# claims

claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:27e541b1d9c15449d157
claim_id: claim:27e541b1d9c15449d157
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
VECs form the vasculature of the placenta and were identified by the expression of canonical markers including CDH5 and PECAM1

summary:
In Homo sapiens, vascular endothelial cells of the placenta are identified by expression of CDH5 and PECAM1.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:8332831d82db70606eb7
claim_id: claim:8332831d82db70606eb7
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
EBs specifically expressed hemoglobin subunit genes such as HBE1 , HBG1 , HBA1 , HBM , HBG2 , HBA2 , and HBZ .

summary:
In Homo sapiens, erythroblasts specifically express hemoglobin subunit genes HBE1, HBG1, HBA1, HBM, HBG2, HBA2, and HBZ.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:5d5ae3731e57695f5362
claim_id: claim:5d5ae3731e57695f5362
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, erythroblasts express glycophorins GYPA, GYPB, and GYPC.
span_literal:
EBs also expressed sialic acid–rich erythrocyte membrane proteins glycophorins ( GYPA , GYPB , and GYPC ).


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:1787ae1ec60df94a4f55
claim_id: claim:1787ae1ec60df94a4f55
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
HCs abundantly and specifically expressed established macrophage markers ( CD163 , CD14 , CSF1R , and CD68 ), the inflammatory cytokines CCL4 and CXCL8 , and allograft inflammatory factor 1 ( AIF1 ).

summary:
In Homo sapiens, Hofbauer cells abundantly and specifically express macrophage markers CD163, CD14, CSF1R, and CD68, as well as CCL4, CXCL8, and AIF1.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:eba61255b3fd158c7506
claim_id: claim:eba61255b3fd158c7506
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, FCGRT is primarily expressed in Hofbauer cells.
span_literal:
The maternal immunoglobulin G transporter FCGRT was primarily expressed in HCs, and to some extent by FBs and VECs, contrary to an earlier report indicating its expression in SCTs


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:5060c142ee66f4580107
claim_id: claim:5060c142ee66f4580107
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
DSCs represented 27% of ECM-expressing cells and are defined by the expression of not only PRL and IGFBP1 , established markers of decidualization

summary:
In Homo sapiens, decidualized stromal cells are defined by the expression of PRL and IGFBP1, established markers of decidualization.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:99e14e074088fd2118f7
claim_id: claim:99e14e074088fd2118f7
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Decidual FB1 (44.5%) and FB2 (21.5%) cells are differentiated by the unique expression of ARC , GEM , BDKRB1 , and PLIN2 in FB2.

summary:
In Homo sapiens, decidual fibroblast 2 is differentiated from decidual fibroblast 1 by unique expression of ARC, GEM, BDKRB1, and PLIN2.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:945294278b3fe715dd19
claim_id: claim:945294278b3fe715dd19
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Vascular SMCs (7%) are differentiated on the basis of their expression of MYH11 , ACTA2 , and RGS5 in addition to PI15 and NDUFA4L2 .

summary:
In Homo sapiens, vascular smooth muscle cells are differentiated by expression of MYH11, ACTA2, RGS5, PI15, and NDUFA4L2.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:3c33e031312f16d00c51
claim_id: claim:3c33e031312f16d00c51
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
EECs are characterized by the abundant expression of PAEP and epithelial markers such as KRT8 and CDH1

summary:
In Homo sapiens, endometrial epithelial cells are characterized by abundant expression of PAEP, KRT8, and CDH1.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:b4ac1551a4a81c745c1b
claim_id: claim:b4ac1551a4a81c745c1b
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
EECs specifically express the monoamine transporter SLC18A2 , along with GPX3 , PCCA , SLPI , DEFB1 , CP , RIMKLB , and LCN2 .

summary:
In Homo sapiens, endometrial epithelial cells specifically express SLC18A2, GPX3, PCCA, SLPI, DEFB1, CP, RIMKLB, and LCN2.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:e1d475376731c6b1325a
claim_id: claim:e1d475376731c6b1325a
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
We also identified three long noncoding RNAs ( LINC01320 , LINC01502 , and LINC01541 ) exclusively expressed by EECs.

summary:
In Homo sapiens, LINC01320, LINC01502, and LINC01541 are exclusively expressed by endometrial epithelial cells.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:47059e3a4af9f2a65260
claim_id: claim:47059e3a4af9f2a65260
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, decidual natural killer cells express GZMA, GZMB, PRF1, XCL1, and XCL2.
span_literal:
the cytotoxic granzyme GZMA and GZMB , perforin PRF1 , and the inflammatory chemokines XCL1 and XCL2 .


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:c7054757400e3cdf1e13
claim_id: claim:c7054757400e3cdf1e13
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, T cells are annotated on the basis of expression of CD3D and CD69.
span_literal:
TCs occurred at 14.2% frequency among all leukocytes and were annotated on the basis of expression of CD3D and CD69


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:3c6e6479662c6040d907
claim_id: claim:3c6e6479662c6040d907
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, T cells show elevated expression of LTB, CXCR4, CCL5, and IL7R.
span_literal:
TCs also showed elevated levels of expression of genes involved in cell-cell signaling such as LTB , CXCR4 , CCL5 , and IL7R .


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:e57de0818524499aed3c
claim_id: claim:e57de0818524499aed3c
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
APCs constituted 19.4% of decidua leukocytes according to expression of CD74 , human leukocyte antigen (HLA) class II α chain ( HLA-DRA and HLA-DPA1 ) and β chain ( HLA-DRB1 and HLA-DPB1 ) genes

summary:
In Homo sapiens, antigen-presenting cells are identified by expression of CD74, HLA-DRA, HLA-DPA1, HLA-DRB1, and HLA-DPB1.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:23a93dfb55d7a52f95d3
claim_id: claim:23a93dfb55d7a52f95d3
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
MACs specifically expressed MS4A4A , STAB1 , SEPP1 , and MS4A7 , characteristic for “alternatively activated” M2 macrophages.

summary:
In Homo sapiens, maternal macrophages specifically express MS4A4A, STAB1, SEPP1, and MS4A7, characteristic of alternatively activated M2 macrophages.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:99f444a489d62522e03d
claim_id: claim:99f444a489d62522e03d
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Dendritic cell types DC1 and DC2 were of the CLEC9A + and CD1C + subtypes, respectively, as described in a recent scRNA-seq study of human blood

summary:
In Homo sapiens, dendritic cell type 1 is of the CLEC9A-positive subtype and dendritic cell type 2 is of the CD1C-positive subtype.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:b59775555f7b67a59e90
claim_id: claim:b59775555f7b67a59e90
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal: LECs, identified by the expression of LYVE1 , and VECs, identified by the expression of CDH5
summary:
In Homo sapiens, lymphatic endothelial cells are identified by expression of LYVE1, and vascular endothelial cells are identified by expression of CDH5.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:aa9286023f56ed5ae7bd
claim_id: claim:aa9286023f56ed5ae7bd
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Expression of STMN1 , CD9 , FABP5 , ADM , and C10orf10 was characteristic for LECs, while VECs expressed ACKR1 , PCDH17 , FAM167B , AQP1 , HP , and IFI27 .

summary:
In Homo sapiens, lymphatic endothelial cells are characterized by expression of STMN1, CD9, FABP5, ADM, and C10orf10.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:08019b741e0ebe2e52be
claim_id: claim:08019b741e0ebe2e52be
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Within villi, EBs, FB3, and VCTs were distinguished by the expression of the Krüppel-like family (KLF) of TFs KLF1 , a known regulator of erythropoiesis ( 25 ), KLF4 , and KLF5 , respectively

summary:
In Homo sapiens, erythroblasts in the placental villi are distinguished by expression of the transcription factor KLF1.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:fb207f27ce248609e434
claim_id: claim:fb207f27ce248609e434
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Within villi, EBs, FB3, and VCTs were distinguished by the expression of the Krüppel-like family (KLF) of TFs KLF1 , a known regulator of erythropoiesis ( 25 ), KLF4 , and KLF5 , respectively

summary:
In Homo sapiens, placental fibroblast 3 in the villi is distinguished by expression of the transcription factor KLF4.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:17ca40deb70967acc96c
claim_id: claim:17ca40deb70967acc96c
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Within villi, EBs, FB3, and VCTs were distinguished by the expression of the Krüppel-like family (KLF) of TFs KLF1 , a known regulator of erythropoiesis ( 25 ), KLF4 , and KLF5 , respectively

summary:
In Homo sapiens, villous cytotrophoblasts in the villi are distinguished by expression of the transcription factor KLF5.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:c6ae7b8d30c5ce0c7275
claim_id: claim:c6ae7b8d30c5ce0c7275
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Within the decidua, ELF3 , PAX8 , and EHF , implicated in epithelial cell survival and function, were abundant and specific in EECs

summary:
In Homo sapiens, ELF3, PAX8, and EHF are abundantly and specifically expressed in endometrial epithelial cells.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:21785aedd40912cf5c67
claim_id: claim:21785aedd40912cf5c67
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, natural killer cells preferentially express the transcription factor EOMES.
span_literal:
Immune cells, such as NK cells, TCs, MACs, and DC1 cells, preferentially expressed known immune cell–specific TFs EOMES , BAFT , KLF2 , and ZNF366 , respectively.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:360db493da668c1e47a6
claim_id: claim:360db493da668c1e47a6
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
summary: In Homo sapiens, FOXL2 and MMP23B are cell-type-specific markers for second heart field.
span_literal:
Many of the top DEGs by z -score have not been identified as cell-specific markers in prior studies, for example, FOXL2 and MMP23B for SHF.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:3147ced4981275f9d295
claim_id: claim:3147ced4981275f9d295
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
summary: In Homo sapiens, SHH is a marker of the floor plate signalling centre.
span_literal:
Our data captured the known signalling molecules in these nine signalling centres, such as SHH in the floor plate 24 , SHH and BMP4 in ZPA 23 and FGF8/9 in AER 23 , demonstrating the fidelity of our data in recovering small anatomical structures (Extended Data Fig. 4d ).


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:4bede2979ebc59446f37
claim_id: claim:4bede2979ebc59446f37
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
span_literal:
At CS15–16, we found that five domains (a, l, m, n and o) are at different degrees of chondrogenesis 52 , 53 (Fig. 3a,e ), including domain m in the zeugopod territory that is distinguished by PTHLH and other DEGs (AUROC 0.94).

summary:
In Homo sapiens, PTHLH is a marker that distinguishes domain m in the zeugopod territory of the limb bud.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:7fdeb11e5f0ce676155b
claim_id: claim:7fdeb11e5f0ce676155b
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
summary: In Homo sapiens, PTHLH and CYP1B1 are specific markers of domain m in the limb bud.
span_literal:
However, specific markers of domain m ( PTHLH and CYP1B1 ) were almost not co-expressed in any cell of E12 mouse (Fig. 3g and Extended Data Fig. 7f ).


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:8aa5b0a8e430943fa300
claim_id: claim:8aa5b0a8e430943fa300
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
span_literal:
More importantly, we found that MSX2 expands its expression ventrally in human compared with mouse (Fig. 4e , roof plate to dp4 in human and roof plate to dp1 in mouse).

summary:
In Homo sapiens, MSX2 is expressed from roof plate to dp4 in the neural tube, expanding ventrally compared with mouse.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:2f3bc5a99bcdbb24fb21
claim_id: claim:2f3bc5a99bcdbb24fb21
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
span_literal:
The expression of MSX2 in human is similar to its paralogue MSX3 in mouse (roof plate to dp4), a gene that is lost in the human genome, suggesting that MSX2 compensates the function of MSX3 in human dp2–4 (Fig. 4e ).

summary:
In Homo sapiens, MSX2 is expressed in dp2–4 neural progenitors, compensating for the loss of MSX3 in the human genome.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:98fe8f574701381e0496
claim_id: claim:98fe8f574701381e0496
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
span_literal:
The dp4 markers ( ASCL1 and GBX2 ) are co-expressed with MSX2 but not with markers of dp1 ( ATOH1 ) or roof plate ( LMX1A ).

summary:
In Homo sapiens, ASCL1 and GBX2 are markers of dp4 neural progenitors, while ATOH1 is a marker of dp1 and LMX1A is a marker of roof plate.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:8d44f1b3c10751d76fa3
claim_id: claim:8d44f1b3c10751d76fa3
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
summary: In Homo sapiens, PAX7 is specifically expressed in floor plate of the neural tube.
span_literal:
A recent scRNA-seq study of human neural tube 63 identified two TFs that are specific to human in some cell types, that is, PAX7 in floor plate and NKX6- 2 in ventral progenitor domains, which are confirmed in our dataset (Extended Data Fig. 8c ).


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:22a4f036f0e0edaab245
claim_id: claim:22a4f036f0e0edaab245
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
summary: In Homo sapiens, RAX is expressed in retinal progenitor cells during eye development.
span_literal:
RAX is initially expressed in the entire vesicle and then restricted to retinal progenitor cells (RPCs) 85 .


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:e8abd0880170ea9145e2
claim_id: claim:e8abd0880170ea9145e2
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
span_literal:
The expression of PMEL and MITF in RPE is important for the differentiation of pigment cells 86 , 87 .

summary:
In Homo sapiens, PMEL and MITF are expressed in retinal pigmented epithelium and are important for pigment cell differentiation.


claim_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6:claim:ffa1eb2681eefb0fa34e
claim_id: claim:ffa1eb2681eefb0fa34e
paper_key: hca:0043_10.1038_s41556-023-01108-w_511ea5e6f6
span_literal:
Although spinal neurons and sclerotome both receive sonic hedgehog signalling from floor plate 32 , we found its antagonist HHIP is specific to sclerotome.

summary:
In Homo sapiens, HHIP is specifically expressed in sclerotome, distinguishing it from spinal neurons.


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:efd5f2b0436490918e48
claim_id: claim:efd5f2b0436490918e48
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
summary: In Homo sapiens, the neural crest derived second heart field is marked by MSC and ISL1.
span_literal:
migratory cell types that would have been difficult to identify without the whole-embryo approach, such as the neural crest derived second heart field (SHF)19 marked by MSC and ISL1


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:9489d4e4f36ef0540371
claim_id: claim:9489d4e4f36ef0540371
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
summary: In Homo sapiens, FOXL2 and MMP23B are cell-specific markers for the second heart field.
span_literal:
Many of the top DEGs by z-score have not been identified as cell specific markers in prior studies, e.g., FOXL2 and MMP23B for SHF.


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:2c48d143bc1ec700a466
claim_id: claim:2c48d143bc1ec700a466
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
span_literal:
Although spinal neurons and sclerotome both receive sonic hedgehog signaling from floor plate31, we found its antagonist HHIP is specific to sclerotome.

summary:
In Homo sapiens, HHIP is specifically expressed in sclerotome, distinguishing it from spinal neuron.


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:f287cda136fd0fbed393
claim_id: claim:f287cda136fd0fbed393
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
span_literal:
we found that MSX2 expands its expression ventrally in human compared to mouse ([Fig. 4E](470583v2_fig4.tif), roof plate to dp4 in human and roof plate to dp1 in mouse).

summary:
In Homo sapiens, MSX2 is expressed from roof plate to dp4 in the neural tube, expanding ventrally compared to mouse.


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:35884111416b4cdbc34c
claim_id: claim:35884111416b4cdbc34c
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
span_literal:
The expression of MSX2 in human is similar to its paralog MSX3 in mouse (roof plate to dp4), a gene that is lost in the human genome, suggesting MSX2 compensates the function of MSX3 in human dp2-4

summary:
In Homo sapiens, MSX2 is expressed in dp2-4 of the neural tube, compensating for the lost MSX3 gene.


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:04a4be85ac5e43eaa299
claim_id: claim:04a4be85ac5e43eaa299
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
summary: In Homo sapiens, dp4 in the neural tube is marked by co-expression of ASCL1 and GBX2.
span_literal:
We located dp4 in the spots in neural tube that co-express dp4 markers (ASCL1 > 0.5 and GBX2 > 0.5).


claim_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c:claim:5242b413c05d5f8e6f89
claim_id: claim:5242b413c05d5f8e6f89
paper_key: hca:0044_10.1101_2021.11.30.470583_4b4329647c
span_literal:
A recent scRNA-seq study of human neural tube63 identified two TFs that are specific to human, namely PAX7 and NKX6-2, which are confirmed in our dataset

summary:
In Homo sapiens, PAX7 and NKX6-2 are transcription factors with human-specific expression in the neural tube.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:bd3b2138b368c3ffd1d1
claim_id: claim:bd3b2138b368c3ffd1d1
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
summary: In Homo sapiens retina, rod photoreceptors are marked by PDE6A, CNGA1, and RHO.
span_literal:
we were able to assign cell identities to 16 of the 18 clusters (Fig 1 A–D), corresponding to rod photoreceptors ( PDE6A, CNGA1, RHO ), cone photoreceptors ( ARR3, GNGT2, GUCA1C ), Müller glia ( RLBP1/CRALBP ), retinal astrocytes ( GFAP ), microglia ( HLA‐DPA1, HLA‐DPB1, HLA‐DRA ), bipolar cells ( VSX2, OTX2 ), retinal ganglion cells ( NEFL, GAP43, SNCG ), amacrine cells ( GAD1, CALB1, CHAT ), and horizontal cells ( ONECUT1, ONECUT2 ).


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:03842b382961b5d00f08
claim_id: claim:03842b382961b5d00f08
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
summary: In Homo sapiens retina, OFF-bipolar cells are marked by GRIK1 expression.
span_literal:
the bipolar clusters can be classified as OFF‐bipolar cells ( GRIK1 + : C6) and ON‐bipolar cells ( ISL1 + : C8, C11).


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:77ae063a9e955ad87df6
claim_id: claim:77ae063a9e955ad87df6
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
Further analysis showed that C8 represents rod bipolar cells based on the marker PRKCA , while C11 expresses the marker TTR corresponding to a diffuse bipolar subtype DB4 (Fig EV1 ).

summary:
In Homo sapiens retina, rod bipolar cells are marked by PRKCA, while diffuse bipolar subtype DB4 is marked by TTR.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:08b77cf2ae3afc03c73e
claim_id: claim:08b77cf2ae3afc03c73e
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
We detected 564 cone photoreceptor cells in our scRNA‐seq data, which are distinguishable from the other cell types by the expression of the cone marker genes ARR3, CNBG3, GNAT2, GNGT2, GRK7, GUCA1C, PDE6C, PDE6H, OPN1LW, RXRG, and THRB (Fig 5 A).

summary:
In Homo sapiens retina, cone photoreceptors are distinguishable from other cell types by expression of ARR3, CNBG3, GNAT2, GNGT2, GRK7, GUCA1C, PDE6C, PDE6H, OPN1LW, RXRG, and THRB.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:76f4efb8f041e25da367
claim_id: claim:76f4efb8f041e25da367
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
OPN1SW ‐positive S‐cones, OPN1MW ‐positive M‐cones, and OPN1LW ‐positive L‐cones respond preferentially to shorter, medium, and longer wavelengths responsible for color vision (Roorda & Williams, 1999 ).

summary:
In Homo sapiens retina, S-cones are marked by OPN1SW, M-cones are marked by OPN1MW, and L-cones are marked by OPN1LW.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:b0a59424ed97dd87793e
claim_id: claim:b0a59424ed97dd87793e
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
Our results identified a panel of genes that differentially marked S‐cones (e.g., CCDC136 , RAMP1 , LY75, CADM3, TFPI2, CRHBP, RAB17, UPB1, RRAD, and SLC12A1 ) and L/M‐cones (e.g., THRB, KIF2A, LBH, PGP, CHRNA3, AHI1, and LIMA1 ; Fig 3 D).

summary:
In Homo sapiens retina, S-cones are differentially marked by CCDC136, RAMP1, LY75, CADM3, TFPI2, CRHBP, RAB17, UPB1, RRAD, and SLC12A1 compared to L/M-cones.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:f8c7bc5939308692d1af
claim_id: claim:f8c7bc5939308692d1af
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
Our results identified a panel of genes that differentially marked S‐cones (e.g., CCDC136 , RAMP1 , LY75, CADM3, TFPI2, CRHBP, RAB17, UPB1, RRAD, and SLC12A1 ) and L/M‐cones (e.g., THRB, KIF2A, LBH, PGP, CHRNA3, AHI1, and LIMA1 ; Fig 3 D).

summary:
In Homo sapiens retina, L/M-cones are differentially marked by THRB, KIF2A, LBH, PGP, CHRNA3, AHI1, and LIMA1 compared to S-cones.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:155871e89634d21c8951
claim_id: claim:155871e89634d21c8951
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
summary: In Homo sapiens retina, TBX2 marks S-cones.
span_literal:
our data showed that TBX2 marks the S‐cones in humans, which is also conserved in macaque (Peng et al , 2019 ).


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:0169fb283a2d97f7147d
claim_id: claim:0169fb283a2d97f7147d
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal: VIM, GLUL , and S100A1 marked both Müller glia and retinal astrocytes at high expression levels.
summary:
In Homo sapiens retina, VIM, GLUL, and S100A1 mark both Müller glia and retinal astrocytes at high expression levels.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:aa0d67626f791e4937c1
claim_id: claim:aa0d67626f791e4937c1
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
summary: In Homo sapiens retina, GFAP represents a reliable marker for retinal astrocytes.
span_literal:
GFAP represents a reliable marker for retinal astrocytes, and its expression is consistent with a previous report (Vecino et al , 2016 ).


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:7a92c055db6e0868e096
claim_id: claim:7a92c055db6e0868e096
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
Notably, Müller glia are low in GFAP expression, indicating they are not in an activated state commonly caused by stresses and reactive gliosis (Fernández‐Sánchez et al , 2015 ).

summary:
In Homo sapiens retina, Müller glia have low GFAP expression, indicating they are not in an activated state.


claim_key: hca:0045_10.15252_embj.2018100811_a99bb4a451:claim:48bbbe18d201fb8b810f
claim_id: claim:48bbbe18d201fb8b810f
paper_key: hca:0045_10.15252_embj.2018100811_a99bb4a451
span_literal:
Conversely, Müller glia can be distinguished from retinal astrocytes by high expression levels of RLBP1 , and RGR to a lesser extent.

summary:
In Homo sapiens retina, Müller glia can be distinguished from retinal astrocytes by high expression levels of RLBP1 and RGR.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:a1579a741144cae73ee4
claim_id: claim:a1579a741144cae73ee4
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
scRNAseq revealed two distinct epithelial cell clusters representing PE (SLC4A4+/TFPI2+/MLANA+ [ 29 ]) and NPE (OPTC+/Best2+ [ 30 , 31 ]), respectively (Fig. 1 A, B ).

summary:
In Homo sapiens ciliary body, pigmented epithelium is marked by SLC4A4, TFPI2, and MLANA, while non-pigmented epithelium is marked by OPTC and Best2.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:b2ce6f00477141b2f2e3
claim_id: claim:b2ce6f00477141b2f2e3
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
summary: In Homo sapiens ciliary body, melanocyte is annotated by its specific expression of MITF.
span_literal:
Of note, melanocyte, which also expressed MLANA, was annotated due to its specific expression of MITF [ 32 ] (Fig. 1 B).


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:1b89943eebfcac839d0f
claim_id: claim:1b89943eebfcac839d0f
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
Furthermore, we identified that the retinal and anterior neural fold homeobox (RAX) gene is specifically expressed in the NPE and PE clusters (Fig. 2 C, D , Suppl. Fig. 3A and Suppl. Table 4), demonstrating a new marker for distinguishing the ciliary epithelium from other ciliary cells.

summary:
In Homo sapiens ciliary body, the retinal and anterior neural fold homeobox (RAX) gene is specifically expressed in the non-pigmented epithelium and pigmented epithelium, serving as a new marker for distinguishing ciliary epithelium from other ciliary cells.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:f9e32ed40a4d07266957
claim_id: claim:f9e32ed40a4d07266957
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
The genes specifically expressed in both PE and NPE also include other homeobox genes, such as PAX6, SIX3 and LHX2 [ 34 – 37 ], common markers for the epithelium, such as DSP (encoding desmoplakin), DSG2 (encoding desmoglein 2) and EGFR, and ion/water channel genes, etc.

summary:
In Homo sapiens ciliary body, the ciliary epithelium (both pigmented epithelium and non-pigmented epithelium) specifically expresses PAX6, SIX3, LHX2, DSP (encoding desmoplakin), DSG2 (encoding desmoglein 2), and EGFR.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:d762880b34421e161774
claim_id: claim:d762880b34421e161774
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
we noted that the expression of lymphatic endothelial cell marker gene Prox1 and LYVE1 were completely absent in the ciliary endothelial cell population that expressed canonical EC genes, such as CLDN5, CDH5, PECAM1, VWF, FLT1, KDR and ERG (Fig. 3 E).

summary:
In Homo sapiens ciliary body, the endothelial cell population expresses canonical endothelial cell genes CLDN5, CDH5, PECAM1, VWF, FLT1, KDR, and ERG, but lacks expression of lymphatic endothelial cell markers PROX1 and LYVE1.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:9e76d08636158135821b
claim_id: claim:9e76d08636158135821b
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
we confirmed that two SMC subclusters with specific expression of the canonical smooth muscle cell markers ACTA2 (encoding αSMA) and MYH11 were present (Fig. 4 C, D ).

summary:
In Homo sapiens ciliary body, smooth muscle cell subclusters specifically express the canonical smooth muscle cell markers ACTA2 (encoding alpha smooth muscle actin) and MYH11.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:f48f3b4c41501266ae36
claim_id: claim:f48f3b4c41501266ae36
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
The larger subcluster was assigned as nonvascular CMC due to its enriched expression of desmin, whereas the smaller sub-cluster was annotated as VSMC [ 39 , 40 ] (Fig. 4 C, D ).

summary:
In Homo sapiens ciliary body, the nonvascular ciliary muscle cell subcluster is distinguished from vascular smooth muscle cell by its enriched expression of desmin.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:214b3a178f7f9b75020e
claim_id: claim:214b3a178f7f9b75020e
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
Analysis of the expression of macrophage surface markers and transcription factors revealed that cells in the relatively larger macrophage subcluster had enriched expression of MHC class II genes, FCGR1A, CD86 and FCGR2A (Fig. 5 B), consistent with a pro-inflammatory (M1) phenotype [ 41 ].

summary:
In Homo sapiens ciliary body, pro-inflammatory (M1) macrophages have enriched expression of MHC class II genes, FCGR1A, CD86, and FCGR2A.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:945eba103c420840bc23
claim_id: claim:945eba103c420840bc23
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
The relatively smaller subcluster was annotated as anti-inflammatory (M2) macrophage [ 41 ] due to higher expression of CD163 and MRC1 genes (Fig. 5 B).

summary:
In Homo sapiens ciliary body, anti-inflammatory (M2) macrophage is marked by higher expression of CD163 and MRC1.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:4883a3f78080126aff9d
claim_id: claim:4883a3f78080126aff9d
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
These macrophage-like microglia possessed significantly higher expression levels of the monocyte/macrophage cell marker CD14 [ 42 ] (Fig. 5 E) and were enriched in pathways responsible for macrophage activation and phagocytosis (Fig. 5 F).

summary:
In Homo sapiens retina, macrophage-like microglia possess significantly higher expression levels of the monocyte/macrophage cell marker CD14.


claim_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba:claim:fe643e53852c11bd4ad8
claim_id: claim:fe643e53852c11bd4ad8
paper_key: hca:0046_10.1007_s00018-022-04559-w_6919bd92ba
span_literal:
Immunofluorescence staining demonstrated that ciliary PE cells lining the outer layer of the ciliary processes with the characteristic brownish black appearance and melanocytes located in the stromal area have strongly enriched expression of tyrosinase (TYR) (Fig. 2 A, B ), a copper-containing enzyme that catalyzes the formation of melanin from tyrosine [ 33 ].

summary:
In Homo sapiens ciliary body, pigmented epithelium cells and melanocytes have strongly enriched expression of tyrosinase (TYR).


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:237f7d4987019fe89d95
claim_id: claim:237f7d4987019fe89d95
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
summary: In Homo sapiens breast tissue, basal cells are positive for CD49f and low/negative for EPCAM.
span_literal:
Flow cytometry based on CD49f and EpCAM staining separates lineage‐negative breast tissue cells into stromal (CD49f – EpCAM – ) and epithelial cells, which includes basal (CD49f + EpCAM lo/– ), luminal progenitor (LP) (CD49f + EpCAM + ), and mature luminal (ML) (CD49f – EpCAM + ) cells.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:03623aca5770b690a115
claim_id: claim:03623aca5770b690a115
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
summary: In Homo sapiens breast, basal cells are marked by KRT5, ACTA2, MYLK, and SNAI2.
span_literal:
Expression of typical mammary lineage marker genes (Lim et al, 2010 ) for basal (e.g., KRT5, ACTA2, MYLK, SNAI2 ), luminal progenitor ( TNFRSF11A (RANK), KIT ), and mature luminal cells ( ESR1, PGR, FOXA1 ) corroborated the identity of the three major cell clusters (Fig 1H ).


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:4068aa797e69c6a9979a
claim_id: claim:4068aa797e69c6a9979a
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
summary: In Homo sapiens breast, B cells are marked by CD79A.
span_literal:
The expression of multiple cell‐specific genes for either pre‐ or post‐menopausal patients was examined: pan‐hematopoietic ( PTPRC/CD45 ), B cells ( CD79A ), T cells ( CD4, CD8a ), NK cells ( HAVR2C ), myeloid/macrophages ( ITGAX/CD11c, ITGAM/CD11b, CD68, CD14 ), pericytes ( RGS5 ), and endothelial cells ( VWF, CD36 ) (Fig 2I ).


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:21e620c3e8804659404c
claim_id: claim:21e620c3e8804659404c
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
The expression of multiple cell‐specific genes for either pre‐ or post‐menopausal patients was examined: pan‐hematopoietic ( PTPRC/CD45 ), B cells ( CD79A ), T cells ( CD4, CD8a ), NK cells ( HAVR2C ), myeloid/macrophages ( ITGAX/CD11c, ITGAM/CD11b, CD68, CD14 ), pericytes ( RGS5 ), and endothelial cells ( VWF, CD36 ) (Fig 2I ).

summary:
In Homo sapiens breast, myeloid cells and macrophages are marked by ITGAX (CD11c), ITGAM (CD11b), CD68, and CD14.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:442b410d8dbe2fb11c7c
claim_id: claim:442b410d8dbe2fb11c7c
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
Moreover, close inspection of the fibroblast population (cluster 1) indicated that a lower proportion of cells expressed key marker genes such as PDGFRA, PDGFRB, CD34, and the matrix‐associated genes POSTN and COL3A1 (also SPARC, COL5A2, COL14A1 ) in post‐menopausal tissue (Fig 3A ).

summary:
In Homo sapiens breast, fibroblasts are marked by PDGFRA, PDGFRB, CD34, POSTN, COL3A1, SPARC, COL5A2, and COL14A1.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:67b94fd2bfe443854865
claim_id: claim:67b94fd2bfe443854865
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
summary: In Homo sapiens breast tumors, T regulatory cells are marked by CD4 and FOXP3.
span_literal:
CD4 + FOXP3 + T regulatory (Treg) cells (Josefowicz et al, 2012 ) were prominent in tumors, while undetectable in preneoplastic tissue.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:b42d5a2fb964137a1044
claim_id: claim:b42d5a2fb964137a1044
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
summary: In Homo sapiens breast tumors, T regulatory cells express CTLA4, TIGIT, and HAVCR2 (TIM-3).
span_literal:
These cells expressed inhibitory markers and genes associated with functional exhaustion (e.g., CTLA4, TIGIT, HAVCR2/TIM‐3 ) (Fig 5D ).


