stage during which amelotin (AMTN) and odontogenic-ameloblast associated protein (ODAM) are produced [ 4 , 35 , 52 , 53 ].

summary:
In Homo sapiens, ameloblast differentiation encompasses a secretory stage marked by amelogenin (AMELX) and ameloblastin (AMBN), and a maturation stage marked by amelotin (AMTN) and odontogenic ameloblast-associated protein (ODAM).


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:24219ac8573003ca44bb
claim_id: claim:24219ac8573003ca44bb
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
The EMPs are proteolytically cleaved by matrix metalloproteinase 20 (MMP20) and kallikrein (KLK4), typically expressed during the secretory and maturation phase, respectively.

summary:
In Homo sapiens, matrix metalloproteinase 20 (MMP20) is typically expressed during the secretory phase and kallikrein 4 (KLK4) during the maturation phase of ameloblast differentiation.


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:4f5acb95efb368a63a57
claim_id: claim:4f5acb95efb368a63a57
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
summary: In Homo sapiens, RUNX2 is expressed in ameloblasts during the late secretory and maturation stages.
span_literal:
RUNX2 expression has been reported in ameloblasts during the late secretory and maturation stages and its deletion suppresses enamel maturation [ 67 ].


claim_key: hca:0245_10.1007_s00018-022-04183-8_4730063570:claim:1b0a61504bfc0285807b
claim_id: claim:1b0a61504bfc0285807b
paper_key: hca:0245_10.1007_s00018-022-04183-8_4730063570
span_literal:
Addition of TGFβ indeed further increased the expression of VIM in the epithelial (CK5 + ) organoids (Fig. 6 a) and also significantly stimulated the expression of the PDL-specific genes periostin ( POSTN ) and collagen type III alpha 1 chain ( COL3A1 ) [ 80 ] (Fig. 6 c).

summary:
In Homo sapiens, periostin (POSTN) and collagen type III alpha 1 chain (COL3A1) are periodontal ligament-specific genes whose expression is stimulated by transforming growth factor-beta in tooth organoids.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:68a9bf0a45885afd5130
claim_id: claim:68a9bf0a45885afd5130
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
summary: In Homo sapiens lung, lymphatic endothelial cells (cluster 6) are marked by PDPN and PROX1.
span_literal:
one set of 85 lymphatic endothelial cells found in tumor and non-malignant samples (cluster 6; marker genes PDPN and PROX1 )


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:c4bb12e0d8bc3f5ab860
claim_id: claim:c4bb12e0d8bc3f5ab860
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal:
5 sets of blood endothelial cells ( FLT1+ ; Fig. 2b ): two were mostly tumor-derived (clusters 3 and 4; IGFBP3+ and SPRY1+ ) and two others were mostly non-malignant lung-derived (clusters 1 and 5; MT2A+ and EDNRB+ )

summary:
In Homo sapiens lung, blood endothelial cells are marked by FLT1, with tumor-derived endothelial cell cluster 3 marked by IGFBP3, tumor-derived endothelial cell cluster 4 marked by SPRY1, non-malignant endothelial cell cluster 1 marked by MT2A, and non-malignant endothelial cell cluster 5 marked by EDNRB.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:a7863ef53873b957bbcb
claim_id: claim:a7863ef53873b957bbcb
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal: follicular B cells expressing high levels of CD20 ( MS4A1 ), CXCR4 and HLA-DRs (clusters 1 and 2)
summary:
In Homo sapiens, follicular B cells (clusters 1 and 2) express high levels of CD20 (MS4A1), CXCR4, and HLA-DR.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:0f1b293f892b2dc28d82
claim_id: claim:0f1b293f892b2dc28d82
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal:
mucosa-associated lymphoid tissue-derived (MALT) B cells expressing immunoglobulins A and M and JCHAIN (clusters 5 and 7)

summary:
In Homo sapiens, mucosa-associated lymphoid tissue-derived B cells (clusters 5 and 7) express JCHAIN.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:c60b77bcfe2611028dad
claim_id: claim:c60b77bcfe2611028dad
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal:
One cluster corresponds to granulocytes (cluster 7; S100A12+ ) and three clusters to dendritic cells: Langerhans cells (cluster 5; CD207+ ), monocyte-derived dendritic cells (cluster 9; FCGR3A+ , CYTIP+ ) and cross-presenting dendritic cells (cluster 12; CLEC9A+ and XCR1+ )

summary:
In Homo sapiens, granulocytes (cluster 7) are positive for S100A12, Langerhans cells (cluster 5) are positive for CD207, monocyte-derived dendritic cells (cluster 9) are positive for FCGR3A and CYTIP, and cross-presenting dendritic cells (cluster 12) are positive for CLEC9A and XCR1.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:60fb2b7337d831fa96c1
claim_id: claim:60fb2b7337d831fa96c1
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
summary: In Homo sapiens, macrophages are positive for CD163 and CD68.
span_literal:
The eight other clusters consisted of CD163+ and CD68+ macrophages and were also less abundant in tumor


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:b6d05dec6e974452640c
claim_id: claim:b6d05dec6e974452640c
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal:
Reclustering revealed nine clusters, which were designated as regulatory T cells ( FOXP3+ , cluster 7), natural killer and natural killer T cells ( FGFBP2+ , cluster 6), CD8+ T cells ( CD8A+ ; 2, 4, 5 and 8) and CD4+ T cells ( CD4+ ; 1, 3 and 9)

summary:
In Homo sapiens, regulatory T cells (cluster 7) are positive for FOXP3, natural killer and natural killer T cells (cluster 6) are positive for FGFBP2, CD8-positive T cells are positive for CD8A, and CD4-positive T cells are positive for CD4.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:8eea285b71a6cfbc8591
claim_id: claim:8eea285b71a6cfbc8591
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal:
we not only detected flat alveolar type 1 (AT1) cells ( AGER, CAV1 ; cluster 3), surfactant-secreting cuboidal alveolar type 2 (AT2) cells ( SFTPC, ABCA3 ; cluster 1) and secretory club cells ( SCGB1A1 ; cluster 6), but also basal cells ( KRT15 ; cluster 7), previously undetected

summary:
In Homo sapiens lung, alveolar type 1 cells (cluster 3) are marked by AGER and CAV1, alveolar type 2 cells (cluster 1) are marked by SFTPC and ABCA3, club cells (cluster 6) are marked by SCGB1A1, and basal cells (cluster 7) are marked by KRT15.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:2630d425b6a85433610a
claim_id: claim:2630d425b6a85433610a
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal: ACTA2 , a myofibroblast marker 26 , showed highest expression in cluster 2.
summary:
In Homo sapiens, ACTA2 is a marker of myofibroblasts, with highest expression in fibroblast cluster 2.


claim_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a:claim:bea2fa1c05066da69ede
claim_id: claim:bea2fa1c05066da69ede
paper_key: hca:0247_10.1038_s41591-018-0096-5_140f8f392a
span_literal:
we detected cells expressing marker genes for COPD-induced injury ( MMP7 , CXCL14 , GDF15 ; cluster 4)

summary:
In Homo sapiens lung, cells associated with chronic obstructive pulmonary disease-induced injury (cluster 4) express MMP7, CXCL14, and GDF15.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:be45bee4b70f48b92e6f
claim_id: claim:be45bee4b70f48b92e6f
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal:
ureteric tip population (U.Tip) was identified based on co-expression of known tip markers such as RET , SOX9 , WNT11 and MUC6

summary:
In Homo sapiens human fetal kidney, ureteric tip cells are identified by co-expression of the markers RET, SOX9, WNT11, and MUC6.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:c9a34ba8a9f54ebea516
claim_id: claim:c9a34ba8a9f54ebea516
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal:
The largest UE subcluster, identified as cortical UE (U.Cortical), exhibited low RET and high AQP2 expression.

summary:
In Homo sapiens human fetal kidney, cortical ureteric epithelium exhibits low RET and high AQP2 expression.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:3aed18b5320202c65d15
claim_id: claim:3aed18b5320202c65d15
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal: medullary UE, which exhibits highest TACSTD2
summary:
In Homo sapiens human fetal kidney, medullary ureteric epithelium exhibits the highest TACSTD2 expression, and inner medullary ureteric epithelium is marked by UPK2, UPK3B, and SNX31.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:48bc1b5c0ab16f7dea1e
claim_id: claim:48bc1b5c0ab16f7dea1e
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal: U.Med_Inner) or absence (U.Med_Outer) of UPK2 , UPK3B and SNX31
summary:
In Homo sapiens human fetal kidney, inner medullary ureteric epithelium is marked by the presence of UPK2, UPK3B, and SNX31.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:adeb4f548591f2064488
claim_id: claim:adeb4f548591f2064488
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal: U.Med_Outer) of UPK2 , UPK3B and SNX31
summary:
In Homo sapiens human fetal kidney, outer medullary ureteric epithelium is marked by the absence of UPK2, UPK3B, and SNX31.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:8635cce49c4be693eddd
claim_id: claim:8635cce49c4be693eddd
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal:
Genes that we identified as specifically expressed in the human UE but not DN included RET , WNT9B , SMIM22 , KANK4 and KCNN4 while those specific to the human DN included BSND , KCNJ1 , FXYD2 and CLCNKB

summary:
In Homo sapiens human fetal kidney, ureteric epithelium specifically expresses RET, WNT9B, SMIM22, KANK4, and KCNN4 but not distal nephron markers.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:dadf0e7a673010081a5e
claim_id: claim:dadf0e7a673010081a5e
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal:
Genes that we identified as specifically expressed in the human UE but not DN included RET , WNT9B , SMIM22 , KANK4 and KCNN4 while those specific to the human DN included BSND , KCNJ1 , FXYD2 and CLCNKB

summary:
In Homo sapiens human fetal kidney, distal nephron specifically expresses BSND, KCNJ1, FXYD2, and CLCNKB but not ureteric epithelium markers.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:c18d14ae661200ba9714
claim_id: claim:c18d14ae661200ba9714
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal:
Notably, UE-specific markers such as RET , KANK4 , MMP7 , MOXD1 , KCNN4 , SLC52A3 , SLC9A2 and WNT11 were upregulated in the cultured mCherry + epithelium while there was a corresponding downregulation of DN markers such as TMEM52B , KCNJ1 , DEFB1 and CLCNKB

summary:
In Homo sapiens, ureteric epithelium is marked by RET, KANK4, MMP7, MOXD1, KCNN4, SLC52A3, SLC9A2, and WNT11, while distal nephron is marked by TMEM52B, KCNJ1, DEFB1, and CLCNKB.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:dceea56154dc23661552
claim_id: claim:dceea56154dc23661552
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
span_literal:
Notably, UE-specific markers such as RET , KANK4 , MMP7 , MOXD1 , KCNN4 , SLC52A3 , SLC9A2 and WNT11 were upregulated in the cultured mCherry + epithelium while there was a corresponding downregulation of DN markers such as TMEM52B , KCNJ1 , DEFB1 and CLCNKB

summary:
In Homo sapiens, distal nephron is marked by TMEM52B, KCNJ1, DEFB1, and CLCNKB, as distinguished from ureteric epithelium.


claim_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c:claim:01740d58ce16b8367866
claim_id: claim:01740d58ce16b8367866
paper_key: hca:0248_10.1016_j.stem.2020.12.001_c5f98f4c3c
summary: In Homo sapiens, principal cells express the vasopressin receptor AVPR2 and AQP2.
span_literal:
PCs express the vasopressin receptor ( AVPR2 ) and respond to vasopressin by relocating AQP2 to the apical luminal membrane of the cell


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:7a45d10b9bbd1c1c8ce7
claim_id: claim:7a45d10b9bbd1c1c8ce7
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
span_literal:
These included two cell type populations at day 11: proliferating and non-proliferating midbrain floorplate progenitors (both expressing LMX1A , FOXA2 and expressing MIK67 , TOP2A when proliferating 18 ).

summary:
In Homo sapiens, midbrain floorplate progenitors express LMX1A and FOXA2, while proliferating midbrain floorplate progenitors additionally express MKI67 and TOP2A.


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:08652eb7fbe7fb94185a
claim_id: claim:08652eb7fbe7fb94185a
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
span_literal:
These included two cell type populations at day 11: proliferating and non-proliferating midbrain floorplate progenitors (both expressing LMX1A , FOXA2 and expressing MIK67 , TOP2A when proliferating 18 ).

summary:
In Homo sapiens, proliferating midbrain floorplate progenitors express LMX1A, FOXA2, MKI67, and TOP2A.


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:d96cb65d99b1902ca56e
claim_id: claim:d96cb65d99b1902ca56e
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
summary: In Homo sapiens, midbrain dopaminergic neurons are marked by TH, NR4A2, PBX1, and TMCC3.
span_literal:
The first neuronal population was annotated as midbrain DA using a comprehensive panel of 75 literature-derived DA marker genes including TH , NR4A2 , PBX1 and TMCC3 18 – 21 ( Extended Data Fig. 1d ).


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:c5ef36f41853ed5e4fee
claim_id: claim:c5ef36f41853ed5e4fee
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
span_literal:
two of which appeared to be neuronal, and two non-neuronal (characterized by expression and lack of the pan-neuronal markers SNAP25 and SYT1, respectively).

summary:
In Homo sapiens, neuronal cells are characterized by expression of the pan-neuronal markers SNAP25 and SYT1, while non-neuronal cells lack these markers.


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:f8103d3f5d5d5de52b76
claim_id: claim:f8103d3f5d5d5de52b76
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
summary: In Homo sapiens, serotonergic-like neurons are enriched for TPH2 and GATA2 markers.
span_literal:
We annotated the second neuronal population as serotonergic-like neurons (Sert), since these cells were enriched TPH2 and GATA2 markers which are also observed in serotonergic neurons in vivo 23 .