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:943cdd6ccef42eebaa00
claim_id: claim:943cdd6ccef42eebaa00
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
summary: In Homo sapiens BRCA1-associated breast tumors, tumor-associated macrophages express CX3CR1.
span_literal:
Interestingly, CX3CR1 ‐expressing cells that resembled tumor‐associated macrophages (TAMs) were restricted to BRCA1 ‐associated tumors (Fig 5G ).


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:38877588bcd55f9d3ad5
claim_id: claim:38877588bcd55f9d3ad5
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
Further examination of cancer‐associated fibroblasts (CAFs) in BRCA1 ‐mutant tumors indicated increased levels of the collagen genes COL1A2 and COL3A1 , the WNT inhibitor SFRP2, and the calmodulin‐ and actin‐binding protein CALD1, which mediates the contractile function of myofibroblasts (Fig 5H ).

summary:
In Homo sapiens BRCA1-mutant breast tumors, cancer-associated fibroblasts show increased levels of COL1A2, COL3A1, SFRP2, and CALD1.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:8fef918c16c542817777
claim_id: claim:8fef918c16c542817777
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
Numerous tumor‐infiltrating myeloid cells expressed abundant MRC1, TREM1, CD68, and SIGLEC1 (Fig 7A–D ), thus sharing features with the breast TAMs recently described through flow cytometry (Cassetta et al, 2019 ).

summary:
In Homo sapiens breast tumors, tumor-infiltrating myeloid cells express MRC1, TREM1, CD68, and SIGLEC1.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:d4f5d6a031cb555d945b
claim_id: claim:d4f5d6a031cb555d945b
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
The expression of immune checkpoint molecules and markers of functional exhaustion in the CD4 + FOXP3 + Treg subset (e.g., CTLA4, BATF, TIGIT, TNFRSF4/18, TIM3, LAG3 ) renders them potential targets of immune checkpoint blockade (Schreiber et al, 2011 ) (Fig EV4C ).

summary:
In Homo sapiens breast tumors, the CD4-positive FOXP3-positive T regulatory cell subset expresses CTLA4, BATF, TIGIT, TNFRSF4, TNFRSF18, TIM3, and LAG3.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:28371c0c061b50bae70d
claim_id: claim:28371c0c061b50bae70d
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
Rather, ER + cancers featured an actively cycling TAM population (Fig 7C and D ; cluster 7), which expressed genes including CD14, FCGR1A , CD11b, MHCII genes , CD68, SIGLEC1, CD74, APOC1, TYROBP, C1QC, FCER1G/3A, and multiple cell cycle genes.

summary:
In Homo sapiens estrogen receptor-positive breast cancers, cycling tumor-associated macrophages express CD14, FCGR1A, CD11b, CD68, SIGLEC1, CD74, APOC1, TYROBP, C1QC, and FCER1G.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:44ce8bf2dfe2330bcee6
claim_id: claim:44ce8bf2dfe2330bcee6
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
Both TNBC and HER2 featured a proliferative CD8 + T‐cell cluster, most likely corresponding to T RM ‐like cells (Savas et al, 2018 ).

summary:
In Homo sapiens triple-negative breast cancer and HER2-positive breast cancer, a proliferative CD8-positive T cell cluster is present, most likely corresponding to tissue-resident memory T cell-like cells.


claim_key: hca:0047_10.15252_embj.2020107333_a4d0f57474:claim:a3e582f62201850163a7
claim_id: claim:a3e582f62201850163a7
paper_key: hca:0047_10.15252_embj.2020107333_a4d0f57474
span_literal:
By contrast, ER + tumors primarily comprised cycling TAMs that expressed markers such as CD163, MARCH1, MRC1, and CX3CR1 , among others.

summary:
In Homo sapiens estrogen receptor-positive breast tumors, cycling tumor-associated macrophages express CD163, MARCH1, MRC1, and CX3CR1.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:b76c74530b467541f5ac
claim_id: claim:b76c74530b467541f5ac
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
we transcriptionally defined chondrocytes in human lungs ( ACAN , CHAD , COL9A3 , HAPLN1 and CYTL1 ; Extended Data Fig. 1d,e )

summary:
In Homo sapiens lung, chondrocytes are defined by expression of ACAN, CHAD, COL9A3, HAPLN1 and CYTL1.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:dc6805b7d8c8912913b9
claim_id: claim:dc6805b7d8c8912913b9
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
summary: In Homo sapiens, immune recruiting fibroblasts express the chemokines CCL19 and CCL21.
span_literal:
IR-fibro cells expressed the chemokines CCL19 and CCL21 and other marker genes of fibroblast reticular cells and follicular dendritic cells (fDC), which together are responsible for T and B cell positioning in secondary lymphoid organs (Fig. 2c )


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:9b74801692d9c09acec9
claim_id: claim:9b74801692d9c09acec9
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
We uncover the transcriptome for human PB-fibro, consistent with the key protein markers COL15A1 and ENTPD1 (Extended Data Fig. 4a,b ).

summary:
In Homo sapiens, peribronchial fibroblasts are marked by the key protein markers COL15A1 and ENTPD1.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:eb89829ae3d2e30dbf6f
claim_id: claim:eb89829ae3d2e30dbf6f
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
summary: In Homo sapiens, perichondrial fibroblasts express the marker gene COL12A1.
span_literal:
We found analogous marker expression of COL12A1 around the cartilage in the Human Protein Atlas (HPA) (Extended Data Fig. 4f ), supporting cell2location mapping of PC-fibro (Fig. 2g ).


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:0cac081e108c4400f022
claim_id: claim:0cac081e108c4400f022
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
summary: In Homo sapiens, immune recruiting venous perivascular cells express ABCC9 and ICAM1 but not CSPG4.
span_literal:
The IR-Ven-Peri expressed ABCC9 and ICAM1 but not CSPG4 , similar to postcapillary venous perivascular cells important for immune cell homing to peripheral lymph nodes


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:b6f4c6db0cacaaeba79d
claim_id: claim:b6f4c6db0cacaaeba79d
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
IR-Ven-Peri markers CCL21 and CCL19 localize adjacent to the venous vessel marker ACKR1 in the airway.

summary:
In Homo sapiens, immune recruiting venous perivascular cells are marked by CCL21 and CCL19, while venous vessel endothelial cells are marked by ACKR1 in the airway.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:fdefaaa5239ac401251d
claim_id: claim:fdefaaa5239ac401251d
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
smFISH staining for ALDH1A3, MIA and RARRES1 validated localization at the SMG and distinguished these cells from other epithelial cells

summary:
In Homo sapiens, submucosal gland duct cells are marked by ALDH1A3, MIA and RARRES1, distinguishing them from other epithelial cells.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:7fcbc9823615710160a3
claim_id: claim:7fcbc9823615710160a3
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
We also identified myoepithelial cells in snRNA-seq, expressing basal epithelium ( TP63 and KRT14 ) and muscle ( ACTA2, TAGLN and CNN1 positive, but DES negative) markers

summary:
In Homo sapiens, myoepithelial cells express basal epithelium markers TP63 and KRT14, and muscle markers ACTA2, TAGLN and CNN1, but are negative for DES.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:9ea0468649051f42c8ef
claim_id: claim:9ea0468649051f42c8ef
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
We identified markers for cell–cell adhesion ( FHOD3 and LAMA1 ) and nerve synapse signaling ( NTRK2 and PLD5 ) and validated marker genes by smFISH (Extended Data Fig. 7i ) and in the HPA (Extended Data Fig. 7j ).

summary:
In Homo sapiens, myoepithelial cells express markers for cell-cell adhesion FHOD3 and LAMA1, and nerve synapse signaling markers NTRK2 and PLD5.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:e1ab5a301399135a284c
claim_id: claim:e1ab5a301399135a284c
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
summary: In Homo sapiens, macro-intermediate cells express the monocyte marker CD14.
span_literal:
We identified a previously undefined cluster expressing monocyte ( CD14 ) and macrophage markers, termed macro-intermediate


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:f4444c60e74caf566dfc
claim_id: claim:f4444c60e74caf566dfc
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal: a cluster expressing metallothioneins (Macro-alv-MT), including MT1G , MT1X and MT1F
summary:
In Homo sapiens, alveolar macrophages expressing metallothioneins (Macro-alv-MT) are marked by MT1G, MT1X and MT1F.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:fabcf3d3b80074f132f4
claim_id: claim:fabcf3d3b80074f132f4
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
summary: In Homo sapiens, Macro-CCL macrophages express the chemokines CXCL8, CCL4 and CCL20.
span_literal:
we identified a rare undescribed population of macrophages expressing chemokines, including CXCL8 , CCL4 and CCL20 , which we named Macro-CCL


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:8fb6ffa64204e1f9bbd3
claim_id: claim:8fb6ffa64204e1f9bbd3
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
Distinguishing markers for IgA plasma cells included CCR10 and B cell maturation antigen BCMA ( TNFRSF17 ; Extended Data Fig. 9b ), which are important for plasma cell localization and survival, respectively

summary:
In Homo sapiens, IgA plasma cells are distinguished by expression of CCR10 and B cell maturation antigen (TNFRSF17).


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:d0c3affe49254565e89a
claim_id: claim:d0c3affe49254565e89a
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
smFISH staining of mucous ( MUC5B ), serous ( LPO) and duct ( ALDH1A3/RARRES1 ) cells in human bronchus.

summary:
In Homo sapiens bronchus, submucosal gland mucous cells are marked by MUC5B, serous cells by LPO, and duct cells by ALDH1A3 and RARRES1.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:04767b64338a1c845d73
claim_id: claim:04767b64338a1c845d73
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
summary: In Homo sapiens, submucosal gland epithelial cells highly express PIGR and CCL28.
span_literal:
Expression of PIGR , which transcytoses polymeric Ig across the surface epithelium, was high across SMG epithelial cells, as was CCL28 , known to recruit IgA plasma cells through CCR10 (Fig. 5a–d and Extended Data Fig. 10a )


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:7c8190886328f7ba96ee
claim_id: claim:7c8190886328f7ba96ee
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
The expression of HLA-DRA and HLA-DRB1 in SMG duct/SMG serous cells was comparable to ciliated cells at the RNA level (Fig. 5i ), but much higher at the protein level (Fig. 5j ).

summary:
In Homo sapiens, submucosal gland duct cells and submucosal gland serous cells express HLA-DRA and HLA-DRB1.


claim_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553:claim:a2d0e58b36677eec83c1
claim_id: claim:a2d0e58b36677eec83c1
paper_key: hca:0048_10.1038_s41588-022-01243-4_ae2af85553
span_literal:
PC-fibros express genes causing skeletal abnormalities in humans (Extended Data Fig. 4i ), including FLNB and FGFR2 , suggesting the relevance of PC-fibros in supporting cartilage functions and related abnormalities

summary:
In Homo sapiens, perichondrial fibroblasts express FLNB and FGFR2, genes causing skeletal abnormalities.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:c2babf0f9d6263ddc3d3
claim_id: claim:c2babf0f9d6263ddc3d3
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal: nuclear expression of the hormone receptors ( ESR1 , AR and PGR ) was specific to the LumHR cells
summary:
In Homo sapiens adult breast, ESR1, AR, and PGR are specifically expressed in luminal hormone-responsive cells.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:7e028f401a50e1fa2bb8
claim_id: claim:7e028f401a50e1fa2bb8
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
The basal cells were highly homogenous, expressing ACTA2 and TP63 , as well as low levels of EPCAM , consistent with their role in basement membrane production and myoepithelial functions

summary:
In Homo sapiens adult breast, basal-myoepithelial cells express ACTA2 and TP63, as well as low levels of EPCAM.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:343289e5bfb4cad01cc7
claim_id: claim:343289e5bfb4cad01cc7
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
LumHR-major was characterized by high EGLN3 expression, whereas LumHR-SCGB showed high expression of secretory genes, including MUCL1 , prolactin-inducible protein ( PIP ) and secretoglobins.

summary:
In Homo sapiens adult breast, luminal hormone-responsive major cell state is characterized by high EGLN3 expression.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:3a1a84230d95517e398c
claim_id: claim:3a1a84230d95517e398c
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
LumHR-major was characterized by high EGLN3 expression, whereas LumHR-SCGB showed high expression of secretory genes, including MUCL1 , prolactin-inducible protein ( PIP ) and secretoglobins.

summary:
In Homo sapiens adult breast, luminal hormone-responsive SCGB cell state shows high expression of MUCL1 and prolactin-inducible protein (PIP).


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:cfabb8a59be0e0013e82
claim_id: claim:cfabb8a59be0e0013e82
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
The LumHR-active cluster had abundant FASN 28 and EREG 29 expression, which are both associated with hormone-dependent proliferation

summary:
In Homo sapiens adult breast, the luminal hormone-responsive active cell state has abundant FASN and EREG expression.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:ee7bd05cf93d9a0bd7e4
claim_id: claim:ee7bd05cf93d9a0bd7e4
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
LumSec-HLA expressed genes encoding MHC class I and MHC class II molecules, as well as the chemokine CCL20 , suggesting a role in immune cell signalling

summary:
In Homo sapiens adult breast, the luminal secretory HLA cell state expresses CCL20 as well as genes encoding MHC class I and MHC class II molecules.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:7fcaca3c6df30d695c4d
claim_id: claim:7fcaca3c6df30d695c4d
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
LumSec-lac was marked by genes encoding caseins ( CSN2 and CSN1S1 ) and showed a high lactation signature 16 score

summary:
In Homo sapiens adult breast, the luminal secretory lactation cell state is marked by CSN2 and CSN1S1.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:4ecd06527895d9726e3b
claim_id: claim:4ecd06527895d9726e3b
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
The LumSec-KIT state showed elevated expression of KIT , as well as transcription factors including SOX4 , HES1 and MAFB

summary:
In Homo sapiens adult breast, the luminal secretory KIT cell state shows elevated expression of KIT, SOX4, HES1, and MAFB.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:a5d2d19dffb307a7e62f
claim_id: claim:a5d2d19dffb307a7e62f
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
LumSec-basal, which expressed both luminal and basal markers (for example, KRT5 , KRT14 ) as reported previously 15 , and LumSec-myo, which expressed genes related to myo-contractile functions such as MYLK

summary:
In Homo sapiens adult breast, the luminal secretory basal cell state expresses KRT5 and KRT14, while the luminal secretory myoepithelial cell state expresses MYLK.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:acc06182de46c2f9ef7f
claim_id: claim:acc06182de46c2f9ef7f
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, naive T cells express SELL.
span_literal:
The CD4 + T cells included naive T cells ( SELL ), T helper (T H ) and T H -like ( IL7R , CCR6 , CCL20 ), T effector memory (T EM ) ( LMNA ) and T regulatory (T reg ) ( FOXP3 , CTLA4 ) cells.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:fff6829d1de80e99c049
claim_id: claim:fff6829d1de80e99c049
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
Two populations of CD8 + T cells were identified, T resident memory (T RM ; ITGA1 ) and T EM ( GZMK ).

summary:
In Homo sapiens adult breast, CD8-positive T resident memory cells express ITGA1 and CD8-positive T effector memory cells express GZMK.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:5ec4ff2f2dbe25cb4ecb
claim_id: claim:5ec4ff2f2dbe25cb4ecb
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, activated T cells display upregulation of PLCG2 and ZNF683.
span_literal:
We detected clusters of activated CD4 + and CD8 + T cells that displayed upregulation of genes associated with TCR engagement ( PLCG2 , ZNF683 ).


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:96f66e7bae9117f1e1c8
claim_id: claim:96f66e7bae9117f1e1c8
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
Our subclustering further resolved populations of NK ( GNLY ), NKT ( GNLY , CD3D ) and innate lymphoid cells (ILCs; IL7R ).

summary:
In Homo sapiens adult breast, natural killer cells express GNLY, natural killer T cells express GNLY and CD3D, and innate lymphoid cells express IL7R.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:f11899ba522386ff196e
claim_id: claim:f11899ba522386ff196e
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, mature dendritic cells express LAMP3.
span_literal:
Four subpopulations of DCs were identified, including mature (mDC) ( LAMP3 ), plasmacytoid (pDC) ( LILRA4 ) and two conventional cell states (cDC1 ( CLEC9A ) and cDC2 ( CLEC10A )).


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:4234b104c1dbbb568ec7
claim_id: claim:4234b104c1dbbb568ec7
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
Among the macrophages, we detected classical (macro-m1) ( IL1B ) and alternatively (macro-m2) ( MRC1 ) activated subsets, which further subclustered by chemokines (macro-m1-CCL and macro-m2-CXCL).

summary:
In Homo sapiens adult breast, classically activated macrophages (macro-m1) express IL1B and alternatively activated macrophages (macro-m2) express MRC1.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:910ac63c24a5a016a2d9
claim_id: claim:910ac63c24a5a016a2d9
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, interferon-response macrophages express IFIT1 and IFIT2.
span_literal:
Macrophages also included a population expressing interferon response genes (macro-IFN) ( IFIT1 , IFIT2 ) and a lipid-associated macrophage subcluster (macro-lipo) ( APOC , LIPA , LPL ).


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:5e5d150855d67a96e16a
claim_id: claim:5e5d150855d67a96e16a
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
We identified populations of classical ( EREG ) and non-classical ( FCGR3A ) monocytes, as well as mast cells ( TPSAB1 ).

summary:
In Homo sapiens adult breast, classical monocytes express EREG, non-classical monocytes express FCGR3A, and mast cells express TPSAB1.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:8f30a8be2ac141724df2
claim_id: claim:8f30a8be2ac141724df2
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, the fibroblast major cell state expresses MMP3, CXCL1, and CXCL2.
span_literal:
The fibro-major ( MMP3 , CXCL1 and CXCL2 ) state was associated with ECM remodelling and immune signalling, whereas the fibro-matrix cells showed high expression of collagen genes ( COL1A1 , COL3A1 ) and scored high for a collagen gene signature, suggesting a role in ECM production


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:b9c5336ccfd731e419c2
claim_id: claim:b9c5336ccfd731e419c2
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
The fibro-major ( MMP3 , CXCL1 and CXCL2 ) state was associated with ECM remodelling and immune signalling, whereas the fibro-matrix cells showed high expression of collagen genes ( COL1A1 , COL3A1 ) and scored high for a collagen gene signature, suggesting a role in ECM production

summary:
In Homo sapiens adult breast, the fibroblast matrix cell state shows high expression of COL1A1 and COL3A1.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:0019dd601f94de593e3b
claim_id: claim:0019dd601f94de593e3b
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
The fibro-prematrix cells ( GPX3 , WISP2 , PCOLE2 ) were associated with pre-collagen formation and vasculogenesis, whereas the fibro-SFRP4 cell state ( SFRP4 , MGP ) was associated with tissue remodelling and WNT signalling

summary:
In Homo sapiens adult breast, the fibroblast prematrix cell state expresses GPX3, WISP2, and PCOLE2.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:a2f03839eb49d7a6e7d6
claim_id: claim:a2f03839eb49d7a6e7d6
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
Collectively, these methods identified ADH1B , CD36 , PLIN1 , PLIN4 , ADIPOQ , FABP 4, LEP and LPL as the top genes expressed in breast adipocytes, which was consistent across the two orthogonal platforms

summary:
In Homo sapiens adult breast, adipocytes express ADH1B, CD36, PLIN1, PLIN4, ADIPOQ, FABP4, LEP, and LPL as top marker genes.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:f4ad2e09f329281cac79
claim_id: claim:f4ad2e09f329281cac79
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, vascular endothelial cells express PECAM1 and VWF.
span_literal:
Our scRNA-seq analysis of 83,651 endothelial cells across 126 women showed that vascular endothelial cells (expressing PECAM1 and VWF ) represent an abundant cell type (11.7% of cells, 7.2% of nuclei) in normal breast tissue


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:0f0f12fc629edb1222d0
claim_id: claim:0f0f12fc629edb1222d0
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
span_literal:
Reclustering of the scRNA-seq vascular endothelial cells identified three major cell states that varied across women and corresponded to arterial endothelial ( SOX17 , GJA4 ), venous endothelial ( ACKR1 , SELP ) and capillary endothelial ( RGCC , CA4 ) cells on the basis of canonical markers 37 , 38 , and further revealed many new top marker genes

summary:
In Homo sapiens adult breast, arterial endothelial cells express SOX17 and GJA4, venous endothelial cells express ACKR1 and SELP, and capillary endothelial cells express RGCC and CA4.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:368eec92a898c460a8a2
claim_id: claim:368eec92a898c460a8a2
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, lymphatic endothelial cells express PROX1 and PDPN.
span_literal:
Our data show that lymphatic endothelial cells ( PROX1 and PDPN ) occur at low frequencies (1.3% of cells, 3.5% of nuclei) in breast tissue.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:0b7604768e9bd2c23457
claim_id: claim:0b7604768e9bd2c23457
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, the lymphatic major cell state expresses LYVE1 and CCL21.
span_literal:
The Lym-major cells ( LYVE1 and CCL21 ) represented the most abundant component of the lymphatic vessels.


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:d763c83ea9bbc14b2d54
claim_id: claim:d763c83ea9bbc14b2d54
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, the lymphatic immune cell state expresses ACKR4 and NTS.
span_literal:
The Lym-immune cells ( ACKR4 and NTS ) resemble cells on the ceiling of subcapsular sinus in human lymph nodes 38 and expressed chemotaxis signatures, suggesting a role in immune cell signalling


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:6c0fe9f6d3c9fbae4824
claim_id: claim:6c0fe9f6d3c9fbae4824
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, lymphatic valve cells express CLDN11.
span_literal:
The two other cell states (Lym-valve1 and Lym-valve2) are lymphatic valve cells that express CLDN11 and are important for preventing lymphatic fluid backflow 39 .


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:7c630f3c3cbcdfb1dfcc
claim_id: claim:7c630f3c3cbcdfb1dfcc
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, pericytes express RGS5, CXCL3, and COL6A3.
span_literal:
Pericytes expressed canonical markers such as RGS5 , but also genes involved in immune signalling (such as CXCL3 ) and matrix production ( COL6A3 )


claim_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6:claim:6f1031073b774caa78e9
claim_id: claim:6f1031073b774caa78e9
paper_key: hca:0049_10.1038_s41586-023-06252-9_3d2f22d6e6
summary: In Homo sapiens adult breast, vascular smooth muscle cells express CNN1, MYH11, SYNM, and ACTG2.
span_literal:
The VSMCs expressed the canonical markers CNN1 and MYH11 , in addition to other smooth muscle ( SYNM , ACTG2 ) marker genes


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:312e4f360c7546926159
claim_id: claim:312e4f360c7546926159
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
Community five is enriched for the marker PVALB and corticotropin releasing factor binding protein ( CRHBP ), markers for distinct populations of GABAergic neurons ( 14 ).

summary:
In Homo sapiens, GABAergic neurons are marked by parvalbumin (PVALB) and corticotropin releasing hormone binding protein (CRHBP), which mark distinct populations.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:3ca46de4c42a272e2181
claim_id: claim:3ca46de4c42a272e2181
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
This community is also enriched for tachykinin, precursor 1 ( TAC1 ) as well as the transcription factor LIM homeobox 6 ( LHX6 ) ( Fig. 2 B ).

summary:
In Homo sapiens, the parvalbumin-expressing community of interneurons is enriched for tachykinin precursor 1 (TAC1) and LIM homeobox 6 (LHX6).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:d19103155dae45c89243
claim_id: claim:d19103155dae45c89243
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
LHX6 is closely related to the transcription factor, SRY (sex determining region Y)-box 6 ( SOX6 ) ( 15 ), which is also enriched in the same neuronal community ( Fig. 2 B ).

summary:
In Homo sapiens, SRY-box 6 (SOX6) is enriched in the parvalbumin-expressing community of interneurons.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:f239216b23b19103754c
claim_id: claim:f239216b23b19103754c
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
summary: In Homo sapiens, excitatory neuronal cells express SLC17A7, NEUROD6, and SATB2 as markers.
span_literal:
We were able to identify two excitatory communities expressing SLC17A7 , NEUROD6 and SATB2 ( Fig. 3 A ), markers for excitatory neuronal cells.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:790d7bbb37bb5af8c354
claim_id: claim:790d7bbb37bb5af8c354
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
The remaining communities of neurons were identified as interneurons based on the lack of expression of excitatory neuronal markers and the strong expression of inhibitory markers such as GAD1 ( Fig. 2 C ).

summary:
In Homo sapiens, interneurons are identified by strong expression of the inhibitory marker glutamate decarboxylase 1 (GAD1).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:deefd067f26fa4f99e84
claim_id: claim:deefd067f26fa4f99e84
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
Among the inhibitory neurons, almost all express GAD1 (the synthetic machinery required to synthesize the inhibitory neurotransmitter, GABA) as well as CCK and CALB2 , with the exception of one community of neurons that exclusively expresses PVALB .

summary:
In Homo sapiens, inhibitory neurons almost all express glutamate decarboxylase 1 (GAD1), cholecystokinin (CCK), and calbindin 2 (CALB2), except for a community that exclusively expresses parvalbumin (PVALB).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:ca779eefa0df007a4d42
claim_id: claim:ca779eefa0df007a4d42
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
Among the inhibitory neurons, almost all express GAD1 (the synthetic machinery required to synthesize the inhibitory neurotransmitter, GABA) as well as CCK and CALB2 , with the exception of one community of neurons that exclusively expresses PVALB .

summary:
In Homo sapiens, the parvalbumin-expressing interneuron community exclusively expresses parvalbumin (PVALB) and lacks cholecystokinin (CCK) and calbindin 2 (CALB2).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:c63dcbec1138d296247e
claim_id: claim:c63dcbec1138d296247e
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
summary: In Homo sapiens, layer I interneurons are enriched for paired box 6 (PAX6).
span_literal:
First, we observed a community of neurons enriched for paired box 6 ( PAX6 ), a gene that has been suggested as a layer I interneuron marker ( 7 ).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:e6af332b0dfb591789ae
claim_id: claim:e6af332b0dfb591789ae
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
summary: In Homo sapiens, the layer I interneuron community strongly coexpresses reelin (RELN).
span_literal:
Our data further support this hypothesis with the strong coexpression of RELN in the same community ( SI Appendix , Fig. S8 ).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:6e774091b9f3b9c788a9
claim_id: claim:6e774091b9f3b9c788a9
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
We next observed a neuronal community enriched for VIP and tachykinin 3 ( TAC3 ), two genes that are expressed in neurons enriched in layers two to four.

summary:
In Homo sapiens, a neuronal community enriched in layers two to four expresses vasoactive intestinal peptide (VIP) and tachykinin 3 (TAC3).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:fd5032b6cc6de15af81a
claim_id: claim:fd5032b6cc6de15af81a
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
Additionally, we found a subpopulation of neurons exhibiting coexpression of genes complexin 3 ( CPLX3 ); secreted protein, acidic, cysteine-rich (osteonectin) ( SPARC ); and synaptic vesicle glycoprotein 2C ( SV2C ) ( SI Appendix , Fig. S8 ), which has been shown to be a human-specific marker for layer three neurons ( 19 ).

summary:
In Homo sapiens, a subpopulation of layer three neurons coexpresses complexin 3 (CPLX3), secreted protein acidic cysteine-rich osteonectin (SPARC), and synaptic vesicle glycoprotein 2C (SV2C).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:769b400498c398a21e0b
claim_id: claim:769b400498c398a21e0b
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
summary: In Homo sapiens, adult neurons express high levels of SNAP25 and glutamate decarboxylase 1 (GAD1).
span_literal:
These include adult neurons, expressing high levels of SNAP25 and GAD1 , as well as actively dividing fetal neuronal progenitors ( MKI67 + and PAX6 + ) and quiescent subplate fetal neurons ( MKI67 − , DCX + , and TUBB3 + ) ( Fig. 4 B ).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:ffc23f7012d69716bf06
claim_id: claim:ffc23f7012d69716bf06
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
These include adult neurons, expressing high levels of SNAP25 and GAD1 , as well as actively dividing fetal neuronal progenitors ( MKI67 + and PAX6 + ) and quiescent subplate fetal neurons ( MKI67 − , DCX + , and TUBB3 + ) ( Fig. 4 B ).

summary:
In Homo sapiens, actively dividing fetal neuronal progenitors are positive for MKI67 and paired box 6 (PAX6).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:f8fb764a13d1312ae6e4
claim_id: claim:f8fb764a13d1312ae6e4
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
These include adult neurons, expressing high levels of SNAP25 and GAD1 , as well as actively dividing fetal neuronal progenitors ( MKI67 + and PAX6 + ) and quiescent subplate fetal neurons ( MKI67 − , DCX + , and TUBB3 + ) ( Fig. 4 B ).

summary:
In Homo sapiens, quiescent subplate fetal neurons are negative for MKI67 and positive for doublecortin (DCX) and tubulin beta 3 class III (TUBB3).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:a9854401136762a691f7
claim_id: claim:a9854401136762a691f7
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
We noticed that in this group of cells we are indeed detecting high levels of genes such as AQP4 and GFAP (astrocyte specific) as well as THY1 , SYT1 , and STMN2 (neuron specific).

summary:
In Homo sapiens, astrocytes specifically express aquaporin 4 (AQP4) and glial fibrillary acidic protein (GFAP).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:07f1d5ccccad29e1f489
claim_id: claim:07f1d5ccccad29e1f489
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
We found that PVALB -expressing neurons are distinct from all other interneuron subtypes and that VIP demarcates a subset of CALB2 cells.

summary:
In Homo sapiens, parvalbumin (PVALB)-expressing neurons are distinct from all other interneuron subtypes, and vasoactive intestinal peptide (VIP) demarcates a subset of calbindin 2 (CALB2)-positive cells.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:190f204dcbcddf36783d
claim_id: claim:190f204dcbcddf36783d
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
We found that PVALB -expressing neurons are distinct from all other interneuron subtypes and that VIP demarcates a subset of CALB2 cells.

summary:
In Homo sapiens, vasoactive intestinal peptide (VIP) demarcates a subset of calbindin 2 (CALB2)-positive interneurons.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:7649bd3b62617fa31ee8
claim_id: claim:7649bd3b62617fa31ee8
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
In addition, we found the genes CRHBP , LHX6 , SOX6 , and TAC1 to be expressed in a subset of PVALB neurons and the gene TAC3 in a subset of VIP-positive cells.

summary:
In Homo sapiens, corticotropin releasing hormone binding protein (CRHBP), LIM homeobox 6 (LHX6), SRY-box 6 (SOX6), and tachykinin precursor 1 (TAC1) are expressed in a subset of parvalbumin (PVALB)-positive neurons.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:559e7efeade1087999ad
claim_id: claim:559e7efeade1087999ad
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
In addition, we found the genes CRHBP , LHX6 , SOX6 , and TAC1 to be expressed in a subset of PVALB neurons and the gene TAC3 in a subset of VIP-positive cells.

summary:
In Homo sapiens, tachykinin 3 (TAC3) is expressed in a subset of vasoactive intestinal peptide (VIP)-positive cells.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:883716651bc405a84ef4
claim_id: claim:883716651bc405a84ef4
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
We identified a subset of neurons most likely belonging to cortical layer I that expresses RELN and PAX6 , which is typically considered a marker for neuronal progenitors but has been recently shown to be a layer I marker in mice.

summary:
In Homo sapiens, a subset of cortical layer I neurons expresses reelin (RELN) and paired box 6 (PAX6).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:076ada1d13f5abe32d92
claim_id: claim:076ada1d13f5abe32d92
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
Finally, we show that CPLX3 is a marker for a distinct subpopulation of NeuN-positive cells and is usually coexpressed with SPARC .

summary:
In Homo sapiens, complexin 3 (CPLX3) is a marker for a distinct subpopulation of NeuN-positive cells and is usually coexpressed with secreted protein acidic cysteine-rich osteonectin (SPARC).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:3b270892b7058e2e707d
claim_id: claim:3b270892b7058e2e707d
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal: Our results show that MHCI genes are clearly expressed in a subset of neurons in the adult brain.
summary:
In Homo sapiens, major histocompatibility complex class I genes are expressed in a subset of adult neurons in the brain.