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:76fa9e9952c75c5ddba6
claim_id: claim:76fa9e9952c75c5ddba6
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
summary: In Homo sapiens, neuroblasts express the pro-neuronal genes NEUROD1, NEUROG2, and NHLH1.
span_literal:
We also identified a neuroblast population specific to day 11 (4% of cells) expressing pro-neuronal genes ( NEUROD1 , NEUROG2 , NHLH1 27 , 28 ), and an additional neuronal population (expressing SNAP25 and SYT1 ) that expressed some midbrain markers but that could not be assigned a specific identity (Unknown neurons 1, present at day 30 and day 52 at around 7%, Extended Data Fig. 1c–e ).


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:7d47c72716c3c2c12bb6
claim_id: claim:7d47c72716c3c2c12bb6
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
summary: In Homo sapiens, induced pluripotent stem cell cluster 2 overexpresses UTF1 and downregulates TAC3.
span_literal:
Cluster 2 overexpressed genes associated with inefficient neuronal differentiation (e.g. UTF1 ), and downregulated genes associated with efficient neuronal differentiation (e.g. TAC3 ; Fig. 3d,e , Extended Data Fig. 5 ).


claim_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf:claim:a8edf8c6fd36ed9a0047
claim_id: claim:a8edf8c6fd36ed9a0047
paper_key: hca:0249_10.1038_s41588-021-00801-6_bd85f761cf
span_literal:
We identified 5 clusters, with all but one (cluster 4) expressing high levels of core pluripotency markers ( NANOG , SOX2 , POU5F1 , Extended Data Fig. 5c ; Methods ).

summary:
In Homo sapiens, induced pluripotent stem cell clusters express high levels of core pluripotency markers NANOG, SOX2, and POU5F1, with the exception of cluster 4.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:3bf6a97a53573807e272
claim_id: claim:3bf6a97a53573807e272
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal: GZMB , PRF1 , GZMH , GNLY , CCL4 , CTSW , FCRL6 , SPON2 , CX3CR1 , S1PR5 , NKG7 , and CD244
summary:
In Homo sapiens, the CD4+ effector memory T cells expressing CD45RA (TEMRA) subset is enriched for GZMB, PRF1, GZMH, GNLY, CCL4, CTSW, FCRL6, SPON2, CX3CR1, S1PR5, NKG7, and CD244 transcripts compared with central memory and effector memory subsets.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:68868aa24268207354fc
claim_id: claim:68868aa24268207354fc
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
ZNF683 (Hobit), and Eomes and T-bet (encoded by TBX21 ) were also expressed at higher levels in single cells from the T EMRA

summary:
In Homo sapiens, the effector memory T cell expressing CD45RA (TEMRA) subset expresses higher levels of ZNF683, EOMES, and TBX21 transcription factor transcripts related to cytotoxic T lymphocyte function.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:814e68abad52d9d87e0e
claim_id: claim:814e68abad52d9d87e0e
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
Cells in clusters 1 and 2 expressed higher levels of KLRG1 ( 40 – 42 ) and CX3CR1 ( 7 , 43 ) transcripts, which are linked to effector status of memory cells, and lower levels of CD27 and CD28 transcripts, which encode costimulation molecules

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte effector cells (clusters 1 and 2) express higher levels of KLRG1 and CX3CR1 and lower levels of CD27 and CD28.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:f88a018294c5ea004b47
claim_id: claim:f88a018294c5ea004b47
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
Compared with cells in clusters 1 and 2 (referred as CD4-CTL effectors), those in clusters 3 and 4 expressed lower levels of KLRG1 transcripts and higher levels of transcripts encoding IL-7R ( IL7R or CD127 ), which is known to play an important role in mediating the long-term homeostatic survival of naive and memory T lymphocytes

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte precursor cells (clusters 3 and 4) express lower levels of KLRG1 and higher levels of IL7R compared with CD4+ cytotoxic T lymphocyte effector cells.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:5c2bff732caaccd8f8ac
claim_id: claim:5c2bff732caaccd8f8ac
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
CD27 and CD28 costimulation molecules, lymphotoxin β ( LTB ), and JUNB TF were also expressed at higher levels in clusters 3 and 4

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte precursor cells (clusters 3 and 4) express higher levels of CD27, CD28, LTB, and JUNB.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:ec35803f97f50c84450e
claim_id: claim:ec35803f97f50c84450e
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
However, cells in both clusters 3 and 4 were still markedly different from T CM cells in that they expressed several transcripts that are specifically enriched in T EMRA cells ( KLRG1 , TBX21 , S1PR5 , FGFBP2 , CCL4 , PRF1 , GZMH , GNLY , NKG7 , ZEB2 , and GPR56 ), albeit at lower levels compared with CD4-CTL effectors (cells in clusters 1 and 2)

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte precursor cells (clusters 3 and 4) express KLRG1, TBX21, S1PR5, FGFBP2, CCL4, PRF1, GZMH, GNLY, NKG7, ZEB2, and GPR56, distinguishing them from central memory T cells.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:6a6770d06812581ba697
claim_id: claim:6a6770d06812581ba697
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
Genes linked to cell survival and CD4-CTL function such as PRSS23 , SPON2 , TCF7 (encodes for TCF1), CRTAM , and ZNF683 (encodes for Hobit) ( 24 , 46 – 51 ) were also highly expressed in single cells from clusters 1 and 2

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte effector cells (clusters 1 and 2) highly express PRSS23, SPON2, TCF7, CRTAM, and ZNF683.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:091ea4ef50e99ceee6f8
claim_id: claim:091ea4ef50e99ceee6f8
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
On the basis of the differential expression pattern of cytotoxicity-related transcripts in cluster 1 ( FADD , IFNG , TNF , IFIT2 , LMNA , CD69 , FOS , JUN , DUSP1 , and DUSP2 ) and cluster 2 ( FGFBP2 , SPON2 , CX3CR1 , GPR56 , and PRF1 ), we hypothesize that their cytotoxic function is preferentially mediated by the FAS/death receptor and perforin pathways, respectively

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte effector cluster 1 is marked by FADD, IFNG, TNF, IFIT2, LMNA, CD69, FOS, JUN, DUSP1, and DUSP2, while CD4+ cytotoxic T lymphocyte effector cluster 2 is marked by FGFBP2, SPON2, CX3CR1, GPR56, and PRF1.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:54697ed6a29cdb453d24
claim_id: claim:54697ed6a29cdb453d24
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
On the basis of the differential expression pattern of cytotoxicity-related transcripts in cluster 1 ( FADD , IFNG , TNF , IFIT2 , LMNA , CD69 , FOS , JUN , DUSP1 , and DUSP2 ) and cluster 2 ( FGFBP2 , SPON2 , CX3CR1 , GPR56 , and PRF1 ), we hypothesize that their cytotoxic function is preferentially mediated by the FAS/death receptor and perforin pathways, respectively

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte effector cluster 2 is marked by FGFBP2, SPON2, CX3CR1, GPR56, and PRF1.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:bbf08cb26468a1914bf2
claim_id: claim:bbf08cb26468a1914bf2
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
IPA and differential expression analysis of the transcripts enriched in clusters 1 and 2 compared with clusters 3 and 4 showed significant overrepresentation of genes encoding products related to cytotoxicity, such as GZMB , GZMH , PRF1 , GNLY , NKG7 , ZNF683 , and FGFBP2

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte effector cells (clusters 1 and 2) are enriched for GZMB, GZMH, PRF1, GNLY, NKG7, ZNF683, and FGFBP2 compared with CD4+ cytotoxic T lymphocyte precursor cells (clusters 3 and 4).


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:6ecf8136f3e1c73785e4
claim_id: claim:6ecf8136f3e1c73785e4
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
These two clusters differentially expressed transcripts characteristic of CD4-CTL effectors ( GZMB and NKG7 ) and precursors ( IL7R , JUNB , and LTB ), respectively

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte effector cells are characterized by GZMB and NKG7, while CD4+ cytotoxic T lymphocyte precursor cells are characterized by IL7R, JUNB, and LTB.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:5d50defd9b2466fc570c
claim_id: claim:5d50defd9b2466fc570c
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
These two clusters differentially expressed transcripts characteristic of CD4-CTL effectors ( GZMB and NKG7 ) and precursors ( IL7R , JUNB , and LTB ), respectively

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte precursor cells are characterized by IL7R, JUNB, and LTB.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:8f474f7974d146d46c76
claim_id: claim:8f474f7974d146d46c76
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
At the single-cell level, CD4-CTL precursors in the CD4-T EMRA subset were distinguished by the high expression levels of IL7R transcripts.

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte precursor cells in the CD4+ effector memory T cell expressing CD45RA subset are distinguished by high expression of IL7R.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:ce6f904c2777fc8cc2b9
claim_id: claim:ce6f904c2777fc8cc2b9
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor

summary:
In Homo sapiens, CD4+ cytotoxic T lymphocyte precursor cells are distinguished from CD4+ cytotoxic T lymphocyte effector cells by high expression of the interleukin-7 receptor.


claim_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903:claim:450e0ce96c797b7d28c1
claim_id: claim:450e0ce96c797b7d28c1
paper_key: hca:0250_10.1126_sciimmunol.aan8664_c5aa305903
span_literal:
Coexpression analysis of T EMRA -enriched transcripts also revealed a number of genes ( PFN1 , PFN1P1 , EFHD2 , VCL , DIP2A , SYNE1 , and PLEK ) ( 29 – 32 ) whose expression was highly correlated with cytotoxicity signature genes, suggesting that the products of these genes may also play important roles in the development or function of CD4-CTLs

summary:
In Homo sapiens, effector memory T cells expressing CD45RA show coexpression of PFN1, PFN1P1, EFHD2, VCL, DIP2A, SYNE1, and PLEK with cytotoxicity signature genes, suggesting roles in CD4+ cytotoxic T lymphocyte function.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:66c76865fbfac6b34fc2
claim_id: claim:66c76865fbfac6b34fc2
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Among the commonalities were genes associated with mesenchymal biology including EDNRB, PDGFRB, ZEB2 and COL4A1

summary:
In Homo sapiens breast tissue, fibroblasts and pericytes share expression of mesenchymal genes EDNRB, PDGFRB, ZEB2, and COL4A1.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:55165c467dab274f9427
claim_id: claim:55165c467dab274f9427
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Among the commonalities were genes associated with mesenchymal biology including EDNRB, PDGFRB, ZEB2 and COL4A1

summary:
In Homo sapiens breast tissue, pericytes share expression of mesenchymal genes EDNRB, PDGFRB, ZEB2, and COL4A1 with fibroblasts.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:9d529123a872e5c6bb47
claim_id: claim:9d529123a872e5c6bb47
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Key differences were observed in genes encoding ECM molecules ( COL1A2 ) and proteolytic remodelers ( MMP2, MMP3, MMP10 ) in fibroblasts, and actin-binding ( TAGLN, ACTA2 ) and factors related to vascular accessory function ( PROCR, ESAM, MCAM, KCNE4 ) in pericytes

summary:
In Homo sapiens breast tissue, fibroblasts are marked by expression of COL1A2, MMP2, MMP3, and MMP10, distinguishing them from pericytes.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:a6a1c407ec7bd4ceb376
claim_id: claim:a6a1c407ec7bd4ceb376
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Key differences were observed in genes encoding ECM molecules ( COL1A2 ) and proteolytic remodelers ( MMP2, MMP3, MMP10 ) in fibroblasts, and actin-binding ( TAGLN, ACTA2 ) and factors related to vascular accessory function ( PROCR, ESAM, MCAM, KCNE4 ) in pericytes

summary:
In Homo sapiens breast tissue, pericytes are marked by expression of TAGLN, ACTA2, PROCR, ESAM, MCAM, and KCNE4, distinguishing them from fibroblasts.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:e6af4a980b8f0c8f00cb
claim_id: claim:e6af4a980b8f0c8f00cb
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Notably, we found that the cell surface markers PROCR and PDPN differentially labeled pericytes and fibroblasts

summary:
In Homo sapiens breast tissue, the cell surface marker PROCR labels pericytes while PDPN labels fibroblasts.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:333e0421e06b78d4c339
claim_id: claim:333e0421e06b78d4c339
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Notably, we found that the cell surface markers PROCR and PDPN differentially labeled pericytes and fibroblasts

summary:
In Homo sapiens breast tissue, the cell surface marker PDPN labels fibroblasts while PROCR labels pericytes.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:9597715adca3d2fdcec5
claim_id: claim:9597715adca3d2fdcec5
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
we next performed detailed differential gene expression analyses within luminal 1 cells, which similarly revealed indicators of altered differentiation such that basal hallmark genes (for example, KRT5, KRT14 ) and luminal progenitor genes (for example, ALDH1A3 ) were upregulated in BRCA1 +/mut luminal 1 cells

summary:
In Homo sapiens BRCA1 mutation carrier breast tissue, luminal 1 cells show upregulation of basal hallmark genes KRT5 and KRT14 and the luminal progenitor gene ALDH1A3.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:6a4ab3a4735b82db9982
claim_id: claim:6a4ab3a4735b82db9982
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
The same subset of luminal 1- ALDH1A3 -positive cells was also found to express mRNA high levels of KRT23

summary:
In Homo sapiens breast tissue, the ALDH1A3-positive luminal 1 cell subset expresses high levels of KRT23.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:7547a7dc74ef11cffe7f
claim_id: claim:7547a7dc74ef11cffe7f
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
we also found indicators of altered epithelial differentiation, including enhanced transcription of genes encoding hallmark luminal cytokeratins such as KRT18, KRT8 and KRT19 in BRCA1 +/mut basal epithelial cells

summary:
In Homo sapiens BRCA1 mutation carrier breast tissue, basal epithelial cells show enhanced transcription of luminal cytokeratins KRT18, KRT8, and KRT19.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:379c469d219a0e5683be
claim_id: claim:379c469d219a0e5683be
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
we found several genes encoding tumor-promoting and proliferation-inducing growth factors enriched in BRCA1 +/mut , including FGF2 (ref. 27 ) and HGF 28 from fibroblasts, and NGF 29 and INHBA 30 from pericytes

summary:
In Homo sapiens BRCA1 mutation carrier breast tissue, fibroblasts express elevated levels of FGF2 and HGF.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:32ad78f461218e5fe3d1
claim_id: claim:32ad78f461218e5fe3d1
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
we found several genes encoding tumor-promoting and proliferation-inducing growth factors enriched in BRCA1 +/mut , including FGF2 (ref. 27 ) and HGF 28 from fibroblasts, and NGF 29 and INHBA 30 from pericytes

summary:
In Homo sapiens BRCA1 mutation carrier breast tissue, pericytes express elevated levels of NGF and INHBA.