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:b66828190a8f61a1eb34
claim_id: claim:b66828190a8f61a1eb34
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal: we found that both of the human fetal cell populations lack expression of HLA-A , -B , and -C .
summary:
In Homo sapiens, fetal neuronal cell populations lack expression of major histocompatibility complex class I A (HLA-A), B (HLA-B), and C (HLA-C).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:8005e78bec50b85442d0
claim_id: claim:8005e78bec50b85442d0
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
Furthermore, fetal cells lack expression of MHCI-associated genes such as TAPBP and ERAP1 , whereas they express genes coding for proteins with more diverse functions such as CALR , HSPA5 , PDIA3 , and members of the SEC61 complex.

summary:
In Homo sapiens, fetal neuronal cells lack expression of tapasin (TAPBP) and endoplasmic reticulum aminopeptidase 1 (ERAP1), while expressing calreticulin (CALR), heat shock protein family A member 5 (HSPA5), and protein disulfide isomerase family A member 3 (PDIA3).


claim_key: hca:0050_10.1073_pnas.1507125112_495172b774:claim:cd06c3f480010df297bd
claim_id: claim:cd06c3f480010df297bd
paper_key: hca:0050_10.1073_pnas.1507125112_495172b774
span_literal:
We observed that CCK , which in the mouse brain is used to define a small subset of neurons with certain electrophysiological characteristics, is ubiquitously expressed at the mRNA level in most human neuronal cells.

summary:
In Homo sapiens, cholecystokinin (CCK) is ubiquitously expressed at the mRNA level in most neuronal cells.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:7b1195b8823c13333d8d
claim_id: claim:7b1195b8823c13333d8d
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
In our datasets, long noncoding RNA LINC01331 was a minimal marker for Exc_L2-3_LINC00507_FREM3, with a beta score of 1, indicating high specificity.

summary:
In Homo sapiens, LINC01331 is a minimal marker for excitatory neuron subtype Exc_L2-3_LINC00507_FREM3 with high specificity in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:7d797f7bbdf00b78cdda
claim_id: claim:7d797f7bbdf00b78cdda
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
By contrast, one of the existing markers for this cell type, PALMD , was more highly expressed in endothelial cells in our datasets (Fig. 3 and Extended Data Fig. 9a,b ).

summary:
In Homo sapiens, PALMD was more highly expressed in endothelial cells than in Exc_L2-3_LINC00507_FREM3 in the temporal cortex datasets.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:65fbf9af3fdeac3befaa
claim_id: claim:65fbf9af3fdeac3befaa
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
Similarly, one of the existing MTG atlas markers for Exc_L5-6 _THEMIS_CRABP1, OLFML2B , was more highly expressed in other layer 5 and 6 neurons in our dataset, whereas our minimal marker, POSTN , showed greater specificity (Fig. 3 and Extended Data Fig. 9c,d ).

summary:
In Homo sapiens, POSTN is a minimal marker for Exc_L5-6_THEMIS_CRABP1 with greater specificity than OLFML2B in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:2dc4c91306a34c6a3a66
claim_id: claim:2dc4c91306a34c6a3a66
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
Visium gene expression profiles (color intensity) for a selection of known cortical layer marker genes in the 31-year-old and 15-year-old temporal cortex tissue sections including AQP4 (layer 1), LAMP5 (layer 2), RORB (layer 4) and CLSTN2 (layers 5 and 6).

summary:
In Homo sapiens temporal cortex, AQP4 is a marker of cortical layer 1, LAMP5 of layer 2, RORB of layer 4, and CLSTN2 of layers 5 and 6.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:1744de69e31b215c782e
claim_id: claim:1744de69e31b215c782e
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
The two astrocyte subtypes were confirmed to have distinct distribution profiles, with Astro_L1-2_FGFR3_GFAP (factor_4) located primarily in layer 1 (Fig. 2c,d ) and the white matter, and Astro_L1-6_FGFR3_SLC14A1 (factor_9) more widely distributed (Extended Data Fig. 5c ).

summary:
In Homo sapiens temporal cortex, Astro_L1-2_FGFR3_GFAP astrocytes are marked by FGFR3 and GFAP, while Astro_L1-6_FGFR3_SLC14A1 astrocytes are marked by FGFR3 and SLC14A1.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:91cefa819014bcab488e
claim_id: claim:91cefa819014bcab488e
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
The two astrocyte subtypes were confirmed to have distinct distribution profiles, with Astro_L1-2_FGFR3_GFAP (factor_4) located primarily in layer 1 (Fig. 2c,d ) and the white matter, and Astro_L1-6_FGFR3_SLC14A1 (factor_9) more widely distributed (Extended Data Fig. 5c ).

summary:
In Homo sapiens temporal cortex, Astro_L1-6_FGFR3_SLC14A1 astrocytes are marked by FGFR3 and SLC14A1.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:172f1ca354bcad74a4db
claim_id: claim:172f1ca354bcad74a4db
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
Several of these biomarkers (for example, FADS2 , AMOT and ALDH6A1 ) were enriched in the two astrocyte subtypes, potentially indicating a prominent role for astrocytes in the host response to TBM.

summary:
In Homo sapiens, FADS2, AMOT, and ALDH6A1 are enriched in astrocyte subtypes in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:14bc7b0ccf8ca075da58
claim_id: claim:14bc7b0ccf8ca075da58
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
These included biomarkers that were associated with Exc_L2_LAMP5_LTK, Exc_L2-4_LINC00507_GLP2R and Exc_L5-6_THEMIS_C1QL3 ( LYNX1 , FAIM2 , MAP1A , TUBB4A ).

summary:
In Homo sapiens, LYNX1, FAIM2, MAP1A, and TUBB4A are biomarkers associated with excitatory neuron subtypes Exc_L2_LAMP5_LTK, Exc_L2-4_LINC00507_GLP2R, and Exc_L5-6_THEMIS_C1QL3 in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:6556ec1f2cec75529289
claim_id: claim:6556ec1f2cec75529289
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
These included biomarkers that were associated with Exc_L2_LAMP5_LTK, Exc_L2-4_LINC00507_GLP2R and Exc_L5-6_THEMIS_C1QL3 ( LYNX1 , FAIM2 , MAP1A , TUBB4A ).

summary:
In Homo sapiens, LYNX1, FAIM2, MAP1A, and TUBB4A are biomarkers associated with excitatory neuron subtype Exc_L2-4_LINC00507_GLP2R in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:0d1fc6f195da59c8f2eb
claim_id: claim:0d1fc6f195da59c8f2eb
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
These included biomarkers that were associated with Exc_L2_LAMP5_LTK, Exc_L2-4_LINC00507_GLP2R and Exc_L5-6_THEMIS_C1QL3 ( LYNX1 , FAIM2 , MAP1A , TUBB4A ).

summary:
In Homo sapiens, LYNX1, FAIM2, MAP1A, and TUBB4A are biomarkers associated with excitatory neuron subtype Exc_L5-6_THEMIS_C1QL3 in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:bfe2c6a64dc99e38efce
claim_id: claim:bfe2c6a64dc99e38efce
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
In Astro_L1-6_FGFR3_SLC14A1, PIK3R3 was upregulated in pediatric samples, whereas PFKFB2 was downregulated.

summary:
In Homo sapiens, PIK3R3 is upregulated in pediatric Astro_L1-6_FGFR3_SLC14A1 astrocytes, whereas PFKFB2 is downregulated in pediatric Astro_L1-6_FGFR3_SLC14A1 astrocytes.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:2838a58702b64cc07efb
claim_id: claim:2838a58702b64cc07efb
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal: In oligodendrocytes, NOTCH2 and RRAS2 were both upregulated in pediatric samples.
summary:
In Homo sapiens, NOTCH2 and RRAS2 are upregulated in pediatric oligodendrocytes in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:08fc40ab7a5d9e8e2a69
claim_id: claim:08fc40ab7a5d9e8e2a69
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
LAMC3 , which encodes a subunit of the extracellular matrix protein laminin, was upregulated in three pediatric subtypes (Exc_L3-5_RORB_ESR1, Exc_L2-3_LINC00507_FREM3 and Exc_L4-5_RORB_FOLH1B) (Fig. 5b–e,h ).

summary:
In Homo sapiens, LAMC3 is upregulated in pediatric excitatory neuron subtypes Exc_L3-5_RORB_ESR1, Exc_L2-3_LINC00507_FREM3, and Exc_L4-5_RORB_FOLH1B in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:baebe17fd088f0d6060a
claim_id: claim:baebe17fd088f0d6060a
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
LAMC3 , which encodes a subunit of the extracellular matrix protein laminin, was upregulated in three pediatric subtypes (Exc_L3-5_RORB_ESR1, Exc_L2-3_LINC00507_FREM3 and Exc_L4-5_RORB_FOLH1B) (Fig. 5b–e,h ).

summary:
In Homo sapiens, LAMC3 is upregulated in pediatric excitatory neuron subtype Exc_L2-3_LINC00507_FREM3 in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:089ed110ce2a88de2cf2
claim_id: claim:089ed110ce2a88de2cf2
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
LAMC3 , which encodes a subunit of the extracellular matrix protein laminin, was upregulated in three pediatric subtypes (Exc_L3-5_RORB_ESR1, Exc_L2-3_LINC00507_FREM3 and Exc_L4-5_RORB_FOLH1B) (Fig. 5b–e,h ).

summary:
In Homo sapiens, LAMC3 is upregulated in pediatric excitatory neuron subtype Exc_L4-5_RORB_FOLH1B in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:d5536b7c9bbbe0be185c
claim_id: claim:d5536b7c9bbbe0be185c
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
S0X11 , encoding a transcription factor that plays a part in embryonic and adult neurogenesis in the mouse brain 38 and decreases in expression in the cerebral cortex during development 39 , 40 , was upregulated in pediatric Exc_L3-5_RORB_ESR1 and Exc_L2-3_LINC00507_FREM3 (Fig. 5b,c,h ).

summary:
In Homo sapiens, SOX11 is upregulated in pediatric excitatory neuron subtypes Exc_L3-5_RORB_ESR1 and Exc_L2-3_LINC00507_FREM3 in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:1a9463ac879157b6ffea
claim_id: claim:1a9463ac879157b6ffea
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
S0X11 , encoding a transcription factor that plays a part in embryonic and adult neurogenesis in the mouse brain 38 and decreases in expression in the cerebral cortex during development 39 , 40 , was upregulated in pediatric Exc_L3-5_RORB_ESR1 and Exc_L2-3_LINC00507_FREM3 (Fig. 5b,c,h ).

summary:
In Homo sapiens, SOX11 is upregulated in pediatric excitatory neuron subtype Exc_L2-3_LINC00507_FREM3 in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:995d96b87871332d4b4d
claim_id: claim:995d96b87871332d4b4d
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal: FNBP1L ( TOCA-1 ) was upregulated in Exc_L2-3_LINC00507_FREM3 and Exc_L2_LAMP5_LTK (Fig. 5c,e,h ).
summary:
In Homo sapiens, FNBP1L is upregulated in pediatric excitatory neuron subtypes Exc_L2-3_LINC00507_FREM3 and Exc_L2_LAMP5_LTK in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:e961d24c1a38fb57cef5
claim_id: claim:e961d24c1a38fb57cef5
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal: FNBP1L ( TOCA-1 ) was upregulated in Exc_L2-3_LINC00507_FREM3 and Exc_L2_LAMP5_LTK (Fig. 5c,e,h ).
summary:
In Homo sapiens, FNBP1L is upregulated in pediatric excitatory neuron subtype Exc_L2_LAMP5_LTK in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:dfe2b098bd5c3933b3f4
claim_id: claim:dfe2b098bd5c3933b3f4
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
Two genes, STEAP2 , encoding a metalloreductase, and TNF receptor gene TNFRSF25 ( DR3 ), showed higher expression in adult Exc_L3-5_RORB_ESR1 and Exc_L4-5_RORB_FOLH1B subtypes (Fig. 5b,d,h ).

summary:
In Homo sapiens, STEAP2 and TNFRSF25 show higher expression in adult excitatory neuron subtypes Exc_L3-5_RORB_ESR1 and Exc_L4-5_RORB_FOLH1B in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:9d5f15b2a1c11411d615
claim_id: claim:9d5f15b2a1c11411d615
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
Two genes, STEAP2 , encoding a metalloreductase, and TNF receptor gene TNFRSF25 ( DR3 ), showed higher expression in adult Exc_L3-5_RORB_ESR1 and Exc_L4-5_RORB_FOLH1B subtypes (Fig. 5b,d,h ).

summary:
In Homo sapiens, STEAP2 and TNFRSF25 show higher expression in adult excitatory neuron subtype Exc_L4-5_RORB_FOLH1B in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:5b64f5b93f083359172e
claim_id: claim:5b64f5b93f083359172e
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal: FGF13 ( FHF2 ) and TENM1 were upregulated in pediatric Exc_L3-5_RORB_ESR1 (Fig. 5b ).
summary:
In Homo sapiens, FGF13 and TENM1 are upregulated in pediatric excitatory neuron subtype Exc_L3-5_RORB_ESR1 in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:2fb0c66b8a720e7ef42c
claim_id: claim:2fb0c66b8a720e7ef42c
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
KCNG1 , which encodes a voltage-gated potassium channel (Kv6.1), was upregulated in pediatric Exc_L2-3_LINC00507_FREM3 neurons (Fig. 5c ), whereas MYO16 ( MYR8 ), coding for an unconventional myosin protein, was upregulated in the Exc_L2_LAMP5_LTK subtype (Fig. 5e ).

summary:
In Homo sapiens, KCNG1 is upregulated in pediatric Exc_L2-3_LINC00507_FREM3 excitatory neurons, and MYO16 is upregulated in pediatric Exc_L2_LAMP5_LTK excitatory neurons in the temporal cortex.


claim_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200:claim:4d5bcd452322ae60df70
claim_id: claim:4d5bcd452322ae60df70
paper_key: hca:0051_10.1038_s41588-024-01990-6_8eb62f3200
span_literal:
KCNG1 , which encodes a voltage-gated potassium channel (Kv6.1), was upregulated in pediatric Exc_L2-3_LINC00507_FREM3 neurons (Fig. 5c ), whereas MYO16 ( MYR8 ), coding for an unconventional myosin protein, was upregulated in the Exc_L2_LAMP5_LTK subtype (Fig. 5e ).

summary:
In Homo sapiens, MYO16 is upregulated in pediatric Exc_L2_LAMP5_LTK excitatory neurons in the temporal cortex.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:c4e43cf190db537227a0
claim_id: claim:c4e43cf190db537227a0
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
summary: In Homo sapiens, alpha cells are marked by GCG, IRX2, and TTR in pancreatic islets.
span_literal:
As a positive control, we verified that we identify established marker genes in all species, which included GCG , IRX2 and TTR for α-, INS , PDX1 and NKX6-1 for β-, SST and HHEX for δ- and PPY for PP-cells.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:379afa05b420c3d07e72
claim_id: claim:379afa05b420c3d07e72
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
we detected high mRNA levels of free fatty acid receptor 4 FFAR4 , as well as calcium-sensing receptor CASR in human β-and δ-cells

summary:
In Homo sapiens, free fatty acid receptor 4 (FFAR4) and calcium-sensing receptor (CASR) are expressed at high levels in beta cells and delta cells of pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:3206e419e9b4ff9623b3
claim_id: claim:3206e419e9b4ff9623b3
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
we detected high mRNA levels of free fatty acid receptor 4 FFAR4 , as well as calcium-sensing receptor CASR in human β-and δ-cells

summary:
In Homo sapiens, free fatty acid receptor 4 (FFAR4) and calcium-sensing receptor (CASR) are expressed at high levels in delta cells of pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:8d644c4eb401078d9489
claim_id: claim:8d644c4eb401078d9489
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal: the synaptic protein neuronal pentraxin-2 ( NPTX2) was strongly expressed in human β-and δ-cells
summary:
In Homo sapiens, neuronal pentraxin-2 (NPTX2) is strongly expressed in beta cells and delta cells of pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:2c7719b8248cb47a8f88
claim_id: claim:2c7719b8248cb47a8f88
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal: the synaptic protein neuronal pentraxin-2 ( NPTX2) was strongly expressed in human β-and δ-cells
summary:
In Homo sapiens, neuronal pentraxin-2 (NPTX2) is strongly expressed in delta cells of pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:03670e7481f5084ef61c
claim_id: claim:03670e7481f5084ef61c
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
summary: In Homo sapiens, UCN3 and NKX6-1 are markers of beta cells in pancreatic islets.
span_literal:
G16, which contained β-cell markers UCN3 and NKX6-1 , also scored highest in the MHC/autoantigen cluster.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:87f5ce2f014a3d2d4d16
claim_id: claim:87f5ce2f014a3d2d4d16
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
In healthy human donors, PCSK1 levels are reportedly higher in β-cells, while PCSK2 levels are higher in α-cells

summary:
In Homo sapiens, PCSK1 is more highly expressed in beta cells, while PCSK2 is more highly expressed in alpha cells in healthy pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:028134f652cc688b28de
claim_id: claim:028134f652cc688b28de
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
In healthy human donors, PCSK1 levels are reportedly higher in β-cells, while PCSK2 levels are higher in α-cells

summary:
In Homo sapiens, PCSK2 is more highly expressed in alpha cells compared to beta cells in healthy pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:2d92bfe0b1a81fec7f87
claim_id: claim:2d92bfe0b1a81fec7f87
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
The high and low velocity clusters were also separated by CD9 and NPY expression ( Figure 3 F). CD9 has been proposed as a marker of functional β-cell heterogeneity, which together with ST8SIA1 separates β-cells into four subpopulations

summary:
In Homo sapiens, CD9 and ST8SIA1 are proposed markers of functional beta cell heterogeneity that separate beta cells into four subpopulations in pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:8512f8fb407611062336
claim_id: claim:8512f8fb407611062336
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
Within this classification scheme, NPY is a marker for CD9 - ST8SIA1 + cells, which showed higher glucose-stimulated insulin secretion capacity consistent with the transcriptional activity in insulin biosynthesis and or secretion observed here.

summary:
In Homo sapiens, NPY is a marker for CD9-negative ST8SIA1-positive beta cells, which show higher glucose-stimulated insulin secretion capacity.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:31342c5589c8e2c25158
claim_id: claim:31342c5589c8e2c25158
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
Multiple developmental markers including SOX4, SOX11, NRG1, ID1-4 , EPHB2 and EPHB6 were increased, while α-cell function genes were decreased.

summary:
In Homo sapiens, immature alpha cells show increased expression of developmental markers SOX4, SOX11, NRG1, ID1-4, EPHB2, and EPHB6 in pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:43cc214dd741b5464824
claim_id: claim:43cc214dd741b5464824
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
For example, we identified the co-regulatory nuclear receptor co-repressor 2 ( NCOR2 ) as well as LIM and calponin-homology domains 1 ( LIMCH1 ) - a positive regulator of non-muscle myosin II promoting focal adhesion assembly - which, to our knowledge, have not been previously associated with β-cell maturation

summary:
In Homo sapiens, nuclear receptor co-repressor 2 (NCOR2) and LIM and calponin-homology domains 1 (LIMCH1) are identified as putative maturation markers of beta cells in pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:99a606234db16993f645
claim_id: claim:99a606234db16993f645
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
Further also ephrinA5 ( EFNA5 ), a well known factor of neurogenesis and potential regulator of insulin secretion in β-cells [ 63 ], showed high velocity in immature cells

summary:
In Homo sapiens, ephrin A5 (EFNA5) is a putative maturation factor of beta cells, showing high velocity in immature beta cells in pancreatic islets.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:a4e68a9d050e13768eb2
claim_id: claim:a4e68a9d050e13768eb2
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
summary: In Homo sapiens, WNT4, BMP5, and PAK3 are known markers of mature beta cells in pancreatic islets.
span_literal:
we predicted high velocity for the signaling proteins WNT4 , BMP5 and PAK3, which are known markers of mature β-cells


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:0d0dd0e06f10cfb9cd49
claim_id: claim:0d0dd0e06f10cfb9cd49
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
Clusters expressing known markers of non-endocrine cells (for example SPP1 for ductal cells , PRSS2 for acinar cells, PLVAP for endothelial cells, PTPRC for immune cells or COL1A1 for fibroblasts and stellate cells)

summary:
In Homo sapiens, SPP1 is a marker of ductal cells, PRSS2 of acinar cells, PLVAP of endothelial cells, PTPRC of immune cells, and COL1A1 of fibroblasts and stellate cells in the pancreas.


claim_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db:claim:5cb8a7c151310249d0e0
claim_id: claim:5cb8a7c151310249d0e0
paper_key: hca:0052_10.1016_j.molmet.2022.101595_3242a2c7db
span_literal:
our analyses revealed novel putative β-cell maturation markers (e.g. NCOR2, LIMCH1, EFNA5 ) and a distinct, conserved immature α-cell state with increased expression of developmental markers (e.g. WNT2, SOX4, SOX11 ), members of the TGF-β signaling pathway (e.g. TGFB1, ID1-3, SOCS3, TNC ), integrins (e.g. ITGA2, ITGA6 ) and a cytokine response.

summary:
In Homo sapiens, immature alpha cells show increased expression of developmental markers WNT2, SOX4, SOX11, transforming growth factor beta signaling pathway members TGFB1, ID1-3, SOCS3, TNC, and integrins ITGA2 and ITGA6 in pancreatic islets.


claim_key: hca:0054_10.1164_rccm.202305-0924oc_e37c5c9bab:claim:586b26ac2a6828e2c4b5
claim_id: claim:586b26ac2a6828e2c4b5
paper_key: hca:0054_10.1164_rccm.202305-0924oc_e37c5c9bab
span_literal: GZMA , GZMB , GZMH
summary:
In Homo sapiens lung, CD8+ KLRG1+ T effector memory CD45RA+ cells express cytotoxic genes GZMA, GZMB, and GZMH.


claim_key: hca:0054_10.1164_rccm.202305-0924oc_e37c5c9bab:claim:1cc54b0216a0d054cb6d
claim_id: claim:1cc54b0216a0d054cb6d
paper_key: hca:0054_10.1164_rccm.202305-0924oc_e37c5c9bab
span_literal: CST7 (cystatin F), possible negative regulators of cytotoxic cells
summary:
In Homo sapiens lung, KLRG1+ T effector memory CD45RA+ cells have enriched expression of CST7 (cystatin F).


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:36a4b6c8f8adbbe14b78
claim_id: claim:36a4b6c8f8adbbe14b78
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
In support of this hypothesis, the cluster is defined by high expression of SLC30A1 , a metal transport protein, and pathway enrichment analysis of DEGs identified cellular responses to metals and mineral absorption pathways

summary:
In Homo sapiens, the metallothionein-expressing airspace macrophage subset (m6) is defined by high expression of SLC30A1, a metal transport protein.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:d60446ab9a1ff531cc73
claim_id: claim:d60446ab9a1ff531cc73
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
clusters (mo0–2) had high expression of both monocyte (e.g., CSF1R ) and macrophage (e.g., MARCO and VSIG4

summary:
In Homo sapiens, monocyte-like airspace macrophage clusters mo0–2 had high expression of the monocyte marker CSF1R and the macrophage markers MARCO and VSIG4.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:b72d1092179994fd486b
claim_id: claim:b72d1092179994fd486b
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
We next examined the defining characteristics of clusters mo0–2 and found that in addition to known monocyte genes such as STAB1 and LGMN , cluster mo2 was uniquely defined by DEGs involved in cell–matrix interactions, such as MMP14 , SPP1 , and ECM1 (Table E3).

summary:
In Homo sapiens, monocyte-like airspace macrophage cluster mo2 is uniquely defined by expression of cell-matrix interaction genes MMP14, SPP1, and ECM1, in addition to monocyte genes STAB1 and LGMN.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:136a4d7b51ba0af806ac
claim_id: claim:136a4d7b51ba0af806ac
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
Examination of DEGs along this trajectory in the direction of resident AMs demonstrates increasing expression of bona fide macrophage markers, such as complement genes, MARCO , and PPARG , over pseudotime

summary:
In Homo sapiens, resident airspace macrophages show increasing expression of macrophage markers MARCO and PPARG along the monocyte-to-macrophage maturation trajectory.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:c6d9dfc9e3b0f43c0e91
claim_id: claim:c6d9dfc9e3b0f43c0e91
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
Furthermore, identification of inferred regulatory networks in each cluster revealed increasing activity of transcription factors associated with macrophage maturation, such as PU.1 ( SPI1 ) and CEBPB moving from mo1 to mo0 to AMs

summary:
In Homo sapiens, airspace macrophages show increasing activity of the transcription factors PU.1 (SPI1) and CEBPB along the monocyte-to-macrophage maturation trajectory.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:9365d2a501c32ea81a60
claim_id: claim:9365d2a501c32ea81a60
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
Five subclusters (p0, 1, 2, 4, 7) were defined by markers of classical, CD14 hi monocytes and included cells from mo0–2 in the BAL (Figure E4).

summary:
In Homo sapiens, classical monocyte subclusters (p0, p1, p2, p4, p7) are defined by markers of CD14-high monocytes.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:2cb81cbfcdd3a2c8947a
claim_id: claim:2cb81cbfcdd3a2c8947a
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
Subcluster p3 was defined by markers of intermediate, CD14 + CD16 + monocytes and contained mainly matrix-associated cells (mo2) from the BAL (Figure E4).

summary:
In Homo sapiens, subcluster p3 is defined by markers of intermediate CD14-positive CD16-positive monocytes.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:cd467e2344cd9d05fa60
claim_id: claim:cd467e2344cd9d05fa60
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
In fact, the DEG profile that defines this cluster, including genes such as CXCL8 , SOD2 , and TNF , mimics the expression profile of human AMs treated with bacterial pathogens in vitro

summary:
In Homo sapiens, the proinflammatory airspace macrophage subset is defined by expression of CXCL8, SOD2, and TNF.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:61b2b5d6d096e6f9ff62
claim_id: claim:61b2b5d6d096e6f9ff62
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
Indeed, this AM subset is also defined by high expression of PTGS2 , CD83 , and TNFAIP3 , which in mice mark a population of classical monocytes that survey the lung and transport antigen to lymph nodes during health

summary:
In Homo sapiens, the proinflammatory airspace macrophage subset is also defined by high expression of PTGS2, CD83, and TNFAIP3.


claim_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484:claim:c85191e422f3fd2c9f9c
claim_id: claim:c85191e422f3fd2c9f9c
paper_key: hca:0055_10.1164_rccm.202005-1989oc_b0c2671484
span_literal:
Together with the CCL22 -expressing or “activated” DC subset in Figure 1 (cluster 10), these three DC subclusters reflect the major conventional DC populations previously described in the healthy human airspaces

summary:
In Homo sapiens, the activated dendritic cell subset (cluster 10) is defined by expression of CCL22.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:32373bc5bd2d8756407d
claim_id: claim:32373bc5bd2d8756407d
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
summary: In Homo sapiens, basal cells are marked by KRT5 in the respiratory epithelium.
span_literal:
We highlight the major types recovered: basal ( KRT5 ) and apical ( KRT8 )—which orient the pseudostratified epithelial division—further specialized ciliated ( FOXJ1 ) and glandular 3 ( LTF ) cells, and supportive endothelial ( DARC ), fibroblast ( COL1A2 ), plasma ( CD79A ), myeloid ( HLA-DRA ), T ( TRBC2 ), and mast cells ( TPSAB1 )


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:da87e5a5ee6644355c57
claim_id: claim:da87e5a5ee6644355c57
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
For example, we found mast cells specifically enriched for HPGDS, PTGS2 , and ALOX5, suggesting they may be a dominant source of prostaglandin D2, implicated in activation of T-helper 2 (Th2) cells 4 .

summary:
In Homo sapiens, mast cells are specifically enriched for HPGDS, PTGS2, and ALOX5 in the respiratory tissue.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:e512a81165e86a8dc364
claim_id: claim:e512a81165e86a8dc364
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
TSLP was uniquely restricted to basal cells, which may link increased basal cell numbers to activation of effector cells

summary:
In Homo sapiens, TSLP expression is uniquely restricted to basal cells in the respiratory epithelium.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:4cd74e4d60a9ea2b90f5
claim_id: claim:4cd74e4d60a9ea2b90f5
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
Second-order effector cytokines were identified in a subset of CD4+ T cells expressing IL4 , IL5 , IL13, and HPGDS , fitting the profile of allergen-specific Th2A cells 23

summary:
In Homo sapiens, a subset of CD4+ T cells expressing IL4, IL5, IL13, and HPGDS fits the profile of allergen-specific T-helper 2A cells.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:f7a4a1de6a6e4ead0404
claim_id: claim:f7a4a1de6a6e4ead0404
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
we observe expression of MUC5B within glandular mucus cells (cluster 13), but MUC5AC in a distinct subset of secretory goblet cells co-expressing SCGB1A1 and FOXA3

summary:
In Homo sapiens, glandular mucus cells express MUC5B, while secretory goblet cells express MUC5AC, SCGB1A1, and FOXA3 in the respiratory epithelium.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:63932a188037e95342f8
claim_id: claim:63932a188037e95342f8
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
we observe expression of MUC5B within glandular mucus cells (cluster 13), but MUC5AC in a distinct subset of secretory goblet cells co-expressing SCGB1A1 and FOXA3

summary:
In Homo sapiens, secretory goblet cells express MUC5AC, SCGB1A1, and FOXA3 in the respiratory epithelium.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:a8b711aa63a4ffffee4a
claim_id: claim:a8b711aa63a4ffffee4a
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
summary: In Homo sapiens, CLC is a pathognomonic gene for eosinophils.
span_literal:
An overlay of CLC displaying binned count-based expression level (log(scaled UMI+1)) amongst myeloid cells (a pathognomonic gene for eosinophils); 811 myeloid cells from n=12 samples.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:5efcc4034d0748f519c2
claim_id: claim:5efcc4034d0748f519c2
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
Violin plots for the count-based expression level (log(scaled UMI+1)) of selected marker genes identified through marker discovery (ROC test) for each subset of glandular cells; 2,114 total cells (791 cells cluster 1; 709 cells LCN2 cluster; 283 cells SERPINB3 cluster; 209 cells MUC5B cluster; 183 cells PRB1 cluster) with representation of every non-polyp patient in each cluster of cells (e.g. no cluster is unique to one patient) and AUC metric 0.800 for LCN2 , 0.736 for SERPINB3 , 0.985 for MUC5B , 0.973 for BPIFB2 , and 0.908 for PRB1 .

summary:
In Homo sapiens, glandular cell subsets are marked by LCN2, SERPINB3, MUC5B, BPIFB2, and PRB1 in the ethmoid sinus.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:4c1af5e218928ade6ccf
claim_id: claim:4c1af5e218928ade6ccf
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
Violin plots for the count-based expression level (log(scaled UMI+1)) for key marker genes using ROC test across cell types identified in ( Fig. 5a ; Supplementary Table 3 ); 1,345 basal; 6,420 secretory; 6,381 hybrid; and 2,027 ciliated cells; from n=2 non-polyp and 2 polyp patients; AUC 0.943 for KRT5 , 0.667 for TP63 , 0.644 for LYPD2 , <0.55 for SPDEF , <0.55 for KRT8 , 0.602 for BPIFA1 , 0.813 for PIFO , 0.73 for FOXJ1 .

summary:
In Homo sapiens air-liquid interface cultures, basal cells are marked by KRT5 (AUC 0.943) and TP63 (AUC 0.667), while ciliated cells are marked by PIFO (AUC 0.813) and FOXJ1 (AUC 0.73).