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:73ad3e529dcc8c27b949
claim_id: claim:73ad3e529dcc8c27b949
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
Our ligand–receptor analysis revealed nerve growth factor (NGF) as a pro-proliferative factor enriched in BRCA1 +/mut pericytes interacting with NGF receptor (NGFR) on basal cells

summary:
In Homo sapiens BRCA1 mutation carrier breast tissue, pericytes express nerve growth factor (NGF), while basal cells express nerve growth factor receptor (NGFR).


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:9897f4bf9c03d0a0848e
claim_id: claim:9897f4bf9c03d0a0848e
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
summary: In Homo sapiens breast tissue, basal cells express NGFR while luminal cells do not.
span_literal:
which was supported by flow cytometric analysis showing that only basal cells, but not luminal cells, express NGFR


claim_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857:claim:200b1abe0281748f66e7
claim_id: claim:200b1abe0281748f66e7
paper_key: hca:0251_10.1038_s41588-023-01298-x_c85e8d4857
span_literal:
expression levels of the gene encoding secreted protease matrix metalloproteinase 3 (MMP3) were one of the top pre-CAF markers found to be elevated in BRCA1 +/mut fibroblasts compared to noncarriers across all individuals

summary:
In Homo sapiens BRCA1 mutation carrier breast tissue, matrix metalloproteinase 3 (MMP3) is a top pre-cancer-associated fibroblast marker elevated in fibroblasts.


claim_key: hca:0252_10.1073_pnas.2025813118_95804f2d74:claim:695ca9e30c6c6e0657cc
claim_id: claim:695ca9e30c6c6e0657cc
paper_key: hca:0252_10.1073_pnas.2025813118_95804f2d74
span_literal:
we found significantly higher levels of CD29 expressed on the surface of murine and human Th17-polarized cells compared to Th2-polarized cells

summary:
In Homo sapiens, T helper 17 cells express significantly higher levels of CD29 (integrin beta-1) compared to T helper 2 cells.


claim_key: hca:0252_10.1073_pnas.2025813118_95804f2d74:claim:0ae0f0d33bb6f8e4eb56
claim_id: claim:0ae0f0d33bb6f8e4eb56
paper_key: hca:0252_10.1073_pnas.2025813118_95804f2d74
span_literal: with higher levels on IL-17 + T cells compared to their IL-17 neg counterpart
summary:
In Homo sapiens, interleukin-17-positive T cells express higher levels of CD29 compared to interleukin-17-negative T cells.


claim_key: hca:0252_10.1073_pnas.2025813118_95804f2d74:claim:f8741e29086b8386fc7f
claim_id: claim:f8741e29086b8386fc7f
paper_key: hca:0252_10.1073_pnas.2025813118_95804f2d74
span_literal:
human T cells display a similar trend along with a significantly higher expression of Vglut1 by Th17-polarized cells

summary:
In Homo sapiens, T helper 17 cells display significantly higher expression of vesicular glutamate transporter 1 (Vglut1) compared to T helper 2 cells.


claim_key: hca:0252_10.1073_pnas.2025813118_95804f2d74:claim:6e5c475da323cfe465fc
claim_id: claim:6e5c475da323cfe465fc
paper_key: hca:0252_10.1073_pnas.2025813118_95804f2d74
span_literal:
all clusters except one (labeled EIF5+ glial cells, less than 5% of total cells) were considered to represent oligodendrocytes or oligodendrocyte progenitors (immature)

summary:
In Homo sapiens, EIF5-positive glial cells are a distinct cluster separate from oligodendrocytes and oligodendrocyte progenitors, marked by EIF5 expression.


claim_key: hca:0252_10.1073_pnas.2025813118_95804f2d74:claim:e91a852c69400e55a336
claim_id: claim:e91a852c69400e55a336
paper_key: hca:0252_10.1073_pnas.2025813118_95804f2d74
span_literal: characterized by high relative expression of PLP1, CNP, MBP, and MOG
summary:
In Homo sapiens, mature oligodendrocytes are characterized by high relative expression of PLP1, CNP, MBP, and MOG.


claim_key: hca:0252_10.1073_pnas.2025813118_95804f2d74:claim:7eadb3270d92c85cbddf
claim_id: claim:7eadb3270d92c85cbddf
paper_key: hca:0252_10.1073_pnas.2025813118_95804f2d74
span_literal: COL4A5 (collagen subunit), FN (fibronectin), and MADCAM1
summary:
In Homo sapiens, oligodendrocytes express high mRNA levels of COL4A5 (collagen type IV alpha 5), FN (fibronectin), and MADCAM1 as CD29 ligands.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:c9576051a19d5e0ce7bc
claim_id: claim:c9576051a19d5e0ce7bc
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
summary: In Homo sapiens, CD34 is a positive marker of hematopoietic stem and progenitor cells.
span_literal:
We applied Palantir to characterize human hematopoietic differentiation using scRNA-seq profiles of ~25,000 cells enriched for CD34, a marker for hematopoietic stem and progenitor cells


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:f1f6f30a5c707905c1f1
claim_id: claim:f1f6f30a5c707905c1f1
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
As expected, CD34 shows a decreasing trend as cells commit in all lineages 11 whereas lineage-specific factors such as CD79A , GATA1 and IRF8 are selectively upregulated in the lymphoid, erythroid and DC lineages, respectively.

summary:
In Homo sapiens, CD79A is selectively upregulated in the lymphoid lineage during hematopoietic differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:020938441b27606b8c05
claim_id: claim:020938441b27606b8c05
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
As expected, CD34 shows a decreasing trend as cells commit in all lineages 11 whereas lineage-specific factors such as CD79A , GATA1 and IRF8 are selectively upregulated in the lymphoid, erythroid and DC lineages, respectively.

summary:
In Homo sapiens, GATA1 is selectively upregulated in the erythroid lineage during hematopoietic differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:e36f6c70497582eef90d
claim_id: claim:e36f6c70497582eef90d
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
As expected, CD34 shows a decreasing trend as cells commit in all lineages 11 whereas lineage-specific factors such as CD79A , GATA1 and IRF8 are selectively upregulated in the lymphoid, erythroid and DC lineages, respectively.

summary:
In Homo sapiens, IRF8 is selectively upregulated in the dendritic cell lineage during hematopoietic differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:e9267cc48bc5b3a9ce75
claim_id: claim:e9267cc48bc5b3a9ce75
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
MPO shows an initial upward trend across all lineages, which is subsequently maintained only in the monocyte lineage

summary:
In Homo sapiens, MPO expression is maintained in the monocyte lineage during hematopoietic differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:624a6d7f67102383440e
claim_id: claim:624a6d7f67102383440e
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
Finally, CD41 expression is consistent with its role as a marker of early erythroid and megakaryocytic precursors, exhibiting continued upregulation in the megakaryocytic lineages

summary:
In Homo sapiens, CD41 is a positive marker of early erythroid and megakaryocytic precursors, with continued upregulation in the megakaryocytic lineage.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:ecf80a2ae4e07f7f8b08
claim_id: claim:ecf80a2ae4e07f7f8b08
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
DP change is also correlated with expression dynamics of THY1 (CD90), a well characterized marker of transition between LT-HSCs to ST-HSCs

summary:
In Homo sapiens, THY1 (CD90) is a well characterized marker of the transition between long-term hematopoietic stem cells and short-term hematopoietic stem cells.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:19dcadda5929c7111cd5
claim_id: claim:19dcadda5929c7111cd5
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
we systematically correlated all TFs with erythroid BP and found the most correlated TFs to be TAL1 , KLF1 and GATA1 (Pearson correlation > 0.99)

summary:
In Homo sapiens, TAL1, KLF1, and GATA1 are the transcription factors most correlated with erythroid cell branch probability during hematopoietic differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:34f9aa6e25deb6b9041e
claim_id: claim:34f9aa6e25deb6b9041e
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
CD34 . Marker of stem and precursor cells and known to be downregulated with differentiation in all cells 11 .

summary:
In Homo sapiens, CD34 is a positive marker of hematopoietic stem and precursor cells and is known to be downregulated with differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:5fbc0d0883126d04975b
claim_id: claim:5fbc0d0883126d04975b
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
MPO . Early marker for myeloid lineages with higher expression during monocyte lineage commitment 38 .

summary:
In Homo sapiens, MPO is an early positive marker for myeloid lineages with higher expression during monocyte lineage commitment.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:0a35ed4ee662be4693f6
claim_id: claim:0a35ed4ee662be4693f6
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
CSF1R . Known to be upregulated in cDCs and downregulated in pDCs following an initial upregulation 40 .

summary:
In Homo sapiens, CSF1R is upregulated in classical dendritic cells during hematopoietic differentiation.


claim_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55:claim:455bc39baa8f5a1fd2d4
claim_id: claim:455bc39baa8f5a1fd2d4
paper_key: hca:0253_10.1038_s41587-019-0068-4_077f63be55
span_literal:
CSF1R . Known to be upregulated in cDCs and downregulated in pDCs following an initial upregulation 40 .

summary:
In Homo sapiens, CSF1R is downregulated in plasmacytoid dendritic cells following an initial upregulation.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:c6ae7300feaf39f3d1eb
claim_id: claim:c6ae7300feaf39f3d1eb
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
summary: In Homo sapiens lung, FABP4-high macrophages are marked by expression of FABP4 and INHBA.
span_literal:
The three different macrophage/monocyte clusters (clusters 0, 1 and 3) can be distinguished in feature plots (panel c, purple intensity indicates level of gene expression) and dot plots (panel d, dot size indicates percent of cells expressing and the intensity of purple the level of expression) by expression of FABP4 and INHBA (FABP4 hi macrophages, cluster 0); SPP1 , MERTK , LGMN and SIGLEC10 (SPP1 hi macrophages, cluster 1); or IL1B and FCN1 (FCN1 hi monocyte/macrophages, cluster 3).


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:dcdd5332373a897caf6e
claim_id: claim:dcdd5332373a897caf6e
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
The three different macrophage/monocyte clusters (clusters 0, 1 and 3) can be distinguished in feature plots (panel c, purple intensity indicates level of gene expression) and dot plots (panel d, dot size indicates percent of cells expressing and the intensity of purple the level of expression) by expression of FABP4 and INHBA (FABP4 hi macrophages, cluster 0); SPP1 , MERTK , LGMN and SIGLEC10 (SPP1 hi macrophages, cluster 1); or IL1B and FCN1 (FCN1 hi monocyte/macrophages, cluster 3).

summary:
In Homo sapiens lung, SPP1-high macrophages are marked by expression of SPP1, MERTK, LGMN, and SIGLEC10.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:4d9a050d2e8b60101431
claim_id: claim:4d9a050d2e8b60101431
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
summary: In Homo sapiens normal lung, monocyte/macrophages express high levels of CD163 and AIF1.
span_literal:
Normal control lungs showed three discrete populations of monocyte/macrophages, all of which expressed high levels of CD163 and AIF1 ( Figures S1 and 1A , clusters 0, 1 and 3).


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:585fcaf0d5abdbfb87e3
claim_id: claim:585fcaf0d5abdbfb87e3
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
The first group of macrophages (FABP4 hi macrophages, Figures 1A – D , cluster 0) expressed high levels of FABP4 and INHBA , and relatively low levels of SPP1 , MERTK, LGMN and SIGLEC10 .

summary:
In Homo sapiens lung, FABP4-high macrophages express high levels of FABP4 and INHBA, and relatively low levels of SPP1, MERTK, LGMN, and SIGLEC10.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:599c39a99e703222a8b4
claim_id: claim:599c39a99e703222a8b4
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
A second group of macrophages (SPP1 hi , Figure 1A – D , cluster 1) expressed relatively high levels of SPP1 , as well as MERTK, LGMN and SIGLEC10 and relatively low levels of FABP4 and INHBA.

summary:
In Homo sapiens lung, SPP1-high macrophages express relatively high levels of SPP1, MERTK, LGMN, and SIGLEC10, and relatively low levels of FABP4 and INHBA.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:df6046322a9dbb97e13f
claim_id: claim:df6046322a9dbb97e13f
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
A third macrophage population ( FCN1 hi monocyte/macrophages) expressed relatively high levels of FCN1 , as well as several marker genes associated with monocytes: CD14 , IL1B, INSIG1 , OSM , IL1R2 and THBS1 [ 14 ], and low to no expression of FABP4, INHBA, MERTK and SPP1 ( Figure 1A – D , cluster 3, and data not shown).

summary:
In Homo sapiens lung, FCN1-high monocyte/macrophages express high levels of FCN1, CD14, IL1B, INSIG1, OSM, IL1R2, and THBS1, and low to no expression of FABP4, INHBA, MERTK, and SPP1.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:698dd734382fd2af9a88
claim_id: claim:698dd734382fd2af9a88
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
summary: In Homo sapiens lung, dendritic cells discretely express CD1C.
span_literal:
A fourth population of cells adjacent to the macrophage populations discretely expressed CD1C and therefore most likely represented dendritic cells ( Figure 1A , S1 and S2 ; cluster 10).