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:235194c2aa609bb26bd6
claim_id: claim:235194c2aa609bb26bd6
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
Violin plots for the count-based expression level (log(scaled UMI+1)) for key marker genes using ROC test across cell types identified in ( Fig. 5a ; Supplementary Table 3 ); 1,345 basal; 6,420 secretory; 6,381 hybrid; and 2,027 ciliated cells; from n=2 non-polyp and 2 polyp patients; AUC 0.943 for KRT5 , 0.667 for TP63 , 0.644 for LYPD2 , <0.55 for SPDEF , <0.55 for KRT8 , 0.602 for BPIFA1 , 0.813 for PIFO , 0.73 for FOXJ1 .

summary:
In Homo sapiens air-liquid interface cultures, ciliated cells are marked by PIFO (AUC 0.813) and FOXJ1 (AUC 0.73).


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:09d1d97bb3fc845a9bad
claim_id: claim:09d1d97bb3fc845a9bad
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
select marker gene overlays displaying count-based (unique molecular identifier (UMI) collapsed) expression level (log(scaled UMI+1)) on a tSNE plot (see Supplementary Table 3 for full gene lists; genes identified via ROC test with AUC 0.689 for S100A8 , 0.763 for CD1C , 0.927 for C1QC )

summary:
In Homo sapiens, myeloid cell subsets are marked by S100A8 (AUC 0.689), CD1C (AUC 0.763), and C1QC (AUC 0.927) in the ethmoid sinus.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:7e626e83b1eb2062e7db
claim_id: claim:7e626e83b1eb2062e7db
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
select marker gene overlays displaying count-based (unique molecular identifier (UMI) collapsed) expression level (log(scaled UMI+1)) on a tSNE plot (see Supplementary Table 3 for full gene lists; genes identified via ROC test with AUC 0.691 for CTGF , 0.683 for CXCL12 , 0.726 for MYH11 )

summary:
In Homo sapiens, fibroblast subsets are marked by CTGF (AUC 0.691), CXCL12 (AUC 0.683), and MYH11 (AUC 0.726) in the ethmoid sinus.


claim_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757:claim:cfffaed15176b763624e
claim_id: claim:cfffaed15176b763624e
paper_key: hca:0056_10.1038_s41586-018-0449-8_fdcc67f757
span_literal:
select marker gene overlays displaying count-based (unique molecular identifier (UMI) collapsed) expression level (log(scaled UMI+1)) on a tSNE plot (see Supplementary Table 3 for full gene lists; genes identified via ROC test with AUC 0.742 for SELE , 0.706 for PODXL , 0.822 for PLAT )

summary:
In Homo sapiens, endothelial cell subsets are marked by SELE (AUC 0.742), PODXL (AUC 0.706), and PLAT (AUC 0.822) in the ethmoid sinus.


claim_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94:claim:0004d924e5d1e277f164
claim_id: claim:0004d924e5d1e277f164
paper_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94
summary: In Homo sapiens, oligodendrocyte precursor cells are marked by PDGFRA, BCAN, and SOX6.
span_literal:
PDGFRA , BCAN and SOX6 for OPCs, APOE and CD74 for immune oligodendroglia (imOLG, see below), CDH20 and RBFOX1 for Oligo1, LURAP1L.AS1 and CDH19 for Oligo2, KLK6 and GJB1 for Oligo5 and OPALIN, LINC00844 for Oligo6.


claim_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94:claim:2b6ed9735972d53b2974
claim_id: claim:2b6ed9735972d53b2974
paper_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94
summary: In Homo sapiens, oligodendrocyte precursor cells express OLIG2 and lack NOGOA (RTN4).
span_literal:
We confirmed the presence of OLIG2 and absence of NOGOA ( RTN4 ) in human OPCs, as used for their identification by neuropathologists 8 ( Extended Fig.4a ).


claim_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94:claim:f4ade6f8f9abfe167f18
claim_id: claim:f4ade6f8f9abfe167f18
paper_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94
span_literal:
Immunohistochemistry (IHC) showed that these OLIG2 + NOGOA - OPCs are also SOX6+ ( Extended Fig.4b,e ).

summary:
In Homo sapiens, oligodendrocyte precursor cells are OLIG2-positive, NOGOA-negative, and SOX6-positive.


claim_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94:claim:3cfb0adec7a17c512cf1
claim_id: claim:3cfb0adec7a17c512cf1
paper_key: hca:0057_10.1038_s41586-019-0903-2_059a54df94
summary: In Homo sapiens, immune oligodendroglia express CD74, HLA-DRA, PTPRC, and C3.
span_literal:
Although ImOLG expressed canonical OL genes, they were slightly separated from the main OL cloud in the tSNE, were closely associated with microglia, and expressed genes such as CD74, HLA.DRA, PTPRC, C3 ( Fig.3d and Extended Fig.8c ).


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:be337d904c63072162b0
claim_id: claim:be337d904c63072162b0
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
Inside the plasmacytoid DC (PDC) cluster, we identified two intriguing additional clusters of precursor T cells (preT; CD3G , CD8A ) and precursor B cells (preB; CD19 , CD79B , PAX5 ), likely because PDCs develop from common lymphoid progenitors

summary:
In Homo sapiens tonsil, precursor T cells are marked by CD3G and CD8A, and precursor B cells are marked by CD19, CD79B, and PAX5.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:8e8015d026b255afcd20
claim_id: claim:8e8015d026b255afcd20
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, precursor T cells and precursor B cells express RAG1, RAG2, and DNTT.
span_literal:
Both preT and preB cells expressed members of the VDJ recombinase, including RAG1 , RAG2 , and DNTT (TdT), supporting T and B cell development within human tonsils


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:7b13c2ac5f474e382ec3
claim_id: claim:7b13c2ac5f474e382ec3
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
Intriguingly, one CM CD4 T cell population expressed higher levels of follicular genes (e.g., IL6ST ), suggesting early signals of Tfh differentiation (CM pre-Tfh cells;

summary:
In Homo sapiens tonsil, central memory pre-T follicular helper cells express higher levels of IL6ST.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:6b6cb5c629308f6bc3ee
claim_id: claim:6b6cb5c629308f6bc3ee
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
We identified a CD4 T cluster that expressed low CCR7 and high IL6ST and TOX , pointing to cells migrating to the border of the follicle, primed to interact with B cells via ICOS-ICOSL (Tfh T:B border;

summary:
In Homo sapiens tonsil, T follicular helper T:B border cells express low CCR7 and high IL6ST and TOX.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:43e38c082611b15bb5b2
claim_id: claim:43e38c082611b15bb5b2
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: Tfh-LZ-GC cells expressed interleukin-21 ( IL-21 ), an inducer of early GC Tfh differentiation
summary:
In Homo sapiens tonsil, T follicular helper light zone germinal center cells express interleukin-21.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:7ca45ec5df7d3bdc48af
claim_id: claim:7ca45ec5df7d3bdc48af
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
Here, the high expression of SH2D1A (SAP) identified one subpopulation as a potent GC B cell (GCBC) state inducer (GC Tfh-SAP;

summary:
In Homo sapiens tonsil, germinal center T follicular helper-SAP cells are identified by high expression of SH2D1A.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:d5a59adbfbb83d947f02
claim_id: claim:d5a59adbfbb83d947f02
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
Tfh memory cells retained stable expression of PDCD1 , MAF , CXCR5 , and upregulated KLRB1 , preserving highly functional follicular characteristics

summary:
In Homo sapiens tonsil, T follicular helper memory cells express PDCD1, MAF, CXCR5, and upregulated KLRB1.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:6d91ac47b39990632b21
claim_id: claim:6d91ac47b39990632b21
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, T follicular regulatory cells downregulate FOXP3, IL2RA, and PRDM1.
span_literal:
The third subpopulation, T follicular regulatory cells (Tfrs), downregulated FOXP3 , IL-2RA (CD25), and PRDM1


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:065640cd9bd192ff3b97
claim_id: claim:065640cd9bd192ff3b97
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
The chemokine receptor CX3CR1 marks the differentiation from CM CD8 T to effector memory T cells (EM CD8 T), a process tightly controlled by TBX21 (TBET).

summary:
In Homo sapiens tonsil, effector memory CD8 T cells are marked by CX3CR1, and their differentiation is controlled by TBX21.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:25ed185629cd05d3cc13
claim_id: claim:25ed185629cd05d3cc13
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, resident memory CD8 T cells are marked by ITGA1 and ITGAE.
span_literal:
Subsequently, we identified two clusters of resident memory (RM) CD8 T cells, marked by the expression of the tissue residency markers ITGA1 and ITGAE (CD103;


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:cab728bb9f482434b1b7
claim_id: claim:cab728bb9f482434b1b7
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: One of these RM CD8 T cells additionally expressed the activation markers HLA-DRB1 and HLA-DPA1
summary:
In Homo sapiens tonsil, a subset of resident memory CD8 T cells additionally express the activation markers HLA-DRB1 and HLA-DPA1.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:7b9abad29aa7931784a0
claim_id: claim:7b9abad29aa7931784a0
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
Both cell types can be activated in a TCR-independent manner and are regulated by PLZF ( ZBTB16 ), 47 a highly specific marker for this cluster

summary:
In Homo sapiens tonsil, mucosal-associated invariant T cells and CD161+ Vδ2+ γδ T cells are marked by ZBTB16.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:0c739c3f0a14e0d9940e
claim_id: claim:0c739c3f0a14e0d9940e
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: NK cells and ILCs differed in their expression of KLRF1 and IL-7R (CD127), respectively
summary:
In Homo sapiens tonsil, natural killer cells are marked by KLRF1, while innate lymphoid cells are marked by IL7R.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:cea152aef5a3e40bdfe0
claim_id: claim:cea152aef5a3e40bdfe0
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: NK cells and ILCs differed in their expression of KLRF1 and IL-7R (CD127), respectively
summary:
In Homo sapiens tonsil, innate lymphoid cells are marked by IL7R, distinguishing them from natural killer cells.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:613f030e67162635691b
claim_id: claim:613f030e67162635691b
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: FCGR3A ) and CD56 ( NCAM1 )—starting from CD16 − CD56 + NK precursors ( SELL
summary:
In Homo sapiens tonsil, natural killer cell differentiation is guided by FCGR3A and NCAM1, with precursors expressing SELL, intermediate cells expressing IKZF3, and terminal cells expressing PRF1, CX3CR1, and TBX21.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:119b20607dc204a1eb9f
claim_id: claim:119b20607dc204a1eb9f
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: ILC1 cells could be distinguished from precursor NK cells by their higher expression of CD200R1
summary:
In Homo sapiens tonsil, innate lymphoid cell 1 is distinguished from precursor natural killer cells by higher expression of CD200R1.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:7d407f64420a139b8d78
claim_id: claim:7d407f64420a139b8d78
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: An early GC-committed subpopulation expressed high levels of MYC , CD69 , EGR2/3 , and CCL3/4
summary:
In Homo sapiens tonsil, early germinal center-committed naive B cells express high levels of MYC, CD69, EGR2, EGR3, CCL3, and CCL4.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:5d25e1684a03e2278b97
claim_id: claim:5d25e1684a03e2278b97
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: GC-committed cells, characterized by CCND2 (a downstream target of MYC), TRAF1/4 , and MIR155HG
summary:
In Homo sapiens tonsil, germinal center-committed cells are characterized by CCND2, TRAF1, and MIR155HG, while pre-germinal center cells express MEF2B and RGS13.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:f65d37d1b43b75e96c64
claim_id: claim:f65d37d1b43b75e96c64
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
PCs originated from LZ-GCBCs, initially overexpressing key PC TFs ( PRDM1 , IRF4 , and XBP1 ) followed by PC phenotypic markers (e.g., SLAMF7 and MZB1

summary:
In Homo sapiens tonsil, plasma cells express the transcription factors PRDM1, IRF4, and XBP1, as well as phenotypic markers SLAMF7 and MZB1.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:0022764ff8cd6443418c
claim_id: claim:0022764ff8cd6443418c
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens, SIX5 is a new marker for mature plasma cells.
span_literal:
Together, these results indicate SIX5 to be a new marker for mature PCs with a potential role in the regulation of MM tumorigenesis.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:b0bcb2f6dab67517d75b
claim_id: claim:b0bcb2f6dab67517d75b
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, marginal reticular cells express high levels of COL1A1, COL1A2, and COL3A1.
span_literal:
MRCs expressed high levels of COL1A1 , COL1A2 , and COL3A1 (among other collagens), which localized mostly at the interfollicular zone


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:f0471bb2e0abd1d1f7bf
claim_id: claim:f0471bb2e0abd1d1f7bf
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, marginal reticular cells express PDGFRB.
span_literal:
Intriguingly, MRCs expressed PDGFRB , which has been shown to be specific to perivascular precursor FDCs in mice


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:eaa799047faa9989e128
claim_id: claim:eaa799047faa9989e128
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, conventional dendritic cell type 1 states are defined by XCR1 expression.
span_literal:
DC1, conventional DC1 (cDC1), divided into precursor and mature states on the basis of XCR1 expression and a proliferation signature


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:a3e7b9cbbd5734c4eed6
claim_id: claim:a3e7b9cbbd5734c4eed6
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: DC4, putatively derived from non-classical monocytes ( FCGR3A
summary:
In Homo sapiens tonsil, DC4 cells are putatively derived from non-classical monocytes and express FCGR3A.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:a16a3755f70fd2df92e4
claim_id: claim:a16a3755f70fd2df92e4
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: AXL and IL-7R but not SIGLEC and additional marker genes, such as IL1RN , IL1B , and CD83
summary:
In Homo sapiens tonsil, a previously uncharacterized dendritic cell cluster expresses AXL, IL7R, IL1RN, IL1B, and CD83 but not SIGLEC.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:e1f72f08b5df52742a36
claim_id: claim:e1f72f08b5df52742a36
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
summary: In Homo sapiens tonsil, activated dendritic cell 2 expresses AIRE.
span_literal:
Noteworthy, aDC2 expressed shallow levels of autoimmune regulator ( AIRE ), which has a role in peripheral tolerance


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:f89d138d0ebee71fe5a2
claim_id: claim:f89d138d0ebee71fe5a2
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal: CD8 T cell cluster expressing CCL4 , XCL1 , and CD99
summary:
In Homo sapiens tonsil, a CD8 T cell cluster that instructs plasmacytoid dendritic cell recruitment expresses CCL4, XCL1, and CD99.


claim_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6:claim:7ec20eb18cd2e4135d7d
claim_id: claim:7ec20eb18cd2e4135d7d
paper_key: hca:0058_10.1016_j.immuni.2024.01.006_4c90d18ac6
span_literal:
PDK1 , TMEM198 , ITM2C , BHLHA15/ MIST1, SLC38A2 , and TSC22D3 /GILZ) showed increased accessibility and selective expression in mature PCs

summary:
In Homo sapiens, the predicted target genes of SIX5 including PDK1, TMEM198, ITM2C, BHLHA15, SLC38A2, and TSC22D3 show selective expression in mature plasma cells.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:3886ffc2ac1549c2377a
claim_id: claim:3886ffc2ac1549c2377a
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
we identified nine major cell clusters present in the healthy and HIV-infected donors based on expression of a unique gene signature: CD4 + T cells ( CD3D + CD8A − IL7R hi ), CD8 + T cells ( CD3D + CD8A + ), natural killer cells (NK; CD3D − CD8A − IL7R − GNLY hi ), B cells ( MS4A1 + ), CD14 + monocytes ( LYZ hi CD14 hi ), CD16 + monocytes ( LYZ hi FCGR3A hi ), conventional dendritic cells (cDCs; LYZ hi FCER1A hi ), plasmacytoid dendritic cells (pDCs; LYZ low IGJ hi ), and megakaryocytes (Mk; PPBP + )

summary:
In Homo sapiens peripheral blood mononuclear cells, CD4-positive T cells are marked by positive expression of CD3D and IL7R and negative expression of CD8A.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:040676275cb850dde1e8
claim_id: claim:040676275cb850dde1e8
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
we identified nine major cell clusters present in the healthy and HIV-infected donors based on expression of a unique gene signature: CD4 + T cells ( CD3D + CD8A − IL7R hi ), CD8 + T cells ( CD3D + CD8A + ), natural killer cells (NK; CD3D − CD8A − IL7R − GNLY hi ), B cells ( MS4A1 + ), CD14 + monocytes ( LYZ hi CD14 hi ), CD16 + monocytes ( LYZ hi FCGR3A hi ), conventional dendritic cells (cDCs; LYZ hi FCER1A hi ), plasmacytoid dendritic cells (pDCs; LYZ low IGJ hi ), and megakaryocytes (Mk; PPBP + )

summary:
In Homo sapiens peripheral blood mononuclear cells, CD8-positive T cells are marked by positive expression of CD3D and CD8A.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:3407f8bf7ca90e296041
claim_id: claim:3407f8bf7ca90e296041
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
we identified nine major cell clusters present in the healthy and HIV-infected donors based on expression of a unique gene signature: CD4 + T cells ( CD3D + CD8A − IL7R hi ), CD8 + T cells ( CD3D + CD8A + ), natural killer cells (NK; CD3D − CD8A − IL7R − GNLY hi ), B cells ( MS4A1 + ), CD14 + monocytes ( LYZ hi CD14 hi ), CD16 + monocytes ( LYZ hi FCGR3A hi ), conventional dendritic cells (cDCs; LYZ hi FCER1A hi ), plasmacytoid dendritic cells (pDCs; LYZ low IGJ hi ), and megakaryocytes (Mk; PPBP + )

summary:
In Homo sapiens peripheral blood mononuclear cells, natural killer cells are marked by negative expression of CD3D, CD8A, and IL7R and positive expression of GNLY.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:75c83260f5cc863d49ce
claim_id: claim:75c83260f5cc863d49ce
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
summary:
In Homo sapiens peripheral blood mononuclear cells, B cells are marked by positive expression of MS4A1.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:945311dbde3ecdc1557d
claim_id: claim:945311dbde3ecdc1557d
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
summary:
In Homo sapiens peripheral blood mononuclear cells, CD14-positive monocytes are marked by high expression of LYZ and CD14.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:c377fb2f3556379b7fbd
claim_id: claim:c377fb2f3556379b7fbd
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
summary:
In Homo sapiens peripheral blood mononuclear cells, CD16-positive monocytes are marked by high expression of LYZ and FCGR3A.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:8d268d8589cfb61f5d67
claim_id: claim:8d268d8589cfb61f5d67
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
summary:
In Homo sapiens peripheral blood mononuclear cells, conventional dendritic cells are marked by high expression of LYZ and FCER1A.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:feb62322d344cbd7786e
claim_id: claim:feb62322d344cbd7786e
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
summary:
In Homo sapiens peripheral blood mononuclear cells, plasmacytoid dendritic cells are marked by low expression of LYZ and high expression of IGJ.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:8e18007867e901e78fbd
claim_id: claim:8e18007867e901e78fbd
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
summary:
In Homo sapiens peripheral blood mononuclear cells, megakaryocytes are marked by positive expression of PPBP.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:a32a03e12a2c545a9383
claim_id: claim:a32a03e12a2c545a9383
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
naïve CD4 + T cells (CD4-Tn: CD8A − CCR7 + IL7R hi ), effector memory CD4 + T cells (CD4-T em : CD8A − IL7R hi CCR7 − GZMA + )

summary:
In Homo sapiens, naïve CD4-positive T cells are marked by negative expression of CD8A and positive expression of CCR7 and IL7R.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:0c8ed83fd028cd0344ff
claim_id: claim:0c8ed83fd028cd0344ff
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
naïve CD4 + T cells (CD4-Tn: CD8A − CCR7 + IL7R hi ), effector memory CD4 + T cells (CD4-T em : CD8A − IL7R hi CCR7 − GZMA + )

summary:
In Homo sapiens, effector memory CD4-positive T cells are marked by negative expression of CD8A and CCR7 and positive expression of IL7R and GZMA.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:63df22432bad382c2437
claim_id: claim:63df22432bad382c2437
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal: a cluster that we defined as precursor memory cells (CD4-Tpm: CD8A − IL7R hi CCR7 low LTB hi )
summary:
In Homo sapiens, precursor memory CD4-positive T cells are marked by negative expression of CD8A, high expression of IL7R and LTB, and low expression of CCR7.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:54a333ec1ada533c9a37
claim_id: claim:54a333ec1ada533c9a37
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
The putative CD4-Tpm cluster showed a similar signature to that of CD4-Tn cells (e.g. TCF7, FOXP1 ) but they did not express effector function-associated genes (e.g. GZMA , CCR5 , NKG7 ), suggesting that they may represent a transitional state between naïve and effector memory status

summary:
In Homo sapiens, precursor memory CD4-positive T cells express TCF7 and FOXP1 but do not express GZMA, CCR5, or NKG7.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:6471112e61b786b073a9
claim_id: claim:6471112e61b786b073a9
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
naïve CD8 + T cells (CD8-Tn: CD8A + CCR7 hi ) and effector memory CD8 + T cells (CD8-Tem: CD8A + IL7R − CCR7 − GZMA + NKG7 + ;

summary:
In Homo sapiens, naïve CD8-positive T cells are marked by positive expression of CD8A and high expression of CCR7.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:890f437c7cb9b568ac87
claim_id: claim:890f437c7cb9b568ac87
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
naïve CD8 + T cells (CD8-Tn: CD8A + CCR7 hi ) and effector memory CD8 + T cells (CD8-Tem: CD8A + IL7R − CCR7 − GZMA + NKG7 + ;

summary:
In Homo sapiens, effector memory CD8-positive T cells are marked by positive expression of CD8A, GZMA, and NKG7 and negative expression of IL7R and CCR7.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:96309f4d0ff54fb0a8ff
claim_id: claim:96309f4d0ff54fb0a8ff
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
The Tex subpopulations were classified based on previous work showing that CD8 + T cells expressing high levels of the exhaustion markers CD160 and TIGIT were enriched in HIV-infected individuals

summary:
In Homo sapiens, exhausted CD8-positive T cells are marked by high expression of the exhaustion markers CD160 and TIGIT.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:63d78a0d57934926f13b
claim_id: claim:63d78a0d57934926f13b
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
Similarly, CD4-Tex cells were characterized by expression of the exhaustion markers TIGIT and CTLA4 .

summary:
In Homo sapiens, exhausted CD4-positive T cells are characterized by expression of the exhaustion markers TIGIT and CTLA4.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:d88b6119aeef16ff3e44
claim_id: claim:d88b6119aeef16ff3e44
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
cells within the CD8-Tem-IFN hi cluster ­ showed enrichment of IFN-stimulated genes such as OASL, ISG15, IFIT2, and IFIT3, consistent with expansion of the host antiviral immune response

summary:
In Homo sapiens, interferon-responsive effector memory CD8-positive T cells show enrichment of interferon-stimulated genes OASL, ISG15, IFIT2, and IFIT3.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:abbdf4c478312b23c785
claim_id: claim:abbdf4c478312b23c785
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
The 24 up-regulated genes in HL-HIV-infected donors included the known exhaustion markers TIGIT and CD160

summary:
In Homo sapiens, exhausted CD8-positive T cells from high-load HIV-infected donors show upregulation of the known exhaustion markers TIGIT and CD160.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:6bd989c43fff41c233e9
claim_id: claim:6bd989c43fff41c233e9
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
CD8-Tex cells from the HL-HIV-infected donors also showed up-regulated expression of another inhibitory receptor, killer cell lectin-like receptor subfamily G member 1 (KLRG1), which contains an immunoreceptor tyrosine-based inhibitory motif in the cytoplasmic domain

summary:
In Homo sapiens, exhausted CD8-positive T cells from high-load HIV-infected donors show upregulated expression of the inhibitory receptor killer cell lectin-like receptor subfamily G member 1 (KLRG1).


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:b821ffc5d6233aa43955
claim_id: claim:b821ffc5d6233aa43955
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
Other genes specifically up-regulated in CD8-Tex cells from HL-HIV-infected donors included CMC1, SH2D1A , COMMD6 , TRAPPC1 , and COTL-1

summary:
In Homo sapiens, exhausted CD8-positive T cells from high-load HIV-infected donors show specific upregulation of CMC1, SH2D1A, COMMD6, TRAPPC1, and COTL1.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:1d761a4d207f76c94fff
claim_id: claim:1d761a4d207f76c94fff
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
Conversely, there were 15 genes commonly down-regulated in CD8-Tex cells from HL-HIV-infected donors, including IRF1, ITGB1, and genes encoding the cytotoxic T cell effector molecules granzyme B (GZMB ) , perforin 1 ( PRF1 ) , and granulysin ( GNLY )

summary:
In Homo sapiens, exhausted CD8-positive T cells from high-load HIV-infected donors show downregulation of IRF1, ITGB1, GZMB, PRF1, and GNLY compared with effector memory CD8-positive T cells.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:9b0b6b88db7ffc40229e
claim_id: claim:9b0b6b88db7ffc40229e
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
Taken together, these results identified novel signatures of KLRG1 , CD160, and TIGIT characterizes exhausted CD8 + T cells in HIV-infected donors.

summary:
In Homo sapiens, exhausted CD8-positive T cells in HIV-infected donors are characterized by novel signatures of KLRG1, CD160, and TIGIT.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:9315e68a1e815398cf99
claim_id: claim:9315e68a1e815398cf99
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal:
An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8 + T cell population expressing KLRG1, TIGIT, and T-bet dim Eomes hi markers.

summary:
In Homo sapiens, an HIV-1 specific exhausted CD8-positive T cell population expresses the inhibitory receptor KLRG1, TIGIT, and T-bet dim Eomes hi markers.


claim_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f:claim:3d858259053cdd1625e6
claim_id: claim:3d858259053cdd1625e6
paper_key: hca:0059_10.1080_22221751.2020.1826361_4a743eba8f
span_literal: the B cell inhibitory receptor LILRB1 was up-regulated in PBMCs from HIV-infected donors
summary:
In Homo sapiens, the B cell inhibitory receptor LILRB1 is upregulated in B cells from HIV-infected donors.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:72d0696293bceea419f2
claim_id: claim:72d0696293bceea419f2
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
summary: In Homo sapiens skin, fibroblasts are marked by COL1A1 and DCN expression.
span_literal:
These cell clusters represented ten main cell types including COL1A1+ DCN+ fibroblasts, KRT5+/KRT10+ keratinocytes, TAGLN+ pericytes/vascular smooth muscle cells (VSMCs), PECAM1+ vascular endothelial cells, LYVE1+ lymphatic endothelial cells, LYZ+ macrophages/dendritic cells (DCs), CXCR4+ T cells, TPSB2+ mast cells, PMEL+ melanocytes and CDH19+ Schwann cells


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:65957f70e06f9f5554d8
claim_id: claim:65957f70e06f9f5554d8
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
Macrophages (cluster 1, Figure 2D ) and DC (cluster 2, Figure 2D ) were distinguished by elevated expression of previously described markers of dermal macrophages ( CD14 , CD68 , CD163 )

summary:
In Homo sapiens skin, dermal macrophages are distinguished from dendritic cells by elevated expression of CD14, CD68, and CD163.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:685b9db2c05db6ad4404
claim_id: claim:685b9db2c05db6ad4404
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
In contrast, cluster 1 showed a prominent reticular gene signature, including MGP , ANGTPL1 , FGF7 , EFEMP1 , MFAP5 , suggesting that these cells represent secretory reticular dermal fibroblasts.

summary:
In Homo sapiens skin, secretory reticular dermal fibroblasts show a prominent reticular gene signature including MGP, ANGTPL1, FGF7, EFEMP1, and MFAP5.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:2f0cb5f8db4b18a3fbf1
claim_id: claim:2f0cb5f8db4b18a3fbf1
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
Specifically, cluster 4 fibroblasts expressed genes involved in anti-oxidative response ( HMOX1 , SOD2 , FTH , SQSTM ) and immunomodulatory ( SQSTM1 , TNFAIP6 , TNFAIP3 , NFKB1 ) cell functions

summary:
In Homo sapiens skin, fibroblast cluster 4 expresses anti-oxidative genes HMOX1, SOD2, FTH, SQSTM and immunomodulatory genes SQSTM1, TNFAIP6, TNFAIP3, NFKB1.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:506c7c79706e20757a11
claim_id: claim:506c7c79706e20757a11
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
summary: In Homo sapiens skin, basal keratinocytes are enriched for the markers KRT5, KRT14, and KRT15.
span_literal:
Keratinocytes in cluster 1 were enriched for known basal keratinocyte markers ( KRT5 , KRT14 , KRT15 )


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:6880d7be660e20411c50
claim_id: claim:6880d7be660e20411c50
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
while cluster 3 keratinocytes, characterized by KRT1 and KRT10 expression, showed a gene signature of suprabasal spinous keratinocytes.

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


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:6dcd994928e7611730e8
claim_id: claim:6dcd994928e7611730e8
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
A differentiated granular keratinocyte cluster (cluster 4) expressed the known differentiation gene markers ( KRT2 , IVL , SBSN , CALML5 , DSC1 ) and contained a small subset of LOR+ FLG + cells which could represent terminally differentiated cells of the cornified envelope

summary:
In Homo sapiens skin, differentiated granular keratinocytes express the differentiation gene markers KRT2, IVL, SBSN, CALML5, and DSC1.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:e6cfe2e902a9779d2aef
claim_id: claim:e6cfe2e902a9779d2aef
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
A differentiated granular keratinocyte cluster (cluster 4) expressed the known differentiation gene markers ( KRT2 , IVL , SBSN , CALML5 , DSC1 ) and contained a small subset of LOR+ FLG + cells which could represent terminally differentiated cells of the cornified envelope

summary:
In Homo sapiens skin, terminally differentiated cells of the cornified envelope express LOR and FLG.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:4ac15ea329779dbcd498
claim_id: claim:4ac15ea329779dbcd498
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
summary: In Homo sapiens skin, vascular smooth muscle cells express ACTA2, TAGLN, MYH11, CNN1, and TPM2.
span_literal:
we identified one cluster of VMSC expressing ACTA2 , TAGLN , MYH11 , CNN1 , TPM2 cells and one cluster of PDGFRB+ pericytes.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:ace3b910be451eade436
claim_id: claim:ace3b910be451eade436
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
summary: In Homo sapiens skin, fibroblasts are marked by DCN expression in the integrated skin atlas.
span_literal:
Specifically, these populations included DCN+ fibroblasts, TAGLN+ pericyte/VSMC, PECAM1+ vascular ECs, CCL21+ lymphatic ECs, SFN+ keratinocytes, CXCL8+/HLA-DRA+ macrophages/DC, CD52+ T cells, TPSAB1+ mast cells, AQP5+ sweat gland cells and a combined cluster of MLANA+ melanocytes, CRYAB+ Schwann cells and GPM6B+ neuronal cells


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:2c05f11402b49764ad13
claim_id: claim:2c05f11402b49764ad13
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
Specifically, these populations included DCN+ fibroblasts, TAGLN+ pericyte/VSMC, PECAM1+ vascular ECs, CCL21+ lymphatic ECs, SFN+ keratinocytes, CXCL8+/HLA-DRA+ macrophages/DC, CD52+ T cells, TPSAB1+ mast cells, AQP5+ sweat gland cells and a combined cluster of MLANA+ melanocytes, CRYAB+ Schwann cells and GPM6B+ neuronal cells

summary:
In Homo sapiens skin, pericyte/vascular smooth muscle cells are marked by TAGLN expression in the integrated skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:d21f43e2347078af2e9f
claim_id: claim:d21f43e2347078af2e9f
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal:
Specifically, these populations included DCN+ fibroblasts, TAGLN+ pericyte/VSMC, PECAM1+ vascular ECs, CCL21+ lymphatic ECs, SFN+ keratinocytes, CXCL8+/HLA-DRA+ macrophages/DC, CD52+ T cells, TPSAB1+ mast cells, AQP5+ sweat gland cells and a combined cluster of MLANA+ melanocytes, CRYAB+ Schwann cells and GPM6B+ neuronal cells

summary:
In Homo sapiens skin, vascular endothelial cells are marked by PECAM1 expression in the integrated skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:1dd01080acb4b32aec89
claim_id: claim:1dd01080acb4b32aec89
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
summary:
In Homo sapiens skin, lymphatic endothelial cells are marked by CCL21 expression in the integrated skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:f050f96a97602fc14028
claim_id: claim:f050f96a97602fc14028
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
summary:
In Homo sapiens skin, macrophages/dendritic cells are marked by CXCL8 and HLA-DRA expression in the integrated skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:37541426d5869240a5be
claim_id: claim:37541426d5869240a5be
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal: FABP4+ lymphatic ECs
summary:
In Homo sapiens skin, lymphatic endothelial cells are marked by FABP4 expression in the fresh and cultured skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:28ab889553f157dc82d5
claim_id: claim:28ab889553f157dc82d5
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal: CALD1+ pericytes/VSMCs
summary:
In Homo sapiens skin, pericytes/vascular smooth muscle cells are marked by CALD1 expression in the fresh and cultured skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:671f85fb29c745c69606
claim_id: claim:671f85fb29c745c69606
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal: CCL3+ macrophages
summary:
In Homo sapiens skin, macrophages are marked by CCL3 expression in the fresh and cultured skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:e98a69fb9fe03205610e
claim_id: claim:e98a69fb9fe03205610e
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal: CCR7+ dendritic cells
summary:
In Homo sapiens skin, dendritic cells are marked by CCR7 expression in the fresh and cultured skin atlas.


claim_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48:claim:62d47bf86ec4c8c86957
claim_id: claim:62d47bf86ec4c8c86957
paper_key: hca:0060_10.3389_fcell.2022.872688_ac00c45d48
span_literal: MUCL1+ sweat gland cells
summary:
In Homo sapiens skin, sweat gland cells are marked by MUCL1 expression in the fresh and cultured skin atlas.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:11359604118e583bca2c
claim_id: claim:11359604118e583bca2c
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
Two of the shared marker genes were TIMP1 and ITLN1 which encode secreted proteins inhibiting neovascularization

summary:
In Homo sapiens white adipose tissue, vascular cell subtype vC08 is marked by TIMP1 and ITLN1, which encode secreted proteins inhibiting neovascularization.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:67c25e6aa577f9e36b65
claim_id: claim:67c25e6aa577f9e36b65
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
vC09 was enriched for genes previously described in “early endothelial progenitor cells” (e.g., TYROBP , FCER1G ), a hematopoietic cell type that promotes angiogenesis via paracrine mechanisms

summary:
In Homo sapiens white adipose tissue, vascular cell subtype vC09 (early endothelial progenitor cell) is enriched for TYROBP and FCER1G.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:e82d03947fe29e562ab9
claim_id: claim:e82d03947fe29e562ab9
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
One vascular subtype (vC05) expressed multiple marker genes for committed preadipocytes (e.g., CXCL14 , APOD, and CFD ) and was the only vascular population that expressed PDGFRA

summary:
In Homo sapiens white adipose tissue, vascular cell subtype vC05 expresses committed preadipocyte marker genes CXCL14, APOD, CFD, and PDGFRA.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:dd634b469d42293bf99a
claim_id: claim:dd634b469d42293bf99a
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
The former included mesothelial-like cells (sfC11), CD74 + stromal cells (sfC13) reported to have antifibrotic properties

summary:
In Homo sapiens subcutaneous white adipose tissue, CD74-positive stromal cells (sfC13) are marked by CD74 expression.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:9124ab64aaff02ea4f27
claim_id: claim:9124ab64aaff02ea4f27
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
One cluster (sfC03) enriched for cell adhesion molecules and was the only FAP that did not express CD34 , PDGFRA, or PDGFRB

summary:
In Homo sapiens subcutaneous white adipose tissue, fibroblast and adipogenic progenitor subtype sfC03 does not express CD34, PDGFRA, or PDGFRB.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:663028e84f0dfcc3f300
claim_id: claim:663028e84f0dfcc3f300
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal: the larger group included multiple extracellular matrix- and CD55 / PI16 -expressing cells
summary:
In Homo sapiens subcutaneous white adipose tissue, the larger fibroblast and adipogenic progenitor group expresses CD55 and PI16.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:a286cd1afbb4087f0e64
claim_id: claim:a286cd1afbb4087f0e64
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
Route 1 ended in sfC0, a cell population enriched for genes that were upregulated at late stages of differentiation (e.g., APOD and CFD ) and most likely represent committed preadipocytes

summary:
In Homo sapiens subcutaneous white adipose tissue, committed preadipocyte subtype sfC0 is enriched for APOD and CFD.


claim_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9:claim:e04ee348cb147f8e80fe
claim_id: claim:e04ee348cb147f8e80fe
paper_key: hca:0061_10.1038_s41467-023-36983-2_7d240f9eb9
span_literal:
These included a cluster of genes encoding proteins involved in lipid metabolism e.g., ABCD2 , ACACB , CD36 , DGAT2 , GPAM , HACD2, and LPL

summary:
In Homo sapiens white adipose tissue, adipocytes display reproducible marker genes including ABCD2, ACACB, CD36, DGAT2, GPAM, HACD2, and LPL.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:9158ecf29cbd17992a16
claim_id: claim:9158ecf29cbd17992a16
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
These cells expressed markers described for endometrial epithelial stem/progenitor cells ( SOX9 , CDH2 , AXIN2 , ALDH1A1 (refs. 9 , 31 – 34 ))

summary:
In Homo sapiens, SOX9 basalis (CDH2+) endometrial epithelial stem/progenitor cells express SOX9, CDH2, AXIN2, and ALDH1A1.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:78cea35cb4339ef3af8f
claim_id: claim:78cea35cb4339ef3af8f
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
The SOX9 functionalis I population expressed CDH2 and high levels of SOX9 and was marked by the expression of PHLDA1 and SLC7A11

summary:
In Homo sapiens, the SOX9 functionalis I epithelial population is marked by expression of CDH2, SOX9, PHLDA1, and SLC7A11 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:9638c7830212a2e820fb
claim_id: claim:9638c7830212a2e820fb
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
It also expressed the WNT inhibitor DKK1 , and, in line with this, AXIN2 was downregulated in both SOX9 functionalis states

summary:
In Homo sapiens, the SOX9 functionalis I epithelial population expresses DKK1, while AXIN2 is downregulated in both SOX9 functionalis states in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:899dc09a83320d509e77
claim_id: claim:899dc09a83320d509e77
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
The SOX9 functionalis II population exhibited lower expression of SOX9 and CDH2 , and distinctly expressed KMO , IHH and EMID1

summary:
In Homo sapiens, the SOX9 functionalis II epithelial population distinctly expresses KMO, IHH, and EMID1 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:2427489fa6d01558d7a5
claim_id: claim:2427489fa6d01558d7a5
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
OPRK1 , SUFU , CBR3 and HPRT1 were specific to the preGlandular population and SULT1E1 to the preLuminal population

summary:
In Homo sapiens, OPRK1, SUFU, CBR3, and HPRT1 are specific markers of the preGlandular epithelial population, and SULT1E1 is a specific marker of the preLuminal epithelial population in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:676b8a6981041a78dae9
claim_id: claim:676b8a6981041a78dae9
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
OPRK1 , SUFU , CBR3 and HPRT1 were specific to the preGlandular population and SULT1E1 to the preLuminal population

summary:
In Homo sapiens, SULT1E1 is a specific marker of the preLuminal epithelial population in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:aed3d3e8918bee914ed8
claim_id: claim:aed3d3e8918bee914ed8
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
We detected a previously described population of MUC5B + epithelial cells 16 expressing MUC5B , TFF3 , SAA1 and BPIFB1

summary:
In Homo sapiens, MUC5B-positive epithelial cells express MUC5B, TFF3, SAA1, and BPIFB1 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:d82d375a040ca1f3a55a
claim_id: claim:d82d375a040ca1f3a55a
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
we further identified a type of eStromal cells (eStromal matrix metalloproteinases (MMPs)) in samples collected during the menstrual and early proliferative phases (Fig. 3a , Extended Data Fig. 1d and Supplementary Note 4 ), characterized by the upregulation of metalloproteases ( MMP1 , MMP10 , MMP3 ) and inhibin A ( INHBA )

summary:
In Homo sapiens, endometrial stromal cells expressing matrix metalloproteinases (eStromal matrix metalloproteinases) are characterized by upregulation of MMP1, MMP10, MMP3, and INHBA in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:ba85e4f76f7af6f08d16
claim_id: claim:ba85e4f76f7af6f08d16
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
Early decidualized stromal cells (dStromal early) were enriched in the early secretory phase samples and upregulated the progesterone-induced gene PLCL1 (ref. 45 )

summary:
In Homo sapiens, early decidualized stromal cells (dStromal early) upregulate PLCL1 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:44b11163c0747007cc4f
claim_id: claim:44b11163c0747007cc4f
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
summary: In Homo sapiens, mid decidualized stromal cells (dStromal mid) upregulate DKK1 in the endometrium.
span_literal:
The mid decidualized stromal population (dStromal mid) mapped to early-mid and mid secretory phase samples and upregulated DKK1


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:6b80c71cbe41232fe91d
claim_id: claim:6b80c71cbe41232fe91d
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
Late decidualized stromal cells (dStromal late) were present in both mid and late secretory phase samples (Fig. 1f ) and upregulated the premenstrual marker LEFTY2 (ref. 46 )

summary:
In Homo sapiens, late decidualized stromal cells (dStromal late) upregulate LEFTY2 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:8260d27e6fa4042cb3d9
claim_id: claim:8260d27e6fa4042cb3d9
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
summary: In Homo sapiens, mid decidualized stromal cells downregulate ESR1 and PGR in the endometrium.
span_literal:
Both the dStromal mid and late populations downregulated estrogen and progesterone receptors ( ESR1 and PGR )


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:0751e5f0e9101a9e435a
claim_id: claim:0751e5f0e9101a9e435a
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
uM1 expressed pro-inflammatory genes such as IL1B and EREG , while uM2 expressed anti-inflammatory genes such as HMOX1 (ref. 52 )

summary:
In Homo sapiens, uterine macrophage 1 (uM1) expresses pro-inflammatory genes IL1B and EREG in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:bcdcedf1e4b6f2bfa741
claim_id: claim:bcdcedf1e4b6f2bfa741
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal:
uM1 expressed pro-inflammatory genes such as IL1B and EREG , while uM2 expressed anti-inflammatory genes such as HMOX1 (ref. 52 )

summary:
In Homo sapiens, uterine macrophage 2 (uM2) expresses the anti-inflammatory gene HMOX1 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:487b1c796524385071e8
claim_id: claim:487b1c796524385071e8
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal: uM2 also expressed tissue-resident macrophage markers such as FOLR2 and LYVE1 (ref. 53 )
summary:
In Homo sapiens, uterine macrophage 2 (uM2) expresses tissue-resident macrophage markers FOLR2 and LYVE1 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:e30109f1dfa603024ee0
claim_id: claim:e30109f1dfa603024ee0
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
span_literal: ePV-1a expressing STEAP4
summary:
In Homo sapiens, endometrial perivascular cell subset ePV-1a expresses STEAP4, ePV-1b expresses STC2, and ePV-2 expresses MMP11 in the endometrium.


claim_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849:claim:ca480765179be06b95b5
claim_id: claim:ca480765179be06b95b5
paper_key: hca:0062_10.1038_s41588-024-01873-w_27bb519849
summary: In Homo sapiens, the glandular secretory epithelial population upregulates FGF7 in the endometrium.
span_literal:
we observed the presence of a glandular secretory population that upregulated FGF7 , a mitogen with a wound healing role in other contexts


claim_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7:claim:bb7d6fc1d5898b9076b8
claim_id: claim:bb7d6fc1d5898b9076b8
paper_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7
span_literal:
Although LGR5 is expressed throughout the stem cell populations of the stomach and intestine, OLFM4 is highly enriched in a subpopulation of small intestine stem cells

summary:
In Homo sapiens, LGR5 is expressed throughout stem cell populations of the stomach and intestine, while OLFM4 is highly enriched in a subpopulation of small intestine stem cells.


claim_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7:claim:5137b5cb1e9d78ab333d
claim_id: claim:5137b5cb1e9d78ab333d
paper_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7
span_literal:
We validated the TF NKX2-3 and secreted factor WNT2 as general markers that distinguish intestine and lung mesenchyme, respectively

summary:
In Homo sapiens, NKX2-3 is a marker of intestine mesenchyme, distinguishing it from lung mesenchyme.


claim_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7:claim:f1de5d8cfa3aedc61138
claim_id: claim:f1de5d8cfa3aedc61138
paper_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7
span_literal:
Further, the TF SALL1 specifically marks F3+ subepithelial mesenchyme (c15, subepithelial, NRG1 +/ F3 +) in the stomach and intestine, whereas the TF PRRX1 marks chondrocyte-like SERPINF1 -high cells and pericytes in the lung

summary:
In Homo sapiens, SALL1 specifically marks F3-positive subepithelial mesenchyme in the stomach and intestine.


claim_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7:claim:e3b531a7eac79982c0f6
claim_id: claim:e3b531a7eac79982c0f6
paper_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7
summary: In Homo sapiens, intestinal stem cells are marked by MKI67, LGR5, and OLFM4.
span_literal:
with proliferative (MKI67+) intestinal stem cells (ISC; LGR5 +/ OLFM4 +) localized to crypt domains and differentiated secretory lineages (CHGA+ enteroendocrine, MUC2+ goblet cells) and FABP2+ absorptive enterocytes along the villus epithelium


claim_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7:claim:ab0df7e0338be7b2199d
claim_id: claim:ab0df7e0338be7b2199d
paper_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7
span_literal:
We noticed that SFRP2 + mesenchyme (c2, SFRP2 +/ PRRX1 +) lacked expression of the intestine marker NKX2-3

summary:
In Homo sapiens, SFRP2-positive mesenchyme is marked by SFRP2 and PRRX1 and lacks expression of the intestine marker NKX2-3.


claim_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7:claim:abcc63be5e1b3b1794f3
claim_id: claim:abcc63be5e1b3b1794f3
paper_key: hca:0063_10.1016_j.cell.2021.04.028_f5e4882de7
summary: In Homo sapiens, GDF10-positive mesenchyme expresses the stem cell niche factor GREM1.
span_literal:
Of note, GDF10 + (c8) and subepithelial mesenchyme (c15) expressed the important stem cell niche factors GREM1 ( McCarthy et al., 2020b ) and NRG1 ( Holloway et al., 2021 ; Jardé et al., 2020 ), respectively


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:5a4803b4c8e0324347e8
claim_id: claim:5a4803b4c8e0324347e8
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
Co-localization immunofluorescent analysis revealed that fibroblasts accounted for around 80% of the total number of CXCL9- and CXCL10-expressing cells in the skin of patients with vitiligo

summary:
In Homo sapiens, fibroblasts are the predominant cell type expressing CXCL9 and CXCL10 in the skin of patients with vitiligo.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:f38978048d5cd6f3a879
claim_id: claim:f38978048d5cd6f3a879
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
Quantification showed that among eight different cell types examined, dermal fibroblasts accounted for most (around 80%) of the pSTAT1 + cells in patient skin

summary:
In Homo sapiens, dermal fibroblasts account for the majority of phosphorylated STAT1-positive cells in vitiligo patient skin.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:ec9caca034848a17d630
claim_id: claim:ec9caca034848a17d630
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
skin recruitment, local aggregation and cytotoxicity of CD8 + T cells that target epidermal melanocytes.
Fig. 2: Paracrine IFNγ

summary:
In Homo sapiens, melanocytes and fibroblasts in the skin of patients with progressive vitiligo are enriched for interferon-gamma signalling pathway genes.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:1595b3da795a01fa4f20
claim_id: claim:1595b3da795a01fa4f20
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal: skin. Our study identifies anatomically distinct fibroblasts with permissive or repressive IFNγ
summary:
In Homo sapiens, fibroblasts in the skin of patients with progressive vitiligo are enriched for interferon-gamma signalling pathway genes.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:a64978614c4a514dcf72
claim_id: claim:a64978614c4a514dcf72
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
Although IFNG was predominantly expressed by cytotoxic T cells (Extended Data Fig. 1p ), T cells in the skin of patients in the progressive state did not show an increased IFNγ response compared to healthy skin.

summary:
In Homo sapiens, IFNG is predominantly expressed by cytotoxic T cells in the skin of patients with vitiligo.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:b3b178fcbc455b583baa
claim_id: claim:b3b178fcbc455b583baa
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
multiple IFNγ-induced chemokine genes—including CXCL9 , CXCL10 and their human-specific variant CXCL11 —were significantly upregulated in fibroblasts that were isolated from anatomic regions with a higher incidence of vitiligo, such as the back of the hand, the back of the foot, the chest and the back

summary:
In Homo sapiens, interferon-gamma-induced chemokine genes CXCL9, CXCL10, and CXCL11 are significantly upregulated in fibroblasts from anatomic regions with higher vitiligo incidence.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:caf77bd2029819825a34
claim_id: claim:caf77bd2029819825a34
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
Quantifications in skin from both patients with vitiligo and vitiligo-affected mice showed that CD8 + T cells constitute the majority of the CXCR3 + immune cells

summary:
In Homo sapiens, CD8-positive T cells constitute the majority of CXCR3-positive immune cells in vitiligo skin.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:f4c12c0d1575dc25d36f
claim_id: claim:f4c12c0d1575dc25d36f
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
In patients in the progressive state, there were significantly more CD8 + cytotoxic T cells, which also expressed significantly higher levels of IFNG

summary:
In Homo sapiens, CD8-positive cytotoxic T cells in the skin of patients with progressive vitiligo express significantly higher levels of IFNG.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:7d8dc3b1465e94ae3fee
claim_id: claim:7d8dc3b1465e94ae3fee
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
fibroblasts from different anatomic skin regions are intrinsically different in their expression of HOX genes

summary:
In Homo sapiens, fibroblasts from different anatomic skin regions differ intrinsically in their expression of HOX genes.


claim_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212:claim:5a3f4702f1704a296299
claim_id: claim:5a3f4702f1704a296299
paper_key: hca:0064_10.1038_s41586-021-04221-8_65d6d3d212
span_literal:
Although fibroblasts from all anatomic regions expressed similar levels of the IFNγ signalling pathway genes IFNGR1 , JAK1 , JAK2 and STAT1

summary:
In Homo sapiens, fibroblasts from all anatomic regions express similar levels of the interferon-gamma signalling pathway genes IFNGR1, JAK1, JAK2, and STAT1.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:684cc8c3a5188ad4e835
claim_id: claim:684cc8c3a5188ad4e835
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
SFTPC, a typical marker for AT2 cells, was strongly expressed in all clusters; however, subtle variations in gene expression among the AT2 clusters were observed

summary:
In Homo sapiens, SFTPC is a typical marker for alveolar type 2 cells, strongly expressed in all alveolar type 2 clusters.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:02074816b60a7b5199de
claim_id: claim:02074816b60a7b5199de
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
Hedgehog interacting protein (HHIP) and inhibitors of Wnt (WIF1) signaling were highly expressed in AT2-A, presumably implicating that they are quiescent AT2.

summary:
In Homo sapiens, Hedgehog interacting protein (HHIP) and WIF1 are highly expressed in alveolar type 2 cell cluster A, implicating a quiescent state.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:b67aa608ff33e964c9f4
claim_id: claim:b67aa608ff33e964c9f4
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
In contrast, WNT5A and detoxification gene, CP were expressed in AT2-B cluster, suggesting that these cells could be alveolar progenitors, AT2-signalling (AT2-s)

summary:
In Homo sapiens, WNT5A and CP are expressed in alveolar type 2 cell cluster B, suggesting these cells could be alveolar progenitors.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:13e4dc20d924d32ad133
claim_id: claim:13e4dc20d924d32ad133
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
Notably, a number of inflammation-related genes, including CXCL1, CXCL8, CCL2, CCL20, and CD274 (PD-L1) were specifically expressed in the AT2-C cluster, and we designated the population inflammatory AT2 (iAT2)

summary:
In Homo sapiens, CXCL1, CXCL8, CCL2, CCL20, and CD274 (programmed death-ligand 1) are specifically expressed in the inflammatory alveolar type 2 cell cluster.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:a835a82b06b2fb81467a
claim_id: claim:a835a82b06b2fb81467a
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal: Additionally, we identified novel markers to classify the iAT2 cluster, such as CLDN1 and TNC
summary:
In Homo sapiens, CLDN1 and TNC are novel markers to classify the inflammatory alveolar type 2 cell cluster.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:63e6561d49f43ba2b9e1
claim_id: claim:63e6561d49f43ba2b9e1
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
INHBA was highly expressed in macrophage-1 but not in macrophage-2; GPR183 was specifically expressed in macrophage-2, although macrophage receptors with collagenous structures (MARCOs) were highly expressed in both clusters

summary:
In Homo sapiens, INHBA is highly expressed in macrophage-1 but not in macrophage-2. In Homo sapiens, MARCO is highly expressed in both macrophage-1 and macrophage-2.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:5a2450e9ad46aa567a5d
claim_id: claim:5a2450e9ad46aa567a5d
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
INHBA was highly expressed in macrophage-1 but not in macrophage-2; GPR183 was specifically expressed in macrophage-2, although macrophage receptors with collagenous structures (MARCOs) were highly expressed in both clusters

summary:
In Homo sapiens, INHBA is not expressed in macrophage-2, in contrast to macrophage-1. In Homo sapiens, GPR183 is specifically expressed in macrophage-2. In Homo sapiens, MARCO is highly expressed in macrophage-2.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:de9e6ac7140ac5a97421
claim_id: claim:de9e6ac7140ac5a97421
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal: All fibroblast clusters expressed general fibroblast markers such as DCN and PDGFRA.
summary:
In Homo sapiens, DCN and PDGFRA are general fibroblast markers expressed in all fibroblast clusters.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:7af7f1eb39ba171c9978
claim_id: claim:7af7f1eb39ba171c9978
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
summary: In Homo sapiens, FGFR4 is highly expressed in alveolar fibroblast.
span_literal:
FGFR4 was highly expressed in alveolar fibroblast, and PDGFRL was specifically expressed in adventitial fibroblast


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:e341591e68ccb910a472
claim_id: claim:e341591e68ccb910a472
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal: the AT1-B clusters, which specifically expressed COL4A1, COL4A2, and COL4A3
summary:
In Homo sapiens, the alveolar type 1 cell cluster B specifically expresses COL4A1, COL4A2, and COL4A3.


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:19afe41035cb67b91630
claim_id: claim:19afe41035cb67b91630
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
summary: In Homo sapiens, goblet cells are marked by MUC5B, MUC5A, and SPDEF.
span_literal:
the cell populations of goblet (MUC5B, MUC5A, and SPDEF), club (SCGB3A1, CYP2F2, and CCKAR), and basal cell (KRT17, KRT5, and TP63) clusters were higher in COPD than in never-smokers


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:0bf3ef4ecba0e3b9a74c
claim_id: claim:0bf3ef4ecba0e3b9a74c
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
summary: In Homo sapiens, ETV5 is a marker of alveolar type 2 cells.
span_literal:
the AT2 cell markers, such as ETV5, were expressed in the predicted early phase, while the CLIC5 and AGER, AT1 cell markers, were highly detected in the late phase


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:75912f35ea014ba19510
claim_id: claim:75912f35ea014ba19510
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
summary: In Homo sapiens, TP63 is a basal cell marker.
span_literal:
we observed that basal cell markers, such as TP63, were expressed early and that ciliated cell markers, such as FOXJ1 and the DNAH family members, were expressed late


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:0fa743c148e18ad76a0e
claim_id: claim:0fa743c148e18ad76a0e
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
summary: In Homo sapiens, EPCAM is a tissue compartment marker for epithelial cells.
span_literal:
Clusters were grouped based on expression of tissue compartment markers (for example, EPCAM for epithelial cells, CLDN5 for endothelial cells, COL1A2 for stromal cells and PTPRC for immune cells)


claim_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424:claim:430b839ce5cd27fecbac
claim_id: claim:430b839ce5cd27fecbac
paper_key: hca:0065_10.1101_2020.12.03.20242412_aa08d1f424
span_literal:
Also, iAT2 cells showed increased expression of NFKB2, a component of NF-κB, and CSF3, an IL-6 superfamily member, further supporting the inflammatory nature of AT2

summary:
In Homo sapiens, inflammatory alveolar type 2 cells show increased expression of NFKB2 and CSF3, supporting their inflammatory nature.


claim_key: hca:0068_10.1093_ibd_izac201_351dddd961:claim:c349d40799b757d63c5f
claim_id: claim:c349d40799b757d63c5f
paper_key: hca:0068_10.1093_ibd_izac201_351dddd961
summary: In Homo sapiens, epithelial cells are marked by shared expression of EPCAM, KRT8, and KRT18.
span_literal:
Epithelial cells were subdivided into 9 cell types with the shared expression of EPCAM , KRT8 , and KRT18 expression in both control subjects and CD patients.


claim_key: hca:0068_10.1093_ibd_izac201_351dddd961:claim:bab54d4f7b86fd448565
claim_id: claim:bab54d4f7b86fd448565
paper_key: hca:0068_10.1093_ibd_izac201_351dddd961
span_literal:
The genes used to define each subcluster of epithelial cells were stem/transit-amplifying (TA)/progenitor cells ( OLFM4 , LGR5 ), TA cells ( OLFM4 , MKI67 , and TOP2A ), early enterocyte cells ( OLFM4 , LCN2 , and ADH1C ), enterocyte cells ( APOA4 and FABP6 ), Goblet cells ( MUC2 , TFF3 , and SPINK4 ), enteroendocrine cells (EECs) ( CHGA , CHGB , PYY , and NTS ), Paneth cells ( DEFA5 , DEFA6 , and LYZ ), BEST4+ enterocyte cells ( BEST4 , OTOP2 , and SPIB ), 15 and tuft cells ( SPIB , SH2D6 , and LRMP ).

summary:
In Homo sapiens, stem/transit-amplifying/progenitor cells are defined by expression of OLFM4 and LGR5.


claim_key: hca:0068_10.1093_ibd_izac201_351dddd961:claim:234fcb34217821f067e2
claim_id: claim:234fcb34217821f067e2
paper_key: hca:0068_10.1093_ibd_izac201_351dddd961
span_literal:
For the immune compartment defined by PTPRC expression, 5 subtypes were defined by the following gene expression patterns: B cells ( MS4A1 ), T cells ( CD3D and NKG7 ), plasma cells ( JCHAIN , MZB1 , IGHA1 , and IGHG1 ), macrophages ( S100A8 , C1QA , and C1QB ), and erythrocytes ( HBB and HBA1 ).

summary:
In Homo sapiens, the immune compartment is defined by PTPRC expression, with B cells marked by MS4A1.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:013d294a1cbd9d11a463
claim_id: claim:013d294a1cbd9d11a463
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal: In humans, GC B cells are commonly identified as CD38 + IgD − and transcription factor BCL6 + .
summary:
In Homo sapiens, germinal center B cells are commonly identified by positive expression of CD38 and BCL6 and negative expression of IgD.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:94d51f9c4047564cd86b
claim_id: claim:94d51f9c4047564cd86b
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
GC B cells can be further divided into centroblasts (dark zone; DZ) and centrocytes (light zone; LZ) through the expression of CXCR4 and CD86, respectively.

summary:
In Homo sapiens, germinal center B cells of the dark zone (centroblasts) are marked by CXCR4 expression, while light zone germinal center B cells (centrocytes) are marked by CD86 expression.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:4fb2f5ce2e1b1453b91d
claim_id: claim:4fb2f5ce2e1b1453b91d
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
GC B cells can be further divided into centroblasts (dark zone; DZ) and centrocytes (light zone; LZ) through the expression of CXCR4 and CD86, respectively.

summary:
In Homo sapiens, light zone germinal center B cells (centrocytes) are marked by CD86 expression, distinguishing them from dark zone germinal center B cells.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:e2ceecd2ea45e4a78aad
claim_id: claim:e2ceecd2ea45e4a78aad
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
In addition, recent studies have indicated Semaphorin 4A (SEMA4A) expression on human GC B cells in SLOs 27 .

summary:
In Homo sapiens, Semaphorin 4A (SEMA4A) is expressed on germinal center B cells in secondary lymphoid organs.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:74d0ab5ac835191282be
claim_id: claim:74d0ab5ac835191282be
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal: T FH cell signature (i.e. high frequency and magnitude of CXCR5, PDCD1, ICOS, CXCL13
summary:
In Homo sapiens, T follicular helper cells are characterized by high expression of CXCR5, PDCD1, ICOS, and CXCL13.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:22b39710da7aee81e6b6
claim_id: claim:22b39710da7aee81e6b6
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
summary: In Homo sapiens, naïve B cells are identified as CD38 negative, IgD positive, and CD27 negative.
span_literal:
we identified seven distinct B cell clusters: naïve B cells (CD38 − IgD + CD27 − ), IgG + switched memory B cells (IgG + CD38 − IgD ‒ CD27 + ), IgG − switched memory B cells (IgG − CD38 − IgD − CD27 + ), activated switched memory (CD38 − IgD − CD27+CD21 − ), GC B cells (CD38 + IgD − BCL6 + SEMA4a + ), tissue-like memory B cells (CD38 − IgD − IgG + CD27 − CD21 − FcRL5 + ) and antibody-secreting cells (CD38 hi CD27 + Ki67 +/− )


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:cc06782bcf88937abf25
claim_id: claim:cc06782bcf88937abf25
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
we identified seven distinct B cell clusters: naïve B cells (CD38 − IgD + CD27 − ), IgG + switched memory B cells (IgG + CD38 − IgD ‒ CD27 + ), IgG − switched memory B cells (IgG − CD38 − IgD − CD27 + ), activated switched memory (CD38 − IgD − CD27+CD21 − ), GC B cells (CD38 + IgD − BCL6 + SEMA4a + ), tissue-like memory B cells (CD38 − IgD − IgG + CD27 − CD21 − FcRL5 + ) and antibody-secreting cells (CD38 hi CD27 + Ki67 +/− )

summary:
In Homo sapiens, IgG positive switched memory B cells are identified as IgG positive, CD38 negative, IgD negative, and CD27 positive.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:221374f1216258a0bec8
claim_id: claim:221374f1216258a0bec8
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
we identified seven distinct B cell clusters: naïve B cells (CD38 − IgD + CD27 − ), IgG + switched memory B cells (IgG + CD38 − IgD ‒ CD27 + ), IgG − switched memory B cells (IgG − CD38 − IgD − CD27 + ), activated switched memory (CD38 − IgD − CD27+CD21 − ), GC B cells (CD38 + IgD − BCL6 + SEMA4a + ), tissue-like memory B cells (CD38 − IgD − IgG + CD27 − CD21 − FcRL5 + ) and antibody-secreting cells (CD38 hi CD27 + Ki67 +/− )

summary:
In Homo sapiens, IgG negative switched memory B cells are identified as IgG negative, CD38 negative, IgD negative, and CD27 positive.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:bcd5ce9ea90a9d365497
claim_id: claim:bcd5ce9ea90a9d365497
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
summary:
In Homo sapiens, activated switched memory B cells are identified as CD38 negative, IgD negative, CD27 positive, and CD21 negative.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:2a52de0ce92d5ac20769
claim_id: claim:2a52de0ce92d5ac20769
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
summary:
In Homo sapiens, germinal center B cells are identified as CD38 positive, IgD negative, BCL6 positive, and SEMA4A positive.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:62df4d004edeed9e9031
claim_id: claim:62df4d004edeed9e9031
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
summary:
In Homo sapiens, tissue-like memory B cells are identified as CD38 negative, IgD negative, IgG positive, CD27 negative, CD21 negative, and FcRL5 positive.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:94f10e3896b82ab7c2f7
claim_id: claim:94f10e3896b82ab7c2f7
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
summary:
In Homo sapiens, antibody-secreting cells are identified as CD38 high, CD27 positive, and Ki67 positive or negative.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:c66cb6b4504a7491d9c8
claim_id: claim:c66cb6b4504a7491d9c8
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal: The key genes that were upregulated on DZ were CXCR4, CD27, CD72, CCR1.
summary:
In Homo sapiens, dark zone germinal center B cells show upregulation of CXCR4, CD27, CD72, and CCR1.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:8fe3b39f5815372c8a0d
claim_id: claim:8fe3b39f5815372c8a0d
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
We identified the upregulation of CD40, CD37, CD7, and CD180 on LZ as well as CD83, ICAM1, CCR6, and CD18 on TZ.