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:11bb1cdca43b0cc95f3f
claim_id: claim:11bb1cdca43b0cc95f3f
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
The cell types identified by marker genes were all inflammatory cells, mostly macrophages, expressing CD163 and AIF1 , but also discrete clusters that included both T cells (expressing CD3D ) and NK cells (expressing KLRF1 , GNLY , and NKG7 , cluster 2), and B cells (expressing MS4A1/ CD20, cluster 4; Figures S7 and S8 ).

summary:
In Homo sapiens bronchoalveolar lavage, macrophages express CD163 and AIF1, T cells express CD3D, natural killer cells express KLRF1, GNLY, and NKG7, and B cells express MS4A1/CD20.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:9c98c4553a343b0e26fd
claim_id: claim:9c98c4553a343b0e26fd
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
MUC5+( MUC5AC and MUC5B ), FoxJ1+( FOXJ1 ) and p63+( TP63 ) expressing cells, which make up honeycomb cysts [ 19 ] associated with, respectively, goblet cells (cluster 9), ciliated cell (cluster 8) and basal cells (cluster 14), as well as club cells were all highly increased in IPF lungs ( Figure 3B ).

summary:
In Homo sapiens lung, goblet cells express MUC5AC and MUC5B, ciliated cells express FOXJ1, and basal cells express TP63.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:6af2517b2ca147a452fa
claim_id: claim:6af2517b2ca147a452fa
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
summary: In Homo sapiens lung, alveolar type 1 cells express AGER and alveolar type 2 cells express SFTPC.
span_literal:
AGER -expressing AT1 and SFTPC -expressing AT2 cells declined in fibrotic lower lobes though not reaching statistical significance ( Figure 3B ), and we did not detect proliferating AT2 cells, though this might represent the relative paucity of AT2 cells surviving digestion [ 20 ].


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:3bfbe0f97a2da85acffe
claim_id: claim:3bfbe0f97a2da85acffe
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
span_literal:
Cells in cluster 6 expressed FCN1 most highly as well as CD14, IL1B, INSIG1, OSM, IL1R2 and THBS1 the other markers shown above to be associated with the FCN1 hi monocyte/macrophage subset in normal lungs.

summary:
In Homo sapiens lung, FCN1-high monocyte/macrophages express FCN1, CD14, IL1B, INSIG1, OSM, IL1R2, and THBS1.


claim_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5:claim:31fbdc3b54fc97f77b85
claim_id: claim:31fbdc3b54fc97f77b85
paper_key: hca:0255_10.1183_13993003.02441-2018_9965f84ef5
summary: In Homo sapiens lung, proliferating cells express MKI67, KIAA0101/PCLAF, BIRC5, and UBE2C.
span_literal:
We found in cluster 15 from Control/IPF lung clustering ( Figure 2B ) cells expressing highest levels of G2/M markers and specific markers of cell proliferation, including MKI67 (i.e. Ki67), KIAA0101 /PCLAF (PCNA-associated factor), BIRC5 (Survivin) and UBE2C /UBCH10 Ubiquitin-conjugating enzyme E2 C ( Figure 6B , 6D ).


claim_key: hca:0256_10.1038_nbt.2859_240ea4136e:claim:7d31f7340307463f2d13
claim_id: claim:7d31f7340307463f2d13
paper_key: hca:0256_10.1038_nbt.2859_240ea4136e
summary: In Homo sapiens, interstitial mesenchymal cells express PDGFRA and SPHK1 and lack myogenic markers.
span_literal:
These cells lacked myogenic markers but expressed PDGFRA and SPHK1 , suggesting that they are contaminating interstitial mesenchymal cells and did not arise from the myoblasts.


claim_key: hca:0256_10.1038_nbt.2859_240ea4136e:claim:388835f914f0768c89c5
claim_id: claim:388835f914f0768c89c5
paper_key: hca:0256_10.1038_nbt.2859_240ea4136e
span_literal:
The first phase of the trajectory was primarily composed of cells collected under high-mitogen conditions and which expressed markers of actively proliferating cells such as CDK1, while the second mainly consisted of cells collected at 24, 48, or 72 hours following serum switch.

summary:
In Homo sapiens, actively proliferating cells express markers such as cyclin-dependent kinase 1 (CDK1).


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:92827a850fb5030322c3
claim_id: claim:92827a850fb5030322c3
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: ILC3s and CD103 + CD196 − CD300LF
summary:
In Homo sapiens tonsils, innate lymphoid cell type 3 is positive for CD196 and CD300LF and negative for CD103.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:670caf54fba9b14889b0
claim_id: claim:670caf54fba9b14889b0
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: intraepithelial ILC1s were CD103 + CD196 − CD300LF
summary:
In Homo sapiens tonsils, intraepithelial innate lymphoid cell type 1 is positive for CD103 and negative for CD196 and CD300LF.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:b04199931591970b5658
claim_id: claim:b04199931591970b5658
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
summary: In Homo sapiens tonsils, innate lymphoid cell type 3a abundantly expresses IL22, IL23R, and IL1R1.
span_literal:
ILC3a abundantly expressed known ILC3 genes, such as IL22 , IL23R and IL1R1 , whereas known ILC1 genes, such as IFNG , GZMK and CCL4 , were more highly expressed by ILC1a


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:2d5d37e8d8c2881f2b73
claim_id: claim:2d5d37e8d8c2881f2b73
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: ILC1a genes ( KLRD1 , TIGIT , CD247 , CD244 , GZMK , GZMB
summary:
In Homo sapiens tonsils, innate lymphoid cell type 1a has core expression of KLRD1, TIGIT, CD247, CD244, GZMK, and GZMB.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:5bda58d832f49b5593ad
claim_id: claim:5bda58d832f49b5593ad
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: ILC3a genes ( RORC , KIT , ICOS , IL1R1 , IL2 , IL7R
summary:
In Homo sapiens tonsils, innate lymphoid cell type 3a expresses RORC, KIT, ICOS, IL1R1, IL2, and IL7R.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:4d61c09c936545c75103
claim_id: claim:4d61c09c936545c75103
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
ILC3a to ILC1a encoded the cytokine receptors CD127 ( IL7R ), IL-1R ( IL1R1 ) and CD117 ( KIT ) ( Fig. 3a ), the costimulatory molecule ICOS and the inhibitory receptors CD33, CD31 ( PECAM1 ) and CD200R1 ( Fig. 3a ), the cytokines and chemokines IL-22, granulocyte-macrophage colony-stimulating factor (GM-CSF) ( CSF2 ), B cell activating factor ( TNFSF13B ), leukemia inhibitory factor and chemokine ligand (CCL)20 ( Fig. 3b ), and the transcription factors RORγt ( RORC