summary:
In Homo sapiens, light zone germinal center B cells show upregulation of CD40, CD37, CD7, and CD180.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:34eaf977d2e3219a6e2b
claim_id: claim:34eaf977d2e3219a6e2b
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
We identified the upregulation of CD40, CD37, CD7, and CD180 on LZ as well as CD83, ICAM1, CCR6, and CD18 on TZ.

summary:
In Homo sapiens, transitional zone germinal center B cells show upregulation of CD83, ICAM1, CCR6, and CD18.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:1777a91d249cc511b5a4
claim_id: claim:1777a91d249cc511b5a4
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
summary: In Homo sapiens, light zone germinal center B cells express canonical genes CD22 and HLA-DRB1.
span_literal:
The first phase consisted of expression of canonical LZ genes such as CD22 and HLA-DRB1 , followed by a wave of transitional genes consisting of CXCR4 and TCL1A , followed by a final wave of cell cycle genes which are consistent with the proliferative nature of DZ B cells.


claim_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4:claim:61940de99addf374dc13
claim_id: claim:61940de99addf374dc13
paper_key: hca:0069_10.1038_s41467-021-23355-x_92232969b4
span_literal:
Regulatory T FH (CXCR5 + FOXP3 + ) was not significantly different between HPV + and HPV − tumors (Fig. 2c ).

summary:
In Homo sapiens, regulatory T follicular helper cells are identified by positive expression of CXCR5 and FOXP3.


claim_key: hca:0070_10.1038_s41587-020-0469-4_55d6a04187:claim:d8b50cf3d73814aa3090
claim_id: claim:d8b50cf3d73814aa3090
paper_key: hca:0070_10.1038_s41587-020-0469-4_55d6a04187
span_literal:
This is illustrated in the monocytes, for which accurate clustering protocols separated the major subpopulations (CD14 + and FCGR3A + ), whereas methods with low ASW did not distinguish between them.

summary:
In Homo sapiens, monocyte subpopulations are distinguished by CD14 and FCGR3A (Fc gamma receptor IIIa), with CD14-positive and FCGR3A-positive marking the major monocyte subpopulations.


claim_key: hca:0070_10.1038_s41587-020-0469-4_55d6a04187:claim:41bc78c3b71e22b86041
claim_id: claim:41bc78c3b71e22b86041
paper_key: hca:0070_10.1038_s41587-020-0469-4_55d6a04187
span_literal:
Similarly, several methods were able to distinguish between CD8 + and natural killer (NK) cells, whereas others were not.

summary:
In Homo sapiens, CD8-positive T cells are marked by CD8, distinguishing them from natural killer cells.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:1292c2fa26951a720332
claim_id: claim:1292c2fa26951a720332
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal: sinusoidal EC genes CTSL, STAB2, and SEPP1
summary:
In Homo sapiens fetal bone marrow, sinusoidal endothelial cells express CTSL, STAB2, and SEPP1, while non-sinusoidal endothelial cells express high levels of VIM and CD34.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:7b643e18986aa7e186f7
claim_id: claim:7b643e18986aa7e186f7
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal: VIM and CD34 , associated with non-sinusoidal EC
summary:
In Homo sapiens fetal bone marrow, non-sinusoidal endothelial cells express high levels of VIM and CD34.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:77cb9987fd207210b90a
claim_id: claim:77cb9987fd207210b90a
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
The non-sinusoidal ‘tip EC’ cells expressed canonical markers for cells at the tips of growing vascular structures, PDGFB, UNC5B and DLL4 20

summary:
In Homo sapiens fetal bone marrow, non-sinusoidal tip endothelial cells express canonical markers PDGFB, UNC5B, and DLL4.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:abf9e0f7261c9c5e37db
claim_id: claim:abf9e0f7261c9c5e37db
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
FBM GMPs expressed higher CEBPA (neutrophil specification), relative to SPI1 (monocyte specification) 9 , than FL GMPs

summary:
In Homo sapiens fetal bone marrow, granulocyte and monocyte progenitors express CEBPA at higher levels relative to SPI1 compared to fetal liver granulocyte and monocyte progenitors.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:1a68793202fac3095a4b
claim_id: claim:1a68793202fac3095a4b
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
FBM sinusoidal ECs had significantly higher expression of SELE , VCAM1 and ICAM2 and concordant surface protein expression than analogous FL sinusoidal ECs.

summary:
In Homo sapiens fetal bone marrow, sinusoidal endothelial cells express higher levels of SELE, VCAM1, and ICAM2 compared to fetal liver sinusoidal endothelial cells.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:3f593f3768536ff91864
claim_id: claim:3f593f3768536ff91864
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal: FBM sinusoidal ECs also expressed more CCL14 , implicated in myeloid progenitor proliferation 25
summary:
In Homo sapiens fetal bone marrow, sinusoidal endothelial cells express CCL14, which is implicated in myeloid progenitor proliferation.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:d2baa9d88a1713ecb7ad
claim_id: claim:d2baa9d88a1713ecb7ad
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
TFs with well-defined roles in early haematopoietic programming ( SPI1 and FLI1 ) 13 , 14 were expressed at lower levels in DS than in non-DS HSC/MPPs and MEMPs, and PySCENIC inferred downregulation of corresponding regulons.

summary:
In Homo sapiens Down syndrome fetal bone marrow, haematopoietic stem cell/multipotent progenitors and megakaryocyte-erythroid-mast cell progenitors express lower levels of SPI1 and FLI1 compared to non-Down syndrome counterparts.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:913acaac51c4332d8c67
claim_id: claim:913acaac51c4332d8c67
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
TFs with well-defined roles in early haematopoietic programming ( SPI1 and FLI1 ) 13 , 14 were expressed at lower levels in DS than in non-DS HSC/MPPs and MEMPs, and PySCENIC inferred downregulation of corresponding regulons.

summary:
In Homo sapiens Down syndrome fetal bone marrow, megakaryocyte-erythroid-mast cell progenitors express lower levels of SPI1 and FLI1 compared to non-Down syndrome counterparts.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:040dec2fde805eda5737
claim_id: claim:040dec2fde805eda5737
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal: MK cells expressed lower levels of FLI1
summary:
In Homo sapiens Down syndrome fetal bone marrow, megakaryocyte cells express lower levels of FLI1, a driver of megakaryocyte differentiation.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:99ed380d98ce0c175e1e
claim_id: claim:99ed380d98ce0c175e1e
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
summary: In Homo sapiens Down syndrome fetal bone marrow, myeloid cells overexpress TNF.
span_literal:
Most myeloid lineages in DS overexpressed TNF (in keeping raised circulating TNFα in DS 18 ) and TNFα signalling pathway genes were over-represented in DS myeloid, erythroid, NK and stromal cells


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:4f3c5e0008c67438f6e9
claim_id: claim:4f3c5e0008c67438f6e9
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
DS megakaryocyte-erythroid-mast cell progenitor (MEMP), MK and B-lineage cells overexpressed chromosome 21 TFs with documented roles in haematopoiesis including U2AF1 (MEMP), U2AF1 and ETS2 (MK) and ETS2 (B-lineage)

summary:
In Homo sapiens Down syndrome fetal bone marrow, megakaryocyte-erythroid-mast cell progenitors overexpress U2AF1.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:9b804c9745b1c9dced6f
claim_id: claim:9b804c9745b1c9dced6f
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
The expression of NOTCH ligands NOV and DLK1, predicted by CellPhoneDB to mediate EC and HSC/MPP interactions ( Extended Data Fig. 10 ), was significantly higher in DS than non-DS endothelium, and expression of NOTCH1 was increased on DS HSC/MPPs

summary:
In Homo sapiens Down syndrome fetal bone marrow, endothelial cells express higher levels of NOTCH ligands NOV and DLK1 compared to non-Down syndrome endothelium.


claim_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954:claim:d9dedae9ebb0c65fe810
claim_id: claim:d9dedae9ebb0c65fe810
paper_key: hca:0071_10.1038_s41586-021-03929-x_6a378f8954
span_literal:
The expression of NOTCH ligands NOV and DLK1, predicted by CellPhoneDB to mediate EC and HSC/MPP interactions ( Extended Data Fig. 10 ), was significantly higher in DS than non-DS endothelium, and expression of NOTCH1 was increased on DS HSC/MPPs

summary:
In Homo sapiens Down syndrome fetal bone marrow, haematopoietic stem cell/multipotent progenitors show increased expression of NOTCH1.


claim_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930:claim:06700ca4ccf0531e5092
claim_id: claim:06700ca4ccf0531e5092
paper_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930
span_literal:
Cluster C2 represents long-lived plasma cells, evident from high expression levels of CXCR4 and TXNIP (Extended Data Fig. 4 )

summary:
In Homo sapiens, long-lived plasma cells are marked by high expression levels of CXCR4 and TXNIP in bone marrow.


claim_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930:claim:da516c0ae9d12be46fbb
claim_id: claim:da516c0ae9d12be46fbb
paper_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930
span_literal:
Cluster C1 shows a similar transcriptional profile, with lower expression levels of CXCR4 and TXNIP and a gradient of CD81 and CD19 protein surface marker expression (Extended Data Fig. 4 ).

summary:
In Homo sapiens, short-lived plasma cells show lower expression levels of CXCR4 and TXNIP compared to long-lived plasma cells.


claim_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930:claim:9a35eabe21be23b9feed
claim_id: claim:9a35eabe21be23b9feed
paper_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930
span_literal:
Aberrant plasma cells were identified either by antigen underexpression (CD19, CD27, CD38, CD45, CD52, CD81) or antigen overexpression (CD56, CD138).

summary:
In Homo sapiens, aberrant plasma cells are identified by underexpression of CD19, CD27, CD38, PTPRC, CD52, and CD81 or overexpression of NCAM1 and SDC1 compared to normal plasma cells.


claim_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930:claim:a6931d9eab6a0b8e02c9
claim_id: claim:a6931d9eab6a0b8e02c9
paper_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930
span_literal:
Long-lived plasma cells are contained within the CD19 − CD38 hi CD138 + subset in human bone marrow.

summary:
In Homo sapiens, long-lived plasma cells are contained within the CD19-negative, CD38-high, SDC1-positive subset in bone marrow.


claim_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930:claim:e52472c3068f78a1a0d6
claim_id: claim:e52472c3068f78a1a0d6
paper_key: hca:0072_10.1038_s41591-018-0269-2_c51f595930
span_literal:
Using flow cytometry in a different cohort of individuals with relapsed multiple myeloma, we showed that circulating tumor cells with an aberrant surface profile have lower protein expression of CD52 compared with non-circulating tumor cells (Extended Data Fig. 10 ).

summary:
In Homo sapiens, circulating tumor cells in multiple myeloma have lower protein expression of CD52 compared with non-circulating tumor cells.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:f5a88f1f15641173028b
claim_id: claim:f5a88f1f15641173028b
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal:
CD47 gene expression was significantly upregulated in both clusters 2 and 3 compared with cluster 0/1

summary:
In Homo sapiens, CD47 gene expression is significantly upregulated in plasmablast clusters 2 and 3 compared with plasmablast cluster 0/1.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:b24927b3c57b66a91eba
claim_id: claim:b24927b3c57b66a91eba
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal:
The top DEGs for cluster 0/1 compared with other clusters were IGLC2 followed by 12 variable region genes and IGJ, indicating that these cells' transcriptional activity is dominated by the production of antibodies.

summary:
In Homo sapiens, plasmablast cluster 0/1 is marked by high expression of IGLC2 and IGJ compared with other plasmablast clusters, indicating transcriptional activity dominated by antibody production.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:d0c4b24f994d56f9d49f
claim_id: claim:d0c4b24f994d56f9d49f
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal: Plasmablasts among total B cells were identified based on CD27, CD38, and PRDM1 expression
summary:
In Homo sapiens, plasmablasts among total B cells were identified based on CD27, CD38, and PRDM1 expression.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:c7d7ac1f244ed7513d6a
claim_id: claim:c7d7ac1f244ed7513d6a
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal:
RPS6, a gene downstream of CD40L ( Luo et al., 2018 ), was expressed significantly higher in clusters 2 and 3 compared with cluster 1

summary:
In Homo sapiens, RPS6 is expressed significantly higher in plasmablast clusters 2 and 3 compared with plasmablast cluster 0/1.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:62d9dae4de930c2cd6d9
claim_id: claim:62d9dae4de930c2cd6d9
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal: HLA-DRB1, an MHC class II gene, was expressed significantly higher in clusters 2 and 3
summary:
In Homo sapiens, HLA-DRB1, a major histocompatibility complex class II gene, is expressed significantly higher in plasmablast clusters 2 and 3.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:1bc4e9766e95fd0aa41f
claim_id: claim:1bc4e9766e95fd0aa41f
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal:
Another plasma cell marker, SDC1 (CD138), showed increased expression in cluster 0/1 compared with cluster 2 and/or 3; IRF4 showed decreased expression, whereas XBP1 expression was not significantly different.

summary:
In Homo sapiens, SDC1 (CD138) showed increased expression in plasmablast cluster 0/1 compared with plasmablast clusters 2 and 3, while IRF4 showed decreased expression in plasmablast cluster 0/1.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:bbe20f645c9fd7ab0577
claim_id: claim:bbe20f645c9fd7ab0577
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal: Clusters 2 and 3 expressed higher levels of blimp-1 (PRDM1) compared with cluster 0/1
summary:
In Homo sapiens, plasmablast clusters 2 and 3 expressed higher levels of PRDM1 (blimp-1) compared with plasmablast cluster 0/1.


claim_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab:claim:dbb6036beddbe43575c7
claim_id: claim:dbb6036beddbe43575c7
paper_key: hca:0073_10.1016_j.isci.2021.102482_6ff6d432ab
span_literal:
Cytochrome c (CYCS) expression was significantly higher in the IgA and IgM fraction compared with the Igneg fraction, and CD47 expression was higher in the IgM fraction

summary:
In Homo sapiens, cytochrome c (CYCS) expression was significantly higher in IgA and IgM plasmablasts compared with immunoglobulin-negative plasmablasts, and CD47 expression was higher in IgM plasmablasts.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:cbd136d5d0a8ffc30e40
claim_id: claim:cbd136d5d0a8ffc30e40
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
TEC progenitors expressed both keratin 5 (KRT5) and KRT8, whose expression is subsequently restricted to mTECs and cTECs, respectively

summary:
In Homo sapiens, medullary thymic epithelial cells are marked by KRT5 expression, while cortical thymic epithelial cells are marked by KRT8 expression.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:65624538b56b0407d332
claim_id: claim:65624538b56b0407d332
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal: Additionally, mTECs are also distinguished from cTECs by the former’s expression of KRT14.
summary:
In Homo sapiens, medullary thymic epithelial cells are distinguished from cortical thymic epithelial cells by expression of KRT14.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:3de8cffcc428c6e30f08
claim_id: claim:3de8cffcc428c6e30f08
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Immunofluorescence analysis shows that human thymic primordium at embryonic week 7 expresses high levels of EPCAM, a marker that is retained in mTECs at embryonic week 15 but substantially downregulated in cTECs

summary:
In Homo sapiens, medullary thymic epithelial cells retain high levels of EPCAM, while cortical thymic epithelial cells substantially downregulate EPCAM.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:5b1140b013c40c5d4d5e
claim_id: claim:5b1140b013c40c5d4d5e
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Immunofluorescence analysis shows that human thymic primordium at embryonic week 7 expresses high levels of EPCAM, a marker that is retained in mTECs at embryonic week 15 but substantially downregulated in cTECs

summary:
In Homo sapiens, cortical thymic epithelial cells substantially downregulate EPCAM compared to medullary thymic epithelial cells.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:a1e017cc8f52fb690450
claim_id: claim:a1e017cc8f52fb690450
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Similarly, the tight junction-forming proteins claudin 3 (CLDN3) and CLDN4 are highly enriched in mTECs

summary:
In Homo sapiens, claudin 3 (CLDN3) and CLDN4 are highly enriched in medullary thymic epithelial cells.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:2ebbc8e4a39de779f622
claim_id: claim:2ebbc8e4a39de779f622
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
FOXN1 is detected mid-week 6 of human development, with its expression restricted to a site within the third pharyngeal pouch that marks the presumptive thymus primordia, in distinction to the presumptive parathyroid which is marked by GCM2 (glial cells missing transcription factor 2)

summary:
In Homo sapiens, FOXN1 marks the presumptive thymus primordia, while GCM2 (glial cells missing transcription factor 2) marks the presumptive parathyroid within the third pharyngeal pouch.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:6749480ae83fe7bb8692
claim_id: claim:6749480ae83fe7bb8692
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
FOXN1 is detected mid-week 6 of human development, with its expression restricted to a site within the third pharyngeal pouch that marks the presumptive thymus primordia, in distinction to the presumptive parathyroid which is marked by GCM2 (glial cells missing transcription factor 2)

summary:
In Homo sapiens, GCM2 (glial cells missing transcription factor 2) marks the presumptive parathyroid within the third pharyngeal pouch.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:9c27a64e2dd225ed33f6
claim_id: claim:9c27a64e2dd225ed33f6
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Studies with these lines showed that FOXN1 :GFP+ cells were marked by co-expression of EPCAM and CD104 (known as ITGB4).

summary:
In Homo sapiens, FOXN1-positive thymic epithelial progenitor cells are marked by co-expression of EPCAM and CD104 (also known as ITGB4).


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:a131603bbf9ddf48af1b
claim_id: claim:a131603bbf9ddf48af1b
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
summary: In Homo sapiens, CLDN4 expression is associated with medullary thymic epithelial cells.
span_literal:
Indeed, we found that CD90- cells showed significantly higher levels of CLDN4 , a gene whose expression is associated with mTECs


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:5dee80cae2576eecc292
claim_id: claim:5dee80cae2576eecc292
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Interestingly, this analysis also showed a consistent trend of increased expression of individual collagen genes in the CD90+ fraction, such COL1A1 , which is also a well-established marker of cells undergoing mesenchymal transition from epithelial cells

summary:
In Homo sapiens, COL1A1 is a well-established marker of cells undergoing epithelial-to-mesenchymal transition.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:5d13b1e6db37fc20a98c
claim_id: claim:5d13b1e6db37fc20a98c
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Conversely, EPCAM-CD104- cells exclusively expressed the mesenchymal cell marker PDGFRB , suggesting a phenotype of conventional fibroblasts.

summary:
In Homo sapiens, EPCAM-negative CD104-negative cells exclusively expressed the mesenchymal cell marker PDGFRB, suggesting a conventional fibroblast phenotype.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:8363f8ffeae776667748
claim_id: claim:8363f8ffeae776667748
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
clusters 0-4 and 6-7 were epithelial cells that expressed E-cadherin ( CDH1 ) and cluster 5 comprised mesenchymal cells that expressed platelet derived growth factor receptor beta ( PDGFRB )

summary:
In Homo sapiens, epithelial cells express E-cadherin (CDH1), while mesenchymal cells express platelet derived growth factor receptor beta (PDGFRB).


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:3173eff90b343c153d5c
claim_id: claim:3173eff90b343c153d5c
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
This contrasts with primary TECs, where expression of both LY75 and PBSM11 was clearly detected in cluster 7, suggesting a cTEC cluster that was effectively absent from cultured TEC populations

summary:
In Homo sapiens, LY75 and PSMB11 expression marks a cortical thymic epithelial cell cluster in primary thymic epithelial cells.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:bfb5724b76fe4cb6c045
claim_id: claim:bfb5724b76fe4cb6c045
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal: Cluster 6 contained cells that expressed CLDN4 and AIRE , suggestive of a mature mTEC phenotype
summary:
In Homo sapiens, expression of CLDN4 and AIRE is suggestive of a mature medullary thymic epithelial cell phenotype.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:7d13c10b01ea3135876f
claim_id: claim:7d13c10b01ea3135876f
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
summary: In Homo sapiens, CD24 is a medullary thymic epithelial cell associated gene.
span_literal:
In addition to CLDN4 , cluster 4 was enriched for the expression of the mTEC associated gene CD24 , a marker that was also broadly expressed at lower levels throughout the culture cell populations


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:e7538bf3245dd84a1e31
claim_id: claim:e7538bf3245dd84a1e31
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
medullary and cortical compartments within these cells were further specified using classical cTEC markers ( LY75 and PSMB11 ) and mTEC markers ( KRT14 , CLDN4 , AIRE and FEZF2 )

summary:
In Homo sapiens, cortical thymic epithelial cells are specified by classical markers LY75 and PSMB11, while medullary thymic epithelial cells are specified by KRT14, CLDN4, AIRE, and FEZF2.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:fb45292ea9aaa1516c01
claim_id: claim:fb45292ea9aaa1516c01
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
medullary and cortical compartments within these cells were further specified using classical cTEC markers ( LY75 and PSMB11 ) and mTEC markers ( KRT14 , CLDN4 , AIRE and FEZF2 )

summary:
In Homo sapiens, medullary thymic epithelial cells are specified by markers KRT14, CLDN4, AIRE, and FEZF2.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:5b1d9e956141e1cde087
claim_id: claim:5b1d9e956141e1cde087
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
This analysis showed that the cTEC functional genes, PSMB11 and PRSS16 , were enriched in the LY75 -high population, whilst the mTEC functional genes, AIRE and FEZF2 , were restricted to a CLDN4 -high population.

summary:
In Homo sapiens, the cortical thymic epithelial cell functional genes PSMB11 and PRSS16 are enriched in the LY75-high population, while the medullary thymic epithelial cell functional genes AIRE and FEZF2 are restricted to a CLDN4-high population.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:83d456e9286ad08789ae
claim_id: claim:83d456e9286ad08789ae
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
This analysis showed that the cTEC functional genes, PSMB11 and PRSS16 , were enriched in the LY75 -high population, whilst the mTEC functional genes, AIRE and FEZF2 , were restricted to a CLDN4 -high population.

summary:
In Homo sapiens, the medullary thymic epithelial cell functional genes AIRE and FEZF2 are restricted to a CLDN4-high population.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:4c4c7c6885fb0ec82c5d
claim_id: claim:4c4c7c6885fb0ec82c5d
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Our results showed that EPCAM and CDH1 (E-cadherin), established epithelial cell surface markers, were upregulated in concert with increasing expression of CLDN4

summary:
In Homo sapiens, EPCAM and CDH1 (E-cadherin) are established epithelial cell surface markers upregulated in medullary thymic epithelial cells marked by CLDN4.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:c890c1d18936fd77e960
claim_id: claim:c890c1d18936fd77e960
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal: Conversely, the EMT-related genes FN1 (fibronectin) and CD90 were strongly associated with LY7 5.
summary:
In Homo sapiens, the epithelial-to-mesenchymal transition-related genes FN1 (fibronectin) and CD90 are strongly associated with cortical thymic epithelial cells marked by LY75.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:eefa307557c72e3c5888
claim_id: claim:eefa307557c72e3c5888
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Similarly, we found that the intracellular signaling molecules, SMAD2 and SMAD3 , were associated with LY75 , suggesting a potential activity of the TGFβ cell signaling pathway in cTECs

summary:
In Homo sapiens, the intracellular signaling molecules SMAD2 and SMAD3 are associated with LY75-expressing cortical thymic epithelial cells, suggesting potential transforming growth factor beta signaling pathway activity.


claim_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9:claim:0895faa0e012896f3409
claim_id: claim:0895faa0e012896f3409
paper_key: hca:0074_10.3389_fimmu.2022.846281_c0060ff2e9
span_literal:
Flow cytometry and gene expression profiling analysis identified CD90 as a potential marker of cells that possessed a mesenchymal-like program within cTEC populations.

summary:
In Homo sapiens, CD90 is identified as a potential marker of cells possessing a mesenchymal-like program within cortical thymic epithelial cell populations.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:c9a42972dfdbca208883
claim_id: claim:c9a42972dfdbca208883
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
ML NK cells expressed CD16, CD57, and high granzyme B and perforin, along with a unique transcription factor profile.

summary:
In Homo sapiens, memory-like natural killer cells express CD16, CD57, and high granzyme B and perforin.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:d97e7af18a84503c1d7e
claim_id: claim:d97e7af18a84503c1d7e
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal: CD56, CD62L, NKG2A, and activating receptors (NKp30, NKp44, NKp46, and DNAM-1) were all increased
summary:
In Homo sapiens, memory-like natural killer cells have increased expression of CD56, CD62L, NKG2A, NKp30, NKp44, NKp46, and DNAM-1.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:dfe92516d9d47642a7e0
claim_id: claim:dfe92516d9d47642a7e0
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
Also consistent with the ML NK cell phenotype are increased effector molecules perforin, granzyme B, tumor necrosis factor (TNF)–related apoptosis-inducing ligand, and proliferation marker Ki-67

summary:
In Homo sapiens, memory-like natural killer cells have increased expression of perforin, granzyme B, tumor necrosis factor-related apoptosis-inducing ligand, and Ki-67.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:8ef1e106480101f70089
claim_id: claim:8ef1e106480101f70089
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
These included high expression of major histocompatibility complex class II–associated genes ( HLA-DRA and CD74 ) and cytotoxicity-associated genes ( GZMA, GZMK , and GNLY ), as well as reduced expression of granzyme M ( GZMM

summary:
In Homo sapiens, memory-like natural killer cells have high expression of HLA-DRA, CD74, GZMA, GZMK, and GNLY, and reduced expression of GZMM compared to other natural killer cells.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:f44142f92ce5dfb65c65
claim_id: claim:f44142f92ce5dfb65c65
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
ML NK cells had a unique NK cell repertoire consisting of increased expression of KLRC1 (NKG2A), KIR2DL4 , and CD300A and decreased expression of the inhibitory receptor KLRB1 (CD161).

summary:
In Homo sapiens, memory-like natural killer cells have increased expression of KLRC1, KIR2DL4, and CD300A, and decreased expression of KLRB1.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:104e34a3f81828425808
claim_id: claim:104e34a3f81828425808
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
summary: In Homo sapiens, memory-like natural killer cells have up-regulation of CD3E.
span_literal:
In addition, ML NK cells had differential expression of intracellular signaling mediators including up-regulation of CD3E


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:1ea51577cfae9917da1e
claim_id: claim:1ea51577cfae9917da1e
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
ML NK cells also had distinct expression of genes encoding cytokines and chemokines including Lymphotoxin beta ( LTB ), chemokine-like factor ( CKLF ), and fibroblast growth factor binding protein 2 ( FGFBP2 )

summary:
In Homo sapiens, memory-like natural killer cells have distinct expression of lymphotoxin beta (LTB), chemokine-like factor (CKLF), and fibroblast growth factor binding protein 2 (FGFBP2).


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:149a27c6051d08aacf0d
claim_id: claim:149a27c6051d08aacf0d
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
Last, ML NK cells had a distinct transcription factor profile including increased HOPX and ID2 expression, which have been reported to play pivotal roles in NK cell sensitivity to IL-15

summary:
In Homo sapiens, memory-like natural killer cells have increased expression of the transcription factors HOPX and ID2.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:66d9e66ce6fffbadedeb
claim_id: claim:66d9e66ce6fffbadedeb
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
summary: In Homo sapiens, memory-like natural killer cells have decreased expression of NR4A2 and ZEB2.
span_literal:
ML NK cells had decreased expression of NR4A2 and ZEB2 , which has been implicated in murine NK cell maturation


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:6d5b6f3374ed3bd8ec51
claim_id: claim:6d5b6f3374ed3bd8ec51
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
In contrast, ML NK cells consistently expressed SH2D1B and FCER1G , with low KLRC2 and variable ZBTB16 (PLZF) expression

summary:
In Homo sapiens, memory-like natural killer cells consistently express SH2D1B and FCER1G, with low KLRC2 expression, distinguishing them from cytomegalovirus-adaptive natural killer cells.


claim_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5:claim:05886acdf5a36e03a99a
claim_id: claim:05886acdf5a36e03a99a
paper_key: hca:0075_10.1126_scitranslmed.abm1375_6de08b3db5
span_literal:
Previously, it has been reported that cytomegalovirus (CMV)–adaptive NK cells up-regulate the gene encoding Killer Cell Lectin Like Receptor 2 (NKG2C), KLRC2 , in CD56 dim NK cells, and down-regulate the genes encoding Promyelocytic Leukemia Zinc Finger [PLZF; gene: Zinc Finger and BTB Domain Containing 16 ( ZBTB16 )], Fc Epsilon Receptor Ig (FcεR1γ;FCER1G), EWS/FLI1 activated transcript 2 [EAT-2; gene: SH2 Domain Containing 1B ( SH2D1B )], and Spleen Tyrosine Kinase (SYK)

summary:
In Homo sapiens, cytomegalovirus-adaptive natural killer cells up-regulate KLRC2 and down-regulate ZBTB16, FCER1G, SH2D1B, and SYK.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:7972dff1e35688fee2ba
claim_id: claim:7972dff1e35688fee2ba
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
XBP1 , POU2AF1 , PRDM1 , and IRF4 were highly expressed in B_c05-MZB1-XBP1 ( Table S2 ), confirming this cluster as plasma cells ( Todd et al., 2009 ).

summary:
In Homo sapiens, plasma cells (B_c05-MZB1-XBP1) are marked by high expression of XBP1, POU2AF1, PRDM1, and IRF4.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:e8948d42637d07563780
claim_id: claim:e8948d42637d07563780
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
Plasmablast cells (B_c06_MKI67), characterized by high expression of MKI67 and thus indicating a proliferative state, were elevated in the peripheral blood of severe COVID-19 patients and shared the most clonotypes with plasma cells ( Figures S2 B and S2C).

summary:
In Homo sapiens, plasmablast cells (B_c06_MKI67) are characterized by high expression of MKI67, indicating a proliferative state.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:8690c5656b89de86382c
claim_id: claim:8690c5656b89de86382c
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
The memory B cell cluster (B_c03-CD27-AIM2), expressing relatively high levels of CD27 , CD80 , AIM2 , GRIP2 , and COCH , was the second major source of plasma B cells and shared a large proportion of clonotypes with plasma cells and plasmablasts ( Figure S2 B).

summary:
In Homo sapiens, memory B cells (B_c03-CD27-AIM2) express relatively high levels of CD27, CD80, AIM2, GRIP2, and COCH.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:fd408f91e6fb09bc6c4b
claim_id: claim:fd408f91e6fb09bc6c4b
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
Two proliferative CD4 + T cell clusters were identified, with T_CD4_c13-MKI67-CCL5 low characterized by high SELL and low CCL5 and T_CD4_c14-MKI67-CCL5 high characterized by low SELL and high CCL5 , among others ( Table S2 ).

summary:
In Homo sapiens, proliferative CD4-positive T cell cluster T_CD4_c13-MKI67-CCL5 low is characterized by high SELL and low CCL5.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:224f535fc17c5827939b
claim_id: claim:224f535fc17c5827939b
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
Two proliferative CD4 + T cell clusters were identified, with T_CD4_c13-MKI67-CCL5 low characterized by high SELL and low CCL5 and T_CD4_c14-MKI67-CCL5 high characterized by low SELL and high CCL5 , among others ( Table S2 ).

summary:
In Homo sapiens, proliferative CD4-positive T cell cluster T_CD4_c14-MKI67-CCL5 high is characterized by low SELL and high CCL5.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:4a1430e31652cbb13e25
claim_id: claim:4a1430e31652cbb13e25
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
T_CD8_c10-MKI67-GZMK, a proliferative effector memory CD8 + T cell group characterized by high STMN1 , HMGB2 , MKI67 , and GZMK , was increased in severe COVID-19 patients, particularly in the convalescence stage ( Figure 2 G).

summary:
In Homo sapiens, proliferative effector memory CD8-positive T cell group T_CD8_c10-MKI67-GZMK is characterized by high expression of STMN1, HMGB2, MKI67, and GZMK.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:9af5855220d1fcb447c9
claim_id: claim:9af5855220d1fcb447c9
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
The significantly decreased T cell clusters included γδT cells (T_c14_gdT-TRDV2) and mucosal-associated invariant T (MAIT) cells (T_CD8_c09-SLC4A10); a CD8 + T cell cluster highly expressing TYROBP , KLRF1 , CD247 , and IL2RB (T_CD8_c08-IL2RB); and three CD4 + T cell clusters showing effector memory characteristics ( Figure 2 A).

summary:
In Homo sapiens, CD8-positive T cell cluster T_CD8_c08-IL2RB highly expresses TYROBP, KLRF1, CD247, and IL2RB.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:ee51b261e27cbd20981f
claim_id: claim:ee51b261e27cbd20981f
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
summary: In Homo sapiens, B cells are identified by expression of MS4A1, CD79A, and CD79B.
span_literal:
In total, we identified 6 major cell types including B cells ( MS4A1 , CD79A , CD79B ), myeloid cells ( CST3 , LYZ ), NK cells ( GNLY , NKG7 , TYROBP ), epithelial cells ( KRT18 , KRT19 ), CD4 and CD8 T cells ( CD3D , CD3E , CD3G , CD40LG , CD8A , CD8B ).


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:cd0aa4ac5ce6cbd3da57
claim_id: claim:cd0aa4ac5ce6cbd3da57
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
summary: In Homo sapiens, megakaryocytes highly express the cell-type identity marker gene PPBP.
span_literal:
Although the inflammatory megakaryocytes highly expressed cell-type identity marker genes such as PPBP ( Zhang et al., 1997 ), the expression level of these genes was decreased in patients compared to healthy controls, indicating a loss of function of these cells after inflammatory activation ( Figures 6 E and 6G).


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:cef046cbd79fdc6466c7
claim_id: claim:cef046cbd79fdc6466c7
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
Notably, the T_CD8_c06-TNF subtype specifically and highly expressed IFNG , a pro-inflammatory cytokine highly enriched in patients at the progression (severe) stage, was also confirmed by plasma cytokine detection ( Figures 6 E, 6G, and S7 F).

summary:
In Homo sapiens, the CD8-positive T cell subtype T_CD8_c06-TNF specifically and highly expresses IFNG.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:be6a390d9bbc4dec9899
claim_id: claim:be6a390d9bbc4dec9899
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
summary: In Homo sapiens, monocyte subtype Mono_c1-CD14-CCL3 highly expresses CCL3, IL1RN, and TNF.
span_literal:
Mono_c1-CD14-CCL3 highly expressed CCL3 , IL1RN , and TNF , which were detected at much higher levels in plasma in another cohort of patients at the severe stage, especially critically ill patients ( Figures 6 E and S7 F).


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:613cdd647ee2bc3f5186
claim_id: claim:613cdd647ee2bc3f5186
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal: Macro_c2-CCL3L1 specifically expressed CCL8 , CXCL10/11 , and IL6 .
summary:
In Homo sapiens, macrophage subtype Macro_c2-CCL3L1 specifically expresses CCL8, CXCL10/11, and IL6.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:232b18ddaa80dd95f0c7
claim_id: claim:232b18ddaa80dd95f0c7
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
Mono_c1-CD14-CCL3, as one of the most notable pro-inflammatory cell types in both peripheral blood and BALF, uniquely expressed high levels of IL1B , CCL20 , CXCL2 , CXCL3 , CCL3 , CCL4 , HBEGF , and TNF .

summary:
In Homo sapiens, monocyte subtype Mono_c1-CD14-CCL3 uniquely expresses high levels of IL1B, CCL20, CXCL2, CXCL3, CCL3, CCL4, HBEGF, and TNF.


claim_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82:claim:0afb9bf445ab5baf67f6
claim_id: claim:0afb9bf445ab5baf67f6
paper_key: hca:0076_10.1016_j.cell.2021.01.053_e0734afb82
span_literal:
Neutrophils also showed multiple uniquely expressed cytokines, including TNFSF13B , CXCL8 , FTH1 , and CXCL16 ( Figure 7 C).

summary:
In Homo sapiens, neutrophils uniquely express cytokines including TNFSF13B, CXCL8, FTH1, and CXCL16.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:faf284b9b1380dadd87e
claim_id: claim:faf284b9b1380dadd87e
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
As the stem cells of the airway epithelium, basal cells ( TP63 + / KRT5 + ) preferentially differentiate into secretory cells that further differentiate into ciliated cells

summary:
In Homo sapiens, basal cells of the airway epithelium are marked by positive expression of TP63 and KRT5.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:edf0f9cf082c86764489
claim_id: claim:edf0f9cf082c86764489
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
In particular, nrMa showed a highly inflammatory profile characterized by the expression of the chemokine encoding genes CCL2 (encoding MCP1) , CCL3 (encoding MIP1α) , CCL20, CXCL1 and CXCL3 and the pro-inflammatory cytokines IL1B, IL8, IL18 and TNF .

summary:
In Homo sapiens, non-resident macrophages showed a highly inflammatory profile characterized by expression of CCL2, CCL3, CCL20, CXCL1, CXCL3, IL1B, IL8, IL18 and TNF.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:1ed46b6e5419242dc5a0
claim_id: claim:1ed46b6e5419242dc5a0
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
moMa were mainly characterized by CCL2, CCL3 and CXCL10 expression, with higher CCL3 expression levels in the patients with critical COVID-19

summary:
In Homo sapiens, monocyte-derived macrophages were mainly characterized by CCL2, CCL3 and CXCL10 expression.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:b7dcf15977751faea702
claim_id: claim:b7dcf15977751faea702
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
In the patients with moderate COVID-19, CTL displayed the characteristic transcriptional profile of anti-viral CD8 + T lymphocytes with high expression of IFNG , TNF , CCL5 and PRF1 (encoding perforin) and GZMB and GZMA (encoding granzymes) together with genes encoding for cytotoxic receptors ( KLRB1 , KLRC1 and KLRD1 )

summary:
In Homo sapiens, cytotoxic T lymphocytes displayed the characteristic transcriptional profile of anti-viral CD8-positive T lymphocytes with high expression of IFNG, TNF, CCL5, PRF1, GZMB, GZMA, KLRB1, KLRC1 and KLRD1.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:091c2b41ca5db4ed6439
claim_id: claim:091c2b41ca5db4ed6439
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
Within the immune cell population, we also found NK cells ( NCAM1 , FCGR3A and KLRD1 ), distinguishable from the NKT population as they were missing the canonical T cell markers.

summary:
In Homo sapiens, natural killer cells are marked by NCAM1, FCGR3A and KLRD1, distinguishable from the natural killer T cell population.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:72f5a3c4accd538dc28d
claim_id: claim:72f5a3c4accd538dc28d
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
summary: In Homo sapiens, plasma cells are marked by expression of CD27, SDC1 and CD79A.
span_literal:
In addition, proliferating NKT as described previously 65 and plasma cells ( CD27 , SDC1 and CD79A ) were observed.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:cfcf9c50d3785c68cfcc
claim_id: claim:cfcf9c50d3785c68cfcc
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
we identified a cell type from the most posterior region of the nasopharynx that we call ‘squamous’ cells that is characterized by a strong expression of SPRR genes essential to squamous cell cornification

summary:
In Homo sapiens, squamous cells from the nasopharynx are characterized by strong expression of SPRR genes.


claim_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835:claim:4089254546e8b059b5b0
claim_id: claim:4089254546e8b059b5b0
paper_key: hca:0077_10.1038_s41587-020-0602-4_e82c5c2835
span_literal:
we show an inflammatory FCN1 + macrophage phenotype in patients with critical COVID-19, which shares similarities with our nrMa population.

summary:
In Homo sapiens, non-resident macrophages display an inflammatory phenotype marked by FCN1 expression in patients with critical COVID-19.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:f3af8ec0f3c8e932192a
claim_id: claim:f3af8ec0f3c8e932192a
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
span_literal:
One subset corresponded to a previously described AT2 to AT1 transitional cell state ( KRT8 + pre-alveolar type (PATS) 1 transitional cell state (PATS/ADI/DATP) 20 – 22 ( Fig. 2b ).

summary:
In Homo sapiens, the pre-alveolar type 1 transitional cell state (PATS/ADI/DATP) is marked by KRT8 expression in the lung.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:e59a36c087221995710f
claim_id: claim:e59a36c087221995710f
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
span_literal:
A subset of PATS program cells, distinct from KRT5 + /TP63 + airway basal cells, expressed canonical ( KRT8/CLDN4/CDKN1A ) and non-canonical ( KRT5/TP63/KRT17 ) PATS markers ( Fig. 2f , Extended Data Fig. 5d , Supplementary Information Table 3 ).

summary:
In Homo sapiens, pre-alveolar type 1 transitional cell state cells express canonical markers KRT8, CLDN4, and CDKN1A and non-canonical markers KRT5, TP63, and KRT17.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:9fd1019f2659dd825522
claim_id: claim:9fd1019f2659dd825522
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
summary: In Homo sapiens, plasmablasts are marked by JCHAIN expression in the lung.
span_literal:
BLIMP-1 high plasma cells 16 , 17 ; BLIMP-1 intermediate plasma cells; B cells; and, JCHAIN -expressing plasmablasts ( Extended Data Fig. 2k , 4b )


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:549588e73b71047609b6
claim_id: claim:549588e73b71047609b6
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
span_literal:
CD14 high CD16 h igh inflammatory monocytes with antimicrobial properties, and five macrophage subsets ( Extended Data Fig. 2j , 4b ) enriched for scavenger receptors, toll-like receptor ligands, inflammatory transcriptional regulators, or metabolism genes

summary:
In Homo sapiens, inflammatory monocytes are marked by high CD14 and high CD16 expression in the lung.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:6ae3bb0a9a463bbae0a3
claim_id: claim:6ae3bb0a9a463bbae0a3
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
summary: In Homo sapiens, FOXP4 has significant expression specificity in alveolar type 1 cells in the lung.
span_literal:
21 had significant (FDR < 0.05) expression specificity in at least one lung cell type, including FOXP4 (chr 6, AT1 and AT2 cells), and CCR1 and CCRL2 (chr 3, macrophages) ( Extended Data Fig. 12e , Supplementary Information Table 11 )


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:4d72a5cd84d9e77a6246
claim_id: claim:4d72a5cd84d9e77a6246
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
span_literal:
18 were differentially expressed (FDR<0.05) in COVID-19 vs . healthy lung ( e.g. , SLC6A20 in goblet cells, CCR5 in CD8 T cells and T regs , and CCR1 in macrophage and CD16 monocytes, ( Extended Data Fig. 12f , Supplementary Information Table 11 ).

summary:
In Homo sapiens, SLC6A20 is differentially expressed in goblet cells in COVID-19 versus healthy lung.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:7af785dc0f18dae0fb97
claim_id: claim:7af785dc0f18dae0fb97
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
span_literal:
18 were differentially expressed (FDR<0.05) in COVID-19 vs . healthy lung ( e.g. , SLC6A20 in goblet cells, CCR5 in CD8 T cells and T regs , and CCR1 in macrophage and CD16 monocytes, ( Extended Data Fig. 12f , Supplementary Information Table 11 ).

summary:
In Homo sapiens, CCR5 is differentially expressed in regulatory T cells in COVID-19 versus healthy lung.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:ff7e6f5a3b5eb5b03329
claim_id: claim:ff7e6f5a3b5eb5b03329
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
summary:
In Homo sapiens, CCR1 is differentially expressed in CD16 monocytes in COVID-19 versus healthy lung.


claim_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b:claim:9050a67d9a2246f5dde3
claim_id: claim:9050a67d9a2246f5dde3
paper_key: hca:0078_10.1038_s41586-021-03570-8_93e4f0be8b
span_literal:
Myeloid cells were the cell category most enriched for SARS-CoV-2 RNA (158 cells following correction for ambient RNA, FDR<0.012, Fig. 3a , Extended Data Fig. 6w – y , Methods ), with particular enrichment in CD 14 high CD 16 high inflammatory monocytes (FDR<0.005) and LDB2 high OSMR high YAP1 high macrophages (FDR<0.02, Extended Data Fig. 6x , 7a , b ), although enrichment scores in individual donors varied.

summary:
In Homo sapiens, LDB2, OSMR, and YAP1 are markers of a macrophage subset enriched for SARS-CoV-2 RNA in the lung.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:5f60ff8fa8cd7ab03361
claim_id: claim:5f60ff8fa8cd7ab03361
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
chromatin accessibility and gene expression of atrial and ventricular cardiomyocyte markers such as NPPA and MYH7

summary:
In Homo sapiens, NPPA and MYH7 are markers of atrial and ventricular cardiomyocytes, respectively, used to classify cardiomyocyte subtypes in the human heart.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:1a2282a179dcb7fcc959
claim_id: claim:1a2282a179dcb7fcc959
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
we found strong enrichment of the binding motif for the macrophage transcription factor SPI1/PU.1 ( 36 ) in macrophage-specific cCREs, and SPI1 was exclusively expressed in macrophages

summary:
In Homo sapiens, SPI1 (also known as PU.1) is exclusively expressed in macrophages in the human heart.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:5449191003beb6e35841
claim_id: claim:5449191003beb6e35841
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
summary: In Homo sapiens, endothelial cells in the heart express GATA2 and GATA6.
span_literal:
endothelial cells and cardiac fibroblasts expressed GATA2 and GATA6 , respectively, whereas cardiomyocytes expressed both GATA4 and GATA6 and endocardial cells expressed GATA2 , GATA4 , and GATA6


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:5366174859dfe3abdc1b
claim_id: claim:5366174859dfe3abdc1b
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
both genes were primarily expressed in cardiac fibroblasts (fig. S7F and table S4), and LUM has been reported to exhibit increased expression in failing hearts compared to control hearts

summary:
In Homo sapiens, lumican (LUM) and decorin (DCN) are primarily expressed in cardiac fibroblasts in the heart.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:54bcc92143afac4d08c0
claim_id: claim:54bcc92143afac4d08c0
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
summary: In Homo sapiens, IRX4 is primarily expressed in cardiomyocytes of the left ventricle.
span_literal:
IRX4 ( Fig. 4D ), which encodes a ventricle-specific transcription factor ( 43 ) and is primarily expressed in cardiomyocytes of the left ventricle


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:5b347bf40e2c4fb2239b
claim_id: claim:5b347bf40e2c4fb2239b
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal: KCNH2 was primarily expressed in ventricular and atrial cardiomyocytes in the adult human heart
summary:
In Homo sapiens, KCNH2 is primarily expressed in ventricular and atrial cardiomyocytes in the adult heart.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:433e1d1dcbfe5eb5c907
claim_id: claim:433e1d1dcbfe5eb5c907
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
We annotated atrial and ventricular cardiomyocytes on the basis of differential chromatin accessibility and gene expression at NPPA , MYH6 , KCNJ3 , MYL7 , MYH7 , HEY2 , MYL2 , and other reported markers of atrial and ventricular cardiomyocytes

summary:
In Homo sapiens, atrial and ventricular cardiomyocytes are annotated using markers NPPA, MYH6, KCNJ3, MYL7, MYH7, HEY2, and MYL2.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:2f1096272e3c2cc619ae
claim_id: claim:2f1096272e3c2cc619ae
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
NRXN3 and GPM6B for a cluster of nervous cells with neuronal and Schwann-like gene expression and chromatin accessibility signatures

summary:
In Homo sapiens, NRXN3 and GPM6B are used as markers to annotate nervous cells with neuronal and Schwann-like signatures in the heart.


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:38c8799803ebf0c91ab2
claim_id: claim:38c8799803ebf0c91ab2
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
summary: In Homo sapiens, NRG3 and NPR3 are specific markers of endocardial cells in the heart.
span_literal:
we identified a population of endothelial-like cells with specific expression of endocardial cell markers NRG3 and NPR3


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:e6100d00a43ec5c04eaa
claim_id: claim:e6100d00a43ec5c04eaa
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
We also identified subtypes of mesenchymal cells that included myofibroblasts with characteristic expression of embryonic smooth muscle actin MYH10

summary:
In Homo sapiens, myofibroblasts in the heart are characterized by expression of MYH10 (embryonic smooth muscle actin).


claim_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed:claim:bd56c24fc113120c89fb
claim_id: claim:bd56c24fc113120c89fb
paper_key: hca:0080_10.1126_sciadv.abf1444_8cb053b6ed
span_literal:
arterial smooth muscle cells with preferential expression of ACTA2 and TAGLN relative to a larger cluster of pericytes

summary:
In Homo sapiens, arterial smooth muscle cells in the heart show preferential expression of ACTA2 and TAGLN relative to pericytes.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:eedd95b0811ca1555198
claim_id: claim:eedd95b0811ca1555198
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
We found three clear photoreceptor clusters: rods, which selectively express rhodopsin; S-cones, which selectively express S-opsin; and M and L cones, which selectively express and M or L-opsin

summary:
In Homo sapiens retina, rod photoreceptors selectively express rhodopsin (RHO), S-cones selectively express S-opsin, and M and L cones selectively express M or L-opsin.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:15af32128fbb7315cd67
claim_id: claim:15af32128fbb7315cd67
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
Similar to macaque H1 and H2, human H1 and H2 were distinguished from each other by selectively expressing transcription factors LHX1 and ISL1 , respectively

summary:
In Homo sapiens retina, horizontal cell type H1 selectively expresses the transcription factor LHX1, distinguishing it from horizontal cell type H2.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:116a16bffe3633a261df
claim_id: claim:116a16bffe3633a261df
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
Similar to macaque H1 and H2, human H1 and H2 were distinguished from each other by selectively expressing transcription factors LHX1 and ISL1 , respectively

summary:
In Homo sapiens retina, horizontal cell type H2 selectively expresses the transcription factor ISL1, distinguishing it from horizontal cell type H1.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:6d30636c2bdda7875c33
claim_id: claim:6d30636c2bdda7875c33
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
ON and OFF bipolars are characterized by expression of genes that encode the metabotropic glutamate receptor 6, GRM6 , and the kainate-type glutamate receptor, GRIK1 , respectively; rod bipolars are distinguished from cone bipolars by expression of PKCα , encoding protein kinase C α

summary:
In Homo sapiens retina, ON bipolar cells are characterized by expression of metabotropic glutamate receptor 6 (GRM6), OFF bipolar cells by GRIK1, and rod bipolar cells are distinguished from cone bipolar cells by expression of protein kinase C alpha (PKCα).


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:17066f159cadddf50412
claim_id: claim:17066f159cadddf50412
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
ON and OFF bipolars are characterized by expression of genes that encode the metabotropic glutamate receptor 6, GRM6 , and the kainate-type glutamate receptor, GRIK1 , respectively; rod bipolars are distinguished from cone bipolars by expression of PKCα , encoding protein kinase C α

summary:
In Homo sapiens retina, OFF bipolar cells are characterized by expression of the kainate-type glutamate receptor GRIK1.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:87d0cb3c1ea60b5c5ae1
claim_id: claim:87d0cb3c1ea60b5c5ae1
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
ON and OFF bipolars are characterized by expression of genes that encode the metabotropic glutamate receptor 6, GRM6 , and the kainate-type glutamate receptor, GRIK1 , respectively; rod bipolars are distinguished from cone bipolars by expression of PKCα , encoding protein kinase C α

summary:
In Homo sapiens retina, rod bipolar cells are distinguished from cone bipolar cells by expression of protein kinase C alpha (PKCα).


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:0a491c442cdc6cae52f4
claim_id: claim:0a491c442cdc6cae52f4
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
By assessing the expression of marker genes for GABAergic (glutamate carboxylase, GAD1 and GAD2 ) and glycinergic ( SLC6A9 , encoding the high affinity glycine transporter GLYT1) amacrines

summary:
In Homo sapiens retina, GABAergic amacrine cells are marked by expression of glutamate decarboxylase GAD1 and GAD2, while glycinergic amacrine cells are marked by SLC6A9 encoding the high affinity glycine transporter GLYT1.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:54fa522b63bb0f2d6361
claim_id: claim:54fa522b63bb0f2d6361
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
By assessing the expression of marker genes for GABAergic (glutamate carboxylase, GAD1 and GAD2 ) and glycinergic ( SLC6A9 , encoding the high affinity glycine transporter GLYT1) amacrines

summary:
In Homo sapiens retina, glycinergic amacrine cells are marked by expression of SLC6A9 encoding the high affinity glycine transporter GLYT1.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:4d7f7fccb4ab4fca45d8
claim_id: claim:4d7f7fccb4ab4fca45d8
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
summary: In Homo sapiens retina, VG3 amacrine cells are marked by SLC17A8.
span_literal:
Several known amacrine types were detected based on key marker genes (Fig. 3d ), including SLC17A8 for VG3 amacrine (an excitatory type that co-releases glycine and glutamate), SLC18A3 for cholinergic starburst amacrines, TH for catecholaminergic CAI/CAII amacrines, and GJD2 for AII amacrines, which mediate transmission of rod signals to RGCs.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:31125da0150f8f490b50
claim_id: claim:31125da0150f8f490b50
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: NPW in C7
summary:
In Homo sapiens retina, amacrine cell type C7 predominantly expresses the neuropeptide NPW, and amacrine cell type C24 predominantly expresses VIP.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:319ad21345d44ae40719
claim_id: claim:319ad21345d44ae40719
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: TRH ) and Natriuretic Peptide B ( NPPB ) in C9
summary:
In Homo sapiens retina, amacrine cell type C9 expresses thyrotropin-releasing hormone (TRH) and Natriuretic Peptide B (NPPB).


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:2c882e98a010a8fcff54
claim_id: claim:2c882e98a010a8fcff54
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: PENK ) and Cholecystokinin ( CCK ) in C15
summary:
In Homo sapiens retina, amacrine cell type C15 expresses Proenkephalin (PENK) and Cholecystokinin (CCK).


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:fb8721ed5a6784e3260d
claim_id: claim:fb8721ed5a6784e3260d
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: FOXP2 (hRGC6
summary:
In Homo sapiens retina, retinal ganglion cell types hRGC6 and hRGC7 express the transcription factor FOXP2, and one of them also expresses FOXP1.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:02af8f800e9ba23eef8d
claim_id: claim:02af8f800e9ba23eef8d
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: FOXP2 (hRGC6 and 7), one of which also expressed FOXP1
summary:
In Homo sapiens retina, retinal ganglion cell type hRGC7 expresses the transcription factors FOXP2 and FOXP1.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:54b92c17443e126f117d
claim_id: claim:54b92c17443e126f117d
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: OPN4 in mice 27 ; others could be included in hRGC5
summary:
In Homo sapiens retina, intrinsically photosensitive retinal ganglion cells (hRGC5 and hRGC12) express melanopsin (OPN4).


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:000887191a9026fc6e8e
claim_id: claim:000887191a9026fc6e8e
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: OPN4 ), the canonical marker of intrinsically photosensitive RGCs (ipRGCs; hRGC5 and hRGC12
summary:
In Homo sapiens retina, intrinsically photosensitive retinal ganglion cell hRGC12 expresses melanopsin (OPN4).


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:334968b2dd6a42e990d7
claim_id: claim:334968b2dd6a42e990d7
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
RBPMS2 was expressed by human but not macaque midget RGCs, while the canonical markers, RBPMS and SLC17A6 (VGLUT2) were expressed by most or all RGCs in both species

summary:
In Homo sapiens retina, RBPMS2 is expressed by midget retinal ganglion cells but not by macaque midget retinal ganglion cells, while RBPMS and SLC17A6 (VGLUT2) are expressed by most or all retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:ca027c0235dfccd452c8
claim_id: claim:ca027c0235dfccd452c8
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
RBPMS2 was expressed by human but not macaque midget RGCs, while the canonical markers, RBPMS and SLC17A6 (VGLUT2) were expressed by most or all RGCs in both species

summary:
In Homo sapiens retina, the canonical markers RBPMS and SLC17A6 (VGLUT2) are expressed by most or all retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:fc92dd1d49778f36e2e0
claim_id: claim:fc92dd1d49778f36e2e0
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
SCGN (green) does not label any CHX10-positive BCs (magenta) in human retina (top two panels), but does label a subset of BCs in macaque retina (bottom two panels).

summary:
In Homo sapiens retina, SCGN does not label any bipolar cells, in contrast to macaque retina where it labels a subset of bipolar cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:5d10b5e988591ef52506
claim_id: claim:5d10b5e988591ef52506
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: HTRA1 , a major susceptibility gene for neovascular AMD 5 , was expressed at high levels in HCs
summary:
In Homo sapiens retina, HTRA1, a major susceptibility gene for neovascular age-related macular degeneration, is expressed at high levels in horizontal cells and Müller glia.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:94d42b92ae29adf2f3b0
claim_id: claim:94d42b92ae29adf2f3b0
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
HTRA1 , a major susceptibility gene for neovascular AMD 5 , was expressed at high levels in HCs and Müller glia

summary:
In Homo sapiens retina, HTRA1, a major susceptibility gene for neovascular age-related macular degeneration, is expressed at high levels in Müller glia.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:5643d2ec468e05dee158
claim_id: claim:5643d2ec468e05dee158
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: EFEMP1 selectively in Müller Glia and TIMP3 selectively in vascular endothelium
summary:
In Homo sapiens retina, EFEMP1 is selectively expressed in Müller glia and TIMP3 is selectively expressed in vascular endothelial cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:4439654ff5edf05f776c
claim_id: claim:4439654ff5edf05f776c
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: OPA1 and OPA3 were predominantly expressed in RGCs
summary:
In Homo sapiens retina, autosomal dominant optic atrophy causative genes OPA1 and OPA3 are predominantly expressed in retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:f58b02c2ddcaa5413f53
claim_id: claim:f58b02c2ddcaa5413f53
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
summary: In Homo sapiens retina, NDP and LRP5 are expressed in Müller glia and in astrocytes.
span_literal:
In addition, however, NDP and LRP5 were also expressed in Müller glia 41 and in astrocytes, a finding compatible with observations of NDP expression in a subset of cortical astrocytes


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:716a7885fe60d842d301
claim_id: claim:716a7885fe60d842d301
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: HS6ST3 45 , DPP10 46 , and VEGFB , were almost exclusively expressed in RGCs
summary:
In Homo sapiens retina, HS6ST3, DPP10, and VEGFB are almost exclusively expressed in retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:b2c242de3a1bf67fe931
claim_id: claim:b2c242de3a1bf67fe931
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
For example, PHGDH and PSPH , encoding enzymes involved in L-serine synthesis, were selectively expressed in RGCs with PHGDH also expressed in Müller glia.

summary:
In Homo sapiens retina, PHGDH and PSPH, encoding enzymes involved in L-serine synthesis, are selectively expressed in retinal ganglion cells, with PHGDH also expressed in Müller glia.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:7878edd171681551cdd5
claim_id: claim:7878edd171681551cdd5
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: RGCs (e.g., OPTN, TMCO1, TBK1
summary:
In Homo sapiens retina, glaucoma-implicated genes OPTN, TMCO1, and TBK1 are expressed predominantly within retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:97dedb06c574332dca2d
claim_id: claim:97dedb06c574332dca2d
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal:
Genes with type-specific RGC expression patterns included the glaucoma-associated genes SIX6 , which was enriched in midget ganglion cells; CAV2 and POU6F2 enriched in ON parasol RGCs and AFAP1 , enriched in peripheral ON parasol RGCs.

summary:
In Homo sapiens retina, the glaucoma-associated gene SIX6 is enriched in midget retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:28e266d61a9b05e8ef9b
claim_id: claim:28e266d61a9b05e8ef9b
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: POU6F2 was expressed at highest levels in RGC types 5, 11 and 12, which include ipRGCs.
summary:
In Homo sapiens retina, POU6F2 is expressed at highest levels in retinal ganglion cell types 5, 11, and 12, which include intrinsically photosensitive retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:2aad7a4bafc4a71ac2f9
claim_id: claim:2aad7a4bafc4a71ac2f9
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: rods (e.g., GNAT1, SLC24A1
summary:
In Homo sapiens retina, congenital stationary night blindness genes GNAT1 and SLC24A1 are expressed in rod photoreceptors, while GRM6 and TRPM1 are expressed in bipolar cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:8cb6476b6d627027c183
claim_id: claim:8cb6476b6d627027c183
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: bipolar cells (e.g., GRM6, TRPM1
summary:
In Homo sapiens retina, congenital stationary night blindness genes GRM6 and TRPM1 are expressed in bipolar cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:7c35695f9e28b52460ce
claim_id: claim:7c35695f9e28b52460ce
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: FABP4 by human but not macaque OFF parasol RGCs
summary:
In Homo sapiens retina, FABP4 is expressed by OFF parasol retinal ganglion cells but not by macaque OFF parasol retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:60bfd135ba9d55172c0a
claim_id: claim:60bfd135ba9d55172c0a
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: RBPMS2 by human but not macaque midget RGCs
summary:
In Homo sapiens retina, RBPMS2 is expressed by midget retinal ganglion cells but not by macaque midget retinal ganglion cells.


claim_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0:claim:06bb9b608bf84f203ab1
claim_id: claim:06bb9b608bf84f203ab1
paper_key: hca:0081_10.1038_s41598-020-66092-9_e23219ced0
span_literal: GPATCH1 and CRHBP by human but not macaque cones
summary:
In Homo sapiens retina, GPATCH1 and CRHBP are expressed by cone photoreceptors but not by macaque cone photoreceptors.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:e454c7b824cfe6d3fc39
claim_id: claim:e454c7b824cfe6d3fc39
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
Magenta, ARR3 antibody (cone marker); green, L/M opsin antibody (cone outer segment marker); white, Hoechst (nucleus marker).

summary:
In Homo sapiens, ARR3 is a positive marker of cone photoreceptor cells, and L/M opsin is a positive marker of cone photoreceptor outer segments in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:c0070308a623e8328399
claim_id: claim:c0070308a623e8328399
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
summary: In Homo sapiens, TRPM1 is a positive marker of ON bipolar cells in the retina.
span_literal:
Magenta, TRPM1 antibody (ON bipolar cell marker); green, GFP antibody (GCaMP6s); white, Hoechst (nucleus marker).