summary:
In Homo sapiens tonsils, innate lymphoid cell type 3a has high expression of IL7R, IL1R1, KIT, ICOS, CD33, PECAM1, CD200R1, IL22, CSF2, TNFSF13B, CCL20, RORC, AHR, and TOX2, which progressively decrease toward innate lymphoid cell type 1a.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:4808d1ee6dd60239c0c8
claim_id: claim:4808d1ee6dd60239c0c8
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
ILC3a to ILC1a encoded surface molecules indicative of TGF-β imprinting, such as TIGIT and CD9 ( Fig. 3a ); cytokines and chemokines, such as IFN-γ, CCL3, CCL4 and CCL5 ( Fig. 3b ); granzymes and perforin ( Fig. 3b ); and the transcription factors T-bet ( TBX21 ), Hobit ( ZNF683 ) and Aiolos ( IKZF3

summary:
In Homo sapiens tonsils, innate lymphoid cell type 1a has high expression of TIGIT, CD9, CCL3, CCL4, CCL5, TBX21, ZNF683, and IKZF3, which progressively increase from innate lymphoid cell type 3a.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:53fc92463f980918460b
claim_id: claim:53fc92463f980918460b
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
summary: In Homo sapiens tonsils, innate lymphoid cell type 3a selectively expresses S100A4.
span_literal:
ILC3a selectively expressed the calcium binding protein S100A4 ( Fig. 3a , d , e ), which is secreted and can upregulate β1-integrin expression on epithelial cells


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:441d3a60931dfd3e9b28
claim_id: claim:441d3a60931dfd3e9b28
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
ILC1b and ILC1a expressed the activating receptor NKG2C (encoded by KLRC2 ), as well as the activating adaptor CD247 (CD3ζ) ( Fig. 3a , f , g ), the expression of which has been associated with memory or adaptive NK cells that are specific for human cytomegalovirus infection.

summary:
In Homo sapiens tonsils, innate lymphoid cell type 1b and innate lymphoid cell type 1a express KLRC2 and CD247.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:2ac25caef9dce99284f0
claim_id: claim:2ac25caef9dce99284f0
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: ILC3 clusters expressed RORC , IL23R , KIT , CD300LF and IL7R
summary:
In Homo sapiens tonsils, innate lymphoid cell type 3 clusters express RORC, IL23R, KIT, CD300LF, and IL7R.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:1ff2109ff48a4d792035
claim_id: claim:1ff2109ff48a4d792035
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: Cells in cluster 5 had high expression of genes encoding cytokines, including IL22 , IL26 and CSF2
summary:
In Homo sapiens tonsils, innate lymphoid cell type 3 cluster 5 has high expression of IL22, IL26, and CSF2.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:59767a4a0dc7b43fa7e9
claim_id: claim:59767a4a0dc7b43fa7e9
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
summary: In Homo sapiens tonsils, innate lymphoid cell type 1a expresses IFNG, TBX21, KLRD1, and CD160.
span_literal:
A large ILC1a cluster (cluster 1) and a small ILC1a-related cluster (cluster 7) that expressed IFNG , TBX21, KLRD1 and CD160 ( Fig. 5a – c ) were identified.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:bcea250a9faf13a2e034
claim_id: claim:bcea250a9faf13a2e034
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
Importantly, cluster 4 expressed CD300LF , IL7R and KLRD1 and represented a transitional population ( Fig. 5b , c ) that probably encompassed the ILC3b and ILC1b subsets.

summary:
In Homo sapiens tonsils, the transitional innate lymphoid cell cluster 4 expresses CD300LF, IL7R, and KLRD1.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:8b2e805ebb4ae9a88cec
claim_id: claim:8b2e805ebb4ae9a88cec
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
Transcripts for IKZF3 , encoding Aiolos, a transcription factor of the Ikaros family 30 , were absent in tonsil ILC3a and detected in ILC3b, and had the highest expression in ILC1b and ILC1a

summary:
In Homo sapiens tonsils, IKZF3 is absent in innate lymphoid cell type 3a and detected in innate lymphoid cell type 3b, with highest expression in innate lymphoid cell type 1b and innate lymphoid cell type 1a.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:55019bae0122bbb23b81
claim_id: claim:55019bae0122bbb23b81
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal: whereas TBX21 , encoding T-bet, was expressed in ILC1b and increased in ILC1a
summary:
In Homo sapiens tonsils, TBX21 is expressed in innate lymphoid cell type 1b and increased in innate lymphoid cell type 1a.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:96a312d42ecc457e5f00
claim_id: claim:96a312d42ecc457e5f00
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
Between the ILC3 and ILC1 clusters a group of cells, cluster 4, could be distinguished, which co-expressed markers of ILC3s and ILC1s, such as IL7R , KIT , IL23R , KLRD1 , NKG7 , KLRC1 , CCL5 , XCL1 and XCL2

summary:
In Homo sapiens ileum lamina propria, the intermediate innate lymphoid cell cluster 4 co-expresses IL7R, KIT, IL23R, KLRD1, NKG7, KLRC1, CCL5, XCL1, and XCL2.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:8f205649e52c2889800c
claim_id: claim:8f205649e52c2889800c
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
A small cluster of actively proliferating cells that mainly expressed ILC1 markers, such as KLRD1 and IFNG , (cluster 7) was more abundant in CD patients than control samples (99 vs 26 cells)

summary:
In Homo sapiens ileum lamina propria, the proliferating innate lymphoid cell cluster 7 expresses KLRD1 and IFNG.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:9b0bc727fdd39d47f1d0
claim_id: claim:9b0bc727fdd39d47f1d0
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
a smaller cluster of ILC1s (cluster 9) that expressed very high amounts of PRF1 and FCGR3A ( Fig. 8c ), and may therefore be closer to NK cells than to ILCs.

summary:
In Homo sapiens ileum lamina propria, innate lymphoid cell type 1 cluster 9 expresses very high amounts of PRF1 and FCGR3A.


claim_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb:claim:195ceb228ae6390cd52f
claim_id: claim:195ceb228ae6390cd52f
paper_key: hca:0259_10.1038_s41590-019-0425-y_86ec5764bb
span_literal:
Although ILC3s share several markers with CD56 bright NK cells, including CD127 and CD117 26 , 43 , we found that ILC3s lacked CD94 and NKG2A, while uniquely expressing CD196, CD300LF and IL-22.

summary:
In Homo sapiens, innate lymphoid cell type 3 lacks CD94 and NKG2A while uniquely expressing CD196, CD300LF, and IL22, distinguishing them from CD56bright natural killer cell.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:e4233d0ab168b9fd83d5
claim_id: claim:e4233d0ab168b9fd83d5
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal: pDCs) produce type I interferon (IFN-I) and are traditionally defined as being BDCA-2 + CD123
summary:
In Homo sapiens, plasmacytoid dendritic cells are traditionally defined by expression of BDCA-2 and CD123.