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:ba863dac35f8d4fdfea4
claim_id: claim:ba863dac35f8d4fdfea4
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
summary: In Homo sapiens, RHO and NRL are positive markers of rod photoreceptor cells in the retina.
span_literal:
the expression of rod markers RHO (week 38, 57.4% of rods expressing; week 46, 42.1%; p = 6 × 10 −33 , Mann-Whitney U of normalized transcript counts) and NRL (week 38, 98.4%; week 46, 38.3%; p = 2 × 10 −308 )


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:5a654e71f41c36b7eaa6
claim_id: claim:5a654e71f41c36b7eaa6
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
summary: In Homo sapiens, GJD2 is a positive marker of AII amacrine cells in the retina.
span_literal:
17 types of amacrine cells including glycinergic types (e.g., AII amacrine cells, GJD2 ) and GABAergic types (e.g., starburst amacrine cells, SLC18A3 )


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:1d00c51f1932cba76a65
claim_id: claim:1d00c51f1932cba76a65
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
Magenta, S opsin antibody (blue cone marker); green, L / M opsin antibody (red/green cone marker); white, Hoechst (nucleus marker).

summary:
In Homo sapiens, S opsin is a positive marker of blue (S) cone photoreceptor cells and L/M opsin is a positive marker of red/green (L/M) cone photoreceptor cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:95b08df5c1974e60e44f
claim_id: claim:95b08df5c1974e60e44f
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
Magenta, S opsin antibody (blue cone marker); green, L / M opsin antibody (red/green cone marker); white, Hoechst (nucleus marker).

summary:
In Homo sapiens, L/M opsin is a positive marker of red/green (L/M) cone photoreceptor cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:abd55f2c5282e32dad82
claim_id: claim:abd55f2c5282e32dad82
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal: ON bipolar cell types not expressing cell type marker PCP2 .
summary:
In Homo sapiens, PCP2 is a positive marker of certain ON bipolar cell types in the retina, while some ON bipolar cell types do not express PCP2.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:e355526a55946e4ae831
claim_id: claim:e355526a55946e4ae831
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
CYP26A1 was expressed in foveal Müller cells and was significantly upregulated relative to the periphery (Mann-Whitney U test, CYP26A1 : 6.3 × upregulated, p = 6 × 10 −176 ).

summary:
In Homo sapiens, CYP26A1 is a positive marker of foveal Müller cells, significantly upregulated relative to peripheral Müller cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:41d5f4956b93db554ea6
claim_id: claim:41d5f4956b93db554ea6
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
ALDH1A3 alone was expressed in pigment epithelial cells, where it was highly upregulated in the periphery relative to the fovea (630 × upregulated, p = 2.5 × 10 −29 ).

summary:
In Homo sapiens, ALDH1A3 is a positive marker of peripheral pigment epithelial cells in the retina, highly upregulated relative to foveal pigment epithelial cells.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:bf04bfd88669467f47b2
claim_id: claim:bf04bfd88669467f47b2
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
Genes associated with type I ( USH1G , USH1C , CDH23 ) and type III ( CLRN1 ) Usher syndromes which had no consensus for the cell type of origin in the human retina as their expression varies across species ( Mathur and Yang, 2015 ; Sahly et al., 2012 ; Siegert et al., 2012 ) are expressed in Müller cells of the adult peripheral and foveal retina and developed organoids.

summary:
In Homo sapiens, USH1G, USH1C, CDH23, and CLRN1 are positive markers of Müller cells in the adult peripheral and foveal retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:cb5281a18887973e92b3
claim_id: claim:cb5281a18887973e92b3
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
Magenta, COL2A1 (peripheral Müller cell marker); Green, RLBP1, (Müller cell marker); White, DAPI (nucleus marker).

summary:
In Homo sapiens, COL2A1 is a positive marker of peripheral Müller cells and RLBP1 is a positive marker of Müller cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:9aa457158d9e2f1f42a4
claim_id: claim:9aa457158d9e2f1f42a4
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
The main periphery-specific genes in Müller cells included ATP1A2 , COL2A1 , KCNK1 , and MT3 and in pigment epithelial cells TFPI2 , FXYD3 , and GAP43 .

summary:
In Homo sapiens, ATP1A2, COL2A1, KCNK1, and MT3 are positive markers of peripheral Müller cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:790fa1f9e6787e365db4
claim_id: claim:790fa1f9e6787e365db4
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
The main periphery-specific genes in Müller cells included ATP1A2 , COL2A1 , KCNK1 , and MT3 and in pigment epithelial cells TFPI2 , FXYD3 , and GAP43 .

summary:
In Homo sapiens, TFPI2, FXYD3, and GAP43 are positive markers of peripheral pigment epithelial cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:e1bf214ae038628c65f1
claim_id: claim:e1bf214ae038628c65f1
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
The main fovea-specific genes in Müller cells included FAM237B , RHCG , PMP2 , CYP26A1 , and EFEMP1 and in pigment epithelial cells WFDC1 , CHI3L1 , and CHN1 .

summary:
In Homo sapiens, FAM237B, RHCG, PMP2, CYP26A1, and EFEMP1 are positive markers of foveal Müller cells in the retina.


claim_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef:claim:967e0282667fa5a9399a
claim_id: claim:967e0282667fa5a9399a
paper_key: hca:0082_10.1016_j.cell.2020.08.013_e864ee2cef
span_literal:
The main fovea-specific genes in Müller cells included FAM237B , RHCG , PMP2 , CYP26A1 , and EFEMP1 and in pigment epithelial cells WFDC1 , CHI3L1 , and CHN1 .

summary:
In Homo sapiens, WFDC1, CHI3L1, and CHN1 are positive markers of foveal pigment epithelial cells in the retina.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:228445696decbca3f725
claim_id: claim:228445696decbca3f725
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
These 28,758 MHCII + cells comprised distinct clusters of IL3RA + plasmacytoid DCs (pDCs), CLEC9A + cDC1s, and FCGR3A + nonclassical monocytes, as well as a central supercluster

summary:
In Homo sapiens intestinal lamina propria, plasmacytoid dendritic cells express IL3RA, conventional type 1 dendritic cells express CLEC9A, and nonclassical monocytes express FCGR3A.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:ae57c48bdf48de7a8672
claim_id: claim:ae57c48bdf48de7a8672
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
summary: In Homo sapiens intestinal lamina propria, monocytes are associated with S100A8 expression.
span_literal:
Cells in distinct regions of this supercluster expressed the monocyte-associated marker S100A8 , the macrophage-associated marker C1QA , CSFR1 or the cDC2-associated marker CD1C , and FLT3


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:7d654d19bb13105c47af
claim_id: claim:7d654d19bb13105c47af
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cells in distinct regions of this supercluster expressed the monocyte-associated marker S100A8 , the macrophage-associated marker C1QA , CSFR1 or the cDC2-associated marker CD1C , and FLT3

summary:
In Homo sapiens intestinal lamina propria, conventional type 2 dendritic cells are associated with CD1C and FLT3 expression.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:3d2b7b6b4f480416c32f
claim_id: claim:3d2b7b6b4f480416c32f
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal: Clusters 1 to 3 expressed the classical monocyte transcription factor (TF) ZBTB16
summary:
In Homo sapiens intestinal lamina propria, classical monocytes express the transcription factor ZBTB16.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:17385852423149257ac4
claim_id: claim:17385852423149257ac4
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
summary: In Homo sapiens intestinal lamina propria, mature macrophages express SEPP1, MERTK, MAF, and ID3.
span_literal:
clusters 15 to 20 expressed high levels of genes associated with mature macrophages, such as SEPP1 , MERTK , and MAF , together with TFs involved in tissue-resident macrophage development such as ID3


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:bbee88e38dc63b54c5db
claim_id: claim:bbee88e38dc63b54c5db
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
clusters 21 to 35 expressed low levels of monocyte- and macrophage-associated genes and high levels of the cDC2-associated genes AP1S3 , FLT3 , SEPT6 , and IRF4

summary:
In Homo sapiens intestinal lamina propria, conventional type 2 dendritic cells express the associated genes AP1S3, FLT3, SEPT6, and IRF4.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:832a041632a1f2bf66df
claim_id: claim:832a041632a1f2bf66df
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
clusters 36 to 39 expressed both cDC2-associated genes, including FLT3 , IRF4 , and CD1C , and mono/mac-associated genes, including CD14 , CD163 , MERTK , S100A9 , and C5AR1 (CD88), albeit at lower levels than observed in the mono/mac clusters

summary:
In Homo sapiens intestinal lamina propria, dendritic cell type 3 cells express FLT3, IRF4, CD1C, CD14, CD163, MERTK, S100A9, and C5AR1.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:8c4dd78f842a44242782
claim_id: claim:8c4dd78f842a44242782
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cluster M1, located at one end of the tSPACE ( Fig. 2A and movie S1), expressed the highest levels of the monocyte-associated genes S100A8 , S100A9 , FCN1 , and VCAN

summary:
In Homo sapiens intestinal lamina propria, monocytes (cluster M1) express the highest levels of S100A8, S100A9, FCN1, and VCAN.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:cc4072e0edd06a78ae13
claim_id: claim:cc4072e0edd06a78ae13
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cluster M6 differentially expressed 1482 genes compared with cluster M7 or M8 (fig. S2C and data file S1), including genes encoding the C-type lectins CLEC7A and CLEC12A, as well as TNFSF10 that encodes tumor necrosis factor (TNF)–related apoptosis-inducing ligand

summary:
In Homo sapiens intestinal lamina propria, macrophage subset M6 differentially expresses CLEC7A, CLEC12A, and TNFSF10.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:19b4cdaa76dcf93c203c
claim_id: claim:19b4cdaa76dcf93c203c
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cluster M7 differentially expressed 1034 genes compared with either cluster M6 or M8 (fig. S2C and data file S1), including several chemokines and the tissue repair and angiogenesis-associated genes VEGFA , PDGFB , and PTGS2 encoding cyclooxygenase-2

summary:
In Homo sapiens intestinal lamina propria, macrophage subset M7 differentially expresses VEGFA, PDGFB, and PTGS2.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:232f4cc55673c4df9e1c
claim_id: claim:232f4cc55673c4df9e1c
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal: cluster M7 lacked expression of the submucosal macrophage markers COLEC12 ( 18 ) and MARCO
summary:
In Homo sapiens intestinal lamina propria, macrophage subset M7 lacks expression of the submucosal macrophage markers COLEC12 and MARCO.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:72159b03d16b5910e5db
claim_id: claim:72159b03d16b5910e5db
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cluster M8 expressed 1140 genes at significantly higher levels than cluster M6 or M7, including the metalloprotease MMP12 ; LGALS3 that encodes galectin-3; and the lipid metabolism–associated genes PLA2G7 , LIPA , and APOC1

summary:
In Homo sapiens intestinal lamina propria, macrophage subset M8 expresses MMP12, LGALS3, PLA2G7, LIPA, and APOC1 at higher levels than macrophage subsets M6 and M7.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:0c0b9c1509f90eebe678
claim_id: claim:0c0b9c1509f90eebe678
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cluster M8 also expressed high levels of ACP5 , a marker of differentiated macrophages locate at the tip of human colonic crypts

summary:
In Homo sapiens, macrophage subset M8 expresses high levels of ACP5, a marker of differentiated macrophages at the tip of colonic crypts.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:66b0fb7c3135b8d3ad2d
claim_id: claim:66b0fb7c3135b8d3ad2d
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
we first analyzed expression of the canonical cDC1 signature genes CLEC9A , CADM1 , XCR1 , BATF3 , and IRF8 , identifying seven clusters with a distinct cDC1 signature score

summary:
In Homo sapiens intestinal lamina propria, conventional type 1 dendritic cells are identified by the canonical signature genes CLEC9A, CADM1, XCR1, BATF3, and IRF8.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:2327afe1903431d60cba
claim_id: claim:2327afe1903431d60cba
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
We also identified a minor population of LAMP3 + cDCs, which expressed high levels of the maturation markers CCR7 and CD40

summary:
In Homo sapiens intestinal lamina propria, LAMP3-positive conventional dendritic cells express high levels of the maturation markers CCR7 and CD40.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:46070a41a41d2d0f51fb
claim_id: claim:46070a41a41d2d0f51fb
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
the top DEGs for the cDC1 cluster included CLEC9A , CADM1 , and ID2 ; the cDC2 cluster expressed high levels of IRF4 , PLAC8 , and CCL22 ; and the DC3 cluster expressed high levels of C1QA , S100A9 , and CD163

summary:
In Homo sapiens intestinal lamina propria, conventional type 1 dendritic cells are marked by CLEC9A, CADM1, and ID2; conventional type 2 dendritic cells express IRF4, PLAC8, and CCL22; and dendritic cell type 3 cells express C1QA, S100A9, and CD163.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:e4c8b01fbd3c074b095b
claim_id: claim:e4c8b01fbd3c074b095b
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
the top DEGs for the cDC1 cluster included CLEC9A , CADM1 , and ID2 ; the cDC2 cluster expressed high levels of IRF4 , PLAC8 , and CCL22 ; and the DC3 cluster expressed high levels of C1QA , S100A9 , and CD163

summary:
In Homo sapiens intestinal lamina propria, conventional type 2 dendritic cells express high levels of IRF4, PLAC8, and CCL22.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:586b65cad15c9249f70e
claim_id: claim:586b65cad15c9249f70e
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
the top DEGs for the cDC1 cluster included CLEC9A , CADM1 , and ID2 ; the cDC2 cluster expressed high levels of IRF4 , PLAC8 , and CCL22 ; and the DC3 cluster expressed high levels of C1QA , S100A9 , and CD163

summary:
In Homo sapiens intestinal lamina propria, dendritic cell type 3 cells express high levels of C1QA, S100A9, and CD163.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:1330964c1ff0219693d1
claim_id: claim:1330964c1ff0219693d1
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
In addition to classical cDC1-associated TFs such as IRF8 , ID2 , and BATF3 , ileal and colonic cDC1s differentially expressed several other TFs including ZEB1

summary:
In Homo sapiens intestinal lamina propria, conventional type 1 dendritic cells express the transcription factors IRF8, ID2, BATF3, and ZEB1.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:0d3430250af85b63762f
claim_id: claim:0d3430250af85b63762f
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
In addition to the cDC2-associated TF IRF4 , cDC2s selectively expressed the Notch pathway gene HES4 and NR4A3 , implicated in cDC activation

summary:
In Homo sapiens intestinal lamina propria, conventional type 2 dendritic cells selectively express IRF4, HES4, and NR4A3.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:951ce3b96ba1462bb0cd
claim_id: claim:951ce3b96ba1462bb0cd
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
As expected, DC3s expressed the highest levels of macrophage-associated TFs, including MAF , MAFB , MAFF , and ZBTB16 , and also the inhibitory TFs NFKBIA and NFKBIZ

summary:
In Homo sapiens intestinal lamina propria, dendritic cell type 3 cells express the highest levels of MAF, MAFB, MAFF, ZBTB16, NFKBIA, and NFKBIZ.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:50d6f4f69234f4a74a67
claim_id: claim:50d6f4f69234f4a74a67
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal: Ambiguous cells expressed the highest levels of KLF4
summary:
In Homo sapiens intestinal lamina propria, ambiguous dendritic cells express the highest levels of KLF4.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:db93f273563d43726616
claim_id: claim:db93f273563d43726616
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cytokines and chemokines were also expressed in a cDC subset–specific manner including high levels of the TNF family members TNF and TNFSF11 (RANK-L) among cDC1s, high levels of CCL19 , CCL22 , and EBI3 among cDC2s, and a wide range of cytokines and chemokines by DC3s

summary:
In Homo sapiens intestinal lamina propria, conventional type 1 dendritic cells express high levels of TNF and TNFSF11.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:79d49858f0c774fe2a7c
claim_id: claim:79d49858f0c774fe2a7c
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
Cytokines and chemokines were also expressed in a cDC subset–specific manner including high levels of the TNF family members TNF and TNFSF11 (RANK-L) among cDC1s, high levels of CCL19 , CCL22 , and EBI3 among cDC2s, and a wide range of cytokines and chemokines by DC3s

summary:
In Homo sapiens intestinal lamina propria, conventional type 2 dendritic cells express high levels of CCL19, CCL22, and EBI3.


claim_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c:claim:85c81d3aa444ca821f26
claim_id: claim:85c81d3aa444ca821f26
paper_key: hca:0083_10.1126_sciimmunol.adz8650_c0046d094c
span_literal:
CCR7 + cDCs differed in their expression of >5000 genes compared with total CCR7 − DCs, including increased expression of the lysosomal gene LAMP3 , maturation markers, and the inhibitory molecules CD273 (encoding PD-L2) and CD274 (encoding PD-L1)

summary:
In Homo sapiens intestinal lamina propria, CCR7-positive conventional dendritic cells show increased expression of LAMP3, CD273, and CD274 compared with CCR7-negative dendritic cells.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:6b9425619d46fbf80d45
claim_id: claim:6b9425619d46fbf80d45
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
We identify CD24 as a marker that distinguishes GALT from other intestinal FB and demonstrate that CD24 + FB consist of distinct subsets that locate within discrete niches.

summary:
In Homo sapiens, CD24 is a positive marker that distinguishes gut-associated lymphoid tissue fibroblasts from other intestinal fibroblasts.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:620a8763b4b1ab4200c5
claim_id: claim:620a8763b4b1ab4200c5
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Cluster 1 expressed transcripts encoding for the chemokines CCL19 , CCL21 , and CXCL13 , the secreted chaperone clusterin ( CLU ), and CD74 , the major histocompatibility complex II (MHCII) invariant chain, all genes previously associated with human ( De Martin et al., 2023 ; Mourcin et al., 2021 ; Verbrugghe et al., 2008 ) and murine ( Cheng et al., 2019 , 2022 ; Prados et al., 2021 ; Rodda et al., 2018 ) FRC, as well as putative FRC-like FB in the human intestine ( Kinchen et al., 2018 ).

summary:
In Homo sapiens, fibroblastic reticular cells express CCL19, CCL21, CXCL13, clusterin (CLU), and CD74.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:f44f4e5b28dac676de95
claim_id: claim:f44f4e5b28dac676de95
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Cluster 1 also expressed the MHCII genes HLA-DRA and HLA-DRB1 as top DEG ( Fig. 1 E and Table S2 ), similar to FRC in murine LN that also express MHCII ( Baptista et al., 2014 ; Nadafi et al., 2020 ; Shaikh et al., 2022 ).

summary:
In Homo sapiens, fibroblastic reticular cells express the major histocompatibility complex class II genes HLA-DRA and HLA-DRB1.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:4b9bc3929fa4b8dbf3ca
claim_id: claim:4b9bc3929fa4b8dbf3ca
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
summary: In Homo sapiens, lamina propria fibroblasts express ADAMDEC1, CCL8, CCL11, and CCL13.
span_literal:
Cluster 2 expressed transcripts encoding the matrix metalloprotease ADAMDEC1 and the chemokines CCL8 , CCL11 , and CCL13 ( Fig. 1, D and E ; and Table S2 ), known markers of LP FB ( Kinchen et al., 2018 ; Martin et al., 2019 ).


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:799ae0dbcfca3ea24ac7
claim_id: claim:799ae0dbcfca3ea24ac7
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
summary: In Homo sapiens, adventitial-type fibroblasts express CD34, PTGS2, and PI16.
span_literal:
Cluster 3 expressed CD34 , PTGS2 , and PI16 ( Fig. 1, D and E ; and Table S2 ), markers previously associated with adventitial-type FB ( Buechler et al., 2021 ; Gong et al., 2022 ; Korsunsky et al., 2022 ; Sitnik et al., 2016 )


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:5237506b4e3eee0e7d37
claim_id: claim:5237506b4e3eee0e7d37
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
summary: In Homo sapiens, subepithelial fibroblasts express F3 (tissue factor).
span_literal:
cluster 4 expressed the cell surface glycoprotein F3 (tissue factor) and genes associated with the Wnt/BMP signaling pathway ( Fig. 1, D and E ; and Table S2 ), previously associated with subepithelial FB (SE-FB) ( Kinchen et al., 2018 ; Smillie et al., 2019 ).


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:6adf5079659a61a4c32d
claim_id: claim:6adf5079659a61a4c32d
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
CD24 (heat stable antigen) was identified as a marker for FB cluster 1, matrix metalloprotease-encoding gene ADAMDEC1 for FB cluster 2, CD34 for FB cluster 3, and F3 for FB cluster 4 ( Fig. 2 A ).

summary:
In Homo sapiens, CD24 is a marker for fibroblastic reticular cells (cluster 1), ADAMDEC1 for lamina propria fibroblasts (cluster 2), CD34 for adventitial-type fibroblasts (cluster 3), and F3 for subepithelial fibroblasts (cluster 4).


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:6efb4205dfd6463b0b38
claim_id: claim:6efb4205dfd6463b0b38
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
PDPN + CD24 + FB were selectively located throughout ileal and large intestinal GALT but were absent from surrounding LP or SM ( Fig. 2 D and Fig. S2 C ), indicating that CD24 is selectively expressed on GALT FRC.

summary:
In Homo sapiens, CD24 is selectively expressed on gut-associated lymphoid tissue fibroblastic reticular cells.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:9b1d0b4caae2561332cd
claim_id: claim:9b1d0b4caae2561332cd
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
FRC subcluster 1 expressed high levels of the T cell chemoattractants CCL19 , CCL21 , and the T cell survival factor IL7 and the cytokine IL6 ( Fig. 3 D ), reminiscent of TRC present in murine secondary lymphoid tissues ( Brown et al., 2019 ; Kapoor et al., 2021 ; Pezoldt et al., 2018 ; Prados et al., 2021 ; Rodda et al., 2018 ) and human tonsils ( De Martin et al., 2023 ; Mourcin et al., 2021 ).

summary:
In Homo sapiens, T cell zone reticular cells (fibroblastic reticular cell subcluster 1) express high levels of CCL19, CCL21, IL7, and IL6.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:bebff4a73a6552552072
claim_id: claim:bebff4a73a6552552072
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Subcluster 2 expressed the B cell chemoattractant CXCL13 , but not the complement receptors CR1 / CR2 indicative for FDC, and expressed lower levels of CCL19 and CCL21 ( Fig. 3 D ), suggesting that these cells represented TBRC ( Lütge et al., 2023 ; Pikor et al., 2020 ).

summary:
In Homo sapiens, T/B border reticular cells (subcluster 2) express CXCL13 but not the complement receptors CR1 and CR2, distinguishing them from follicular dendritic cells.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:ff6ccab813a237ca3554
claim_id: claim:ff6ccab813a237ca3554
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Subcluster 3 expressed the highest levels of the myeloid chemoattractant CXCL14 ( Fig. 3 D ), previously associated with a subepithelial location in mice ( Muhl et al., 2020 ) and humans ( Elmentaite et al., 2021 ; Kinchen et al., 2018 ), TCF21 ( Fig. 3 D ), a marker of SED-FB in mice ( Ding et al., 2020 ), and the oxysterol synthesizing enzyme CH25H ( Fig. 3 D ), produced by FRC in the outer follicle and interfollicular areas of murine secondary lymphoid tissues ( Rodda et al., 2018 ).

summary:
In Homo sapiens, subepithelial dome fibroblastic reticular cells (subcluster 3) express the highest levels of CXCL14, as well as TCF21 and CH25H.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:bba123c2a3386e0b39b0
claim_id: claim:bba123c2a3386e0b39b0
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Subcluster 4 expressed the highest levels of CXCL13 and the FDC-associated genes CR2 and FDCSP ( Fig. 3 D )

summary:
In Homo sapiens, follicular dendritic cells (subcluster 4) express the highest levels of CXCL13 and the follicular dendritic cell-associated genes CR2 and FDCSP.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:f2a0a31b91b696a89faa
claim_id: claim:f2a0a31b91b696a89faa
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
subcluster 5 expressed interferon-stimulated genes including GBP4 , GBP5 ( Tretina et al., 2019 ), CXCL9 , and CXCL10 ( Tokunaga et al., 2018 ) ( Fig. 3 D )

summary:
In Homo sapiens, CXCL9+ CXCL10+ fibroblastic reticular cells (subcluster 5) express interferon-stimulated genes including GBP4, GBP5, CXCL9, and CXCL10.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:cfeda9d260395b77a7da
claim_id: claim:cfeda9d260395b77a7da
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
subcluster 6, while expressing the GALT FRC-associated markers CD24 and CLU ( Fig. 3 C ), also expressed high levels of the SE-FB–associated markers F3, AGT , and POSTN ( Fig. 1, D and E ; Fig. 3 D ; and Table S2 [ Kinchen et al., 2018 ]), as well as the MRC-associated marker TNFSF11 ( Fig. 3 D ) ( Nagashima et al., 2017 ; Prados et al., 2021 ).

summary:
In Homo sapiens, marginal reticular cells (subcluster 6) express the gut-associated lymphoid tissue fibroblastic reticular cell markers CD24 and CLU, the subepithelial fibroblast markers F3, AGT, and POSTN, and the marginal reticular cell marker TNFSF11.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:1da3143bc65305415fb1
claim_id: claim:1da3143bc65305415fb1
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
summary: In Homo sapiens, T cell zone reticular cells are CCL19-positive fibroblastic reticular cells.
span_literal:
Considering our scRNA-seq and immunohistochemical analyses, we identified the CCL19 + FRC subcluster 1 as TRC, the CXCL13 + CR1 − /2 − FRC subcluster 2 as TBRC, the CXCL14 + FRC subcluster 3 as SED-FRC, the CXCL13 + CR1 + /2 + FRC subcluster 4 as FDC, the CXCL9 + CXCL10 + FRC subcluster 5 as CXCL9 + CXCL10 + FRC, and the F3 + TNFSF11 + FRC subcluster 6 as MRC ( Fig. 3 F ).


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:b2e18b0c8aa668dd1278
claim_id: claim:b2e18b0c8aa668dd1278
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Considering our scRNA-seq and immunohistochemical analyses, we identified the CCL19 + FRC subcluster 1 as TRC, the CXCL13 + CR1 − /2 − FRC subcluster 2 as TBRC, the CXCL14 + FRC subcluster 3 as SED-FRC, the CXCL13 + CR1 + /2 + FRC subcluster 4 as FDC, the CXCL9 + CXCL10 + FRC subcluster 5 as CXCL9 + CXCL10 + FRC, and the F3 + TNFSF11 + FRC subcluster 6 as MRC ( Fig. 3 F ).

summary:
In Homo sapiens, T/B border reticular cells are CXCL13-positive, CR1-negative, CR2-negative fibroblastic reticular cells.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:6f23b17816b217acf69b
claim_id: claim:6f23b17816b217acf69b
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
summary:
In Homo sapiens, follicular dendritic cells are CXCL13-positive, CR1-positive, CR2-positive fibroblastic reticular cells.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:147c0b9fbf45d252d499
claim_id: claim:147c0b9fbf45d252d499
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
summary:
In Homo sapiens, marginal reticular cells are F3-positive and TNFSF11-positive fibroblastic reticular cells.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:5175523c2bd6e1b9e8ed
claim_id: claim:5175523c2bd6e1b9e8ed
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Notably, CD24 expression overlapped with TRC and BRC/FDC in both tonsils and cervical LN ( Fig. 6 B and Fig. S5 C ), as well as with interfollicular and medullary FB within cervical LN ( Fig. 6 B and Fig. S5 C ), that also express CCL19 , CCL21 , and CLU ( Lütge et al., 2025 ).

summary:
In Homo sapiens, CD24 expression overlaps with T cell zone reticular cells and B cell zone reticular cells/follicular dendritic cells in tonsils and cervical lymph nodes, as well as with interfollicular and medullary fibroblasts that also express CCL19, CCL21, and CLU.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:145140fba4ab9266cb8b
claim_id: claim:145140fba4ab9266cb8b
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Notably, CD24 expression overlapped with TRC and BRC/FDC in both tonsils and cervical LN ( Fig. 6 B and Fig. S5 C ), as well as with interfollicular and medullary FB within cervical LN ( Fig. 6 B and Fig. S5 C ), that also express CCL19 , CCL21 , and CLU ( Lütge et al., 2025 ).

summary:
In Homo sapiens, CD24 expression overlaps with follicular dendritic cells in tonsils and cervical lymph nodes.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:3ae53aef6d448311409b
claim_id: claim:3ae53aef6d448311409b
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Notably, CD24 expression overlapped with TRC and BRC/FDC in both tonsils and cervical LN ( Fig. 6 B and Fig. S5 C ), as well as with interfollicular and medullary FB within cervical LN ( Fig. 6 B and Fig. S5 C ), that also express CCL19 , CCL21 , and CLU ( Lütge et al., 2025 ).

summary:
In Homo sapiens, interfollicular and medullary fibroblasts in cervical lymph nodes express CD24, CCL19, CCL21, and CLU.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:ea8f31daac71530a7ba6
claim_id: claim:ea8f31daac71530a7ba6
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Collectively, these results indicate that human GALT, LN, and tonsils harbor partially overlapping, but also distinct, FRC clusters, and that CD24 serves as a marker of lymphoid tissue FRC across multiple human secondary lymphoid tissues.

summary:
In Homo sapiens, CD24 serves as a marker of lymphoid tissue fibroblastic reticular cells across multiple secondary lymphoid tissues.


claim_key: hca:0084_10.1084_jem.20250471_14ff4cfa40:claim:244889642695c3567ce9
claim_id: claim:244889642695c3567ce9
paper_key: hca:0084_10.1084_jem.20250471_14ff4cfa40
span_literal:
Our study identified the GPI-anchored sialoglycoprotein CD24 ( Altevogt et al., 2021 ) as a novel marker that distinguished GALT FRC from other intestinal FB populations.

summary:
In Homo sapiens, CD24 is a novel marker that distinguishes gut-associated lymphoid tissue fibroblastic reticular cells from other intestinal fibroblast populations.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:a59629a4c34c0e461d10
claim_id: claim:a59629a4c34c0e461d10
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal: Among corneal epithelial clusters, defined by a high expression of PAX6 , KRT12 , and TACSTD2
summary:
In Homo sapiens, corneal epithelial cells are defined by high expression of PAX6, KRT12, and TACSTD2.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:5ec8e73a5c1173850d7e
claim_id: claim:5ec8e73a5c1173850d7e
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, corneal basal epithelial cells are characterized by enriched expression of LAMA3.
span_literal:
The basal cluster was characterized by an enriched expression of extracellular matrix (ECM)- and adhesion-related genes including LAMA3


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:608870f471617ab29fa4
claim_id: claim:608870f471617ab29fa4
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
The transit amplifying cells were distinguished from committed basal cells by selective expression of the cell proliferation marker MKI67 and other genes involved in DNA replication and cell division including BIRC5 , UBE2C , and TOP2A

summary:
In Homo sapiens, transit amplifying cells are distinguished from committed basal cells by selective expression of MKI67, BIRC5, UBE2C, and TOP2A.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:ea2ad873b471f5dd0be7
claim_id: claim:ea2ad873b471f5dd0be7
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
The superficial-most squamous epithelial cells were characterized by the expression of multiple keratins ( KRT4 , KRT24 , KRT78 ) and mucins ( MUC4 , MUC16 , MUC21 , MUC22 ), as well as BCAS1

summary:
In Homo sapiens, corneal superficial squamous epithelial cells are characterized by expression of KRT4, KRT24, KRT78, MUC4, MUC16, MUC21, MUC22, and BCAS1.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:7165908f0df5c19fe99a
claim_id: claim:7165908f0df5c19fe99a
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, corneal wing cells are characterized by higher levels of KRT3 expression.
span_literal:
The middle layer wing cells were characterized by higher levels of KRT3 expression and graded expression of multiple genes, representing the transitional state between basal and superficial cells


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:8cf663b4a28f223b378c
claim_id: claim:8cf663b4a28f223b378c
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Two other clusters corresponded to the corneal endothelium ( CA3 ; Fig. 1 F and L ) and corneal stromal keratocytes ( ANGPTL7 ; Fig. 1 F and K ).

summary:
In Homo sapiens, corneal endothelium is marked by CA3 and corneal stromal keratocytes are marked by ANGPTL7.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:5bfce82a4ea10e148110
claim_id: claim:5bfce82a4ea10e148110
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
the small cluster of immune cells contained both macrophages (likely corneal dendritic cells) and lymphocytes; DE genes within the cluster included PTPRC / CD45 , CYTIP , FYB1 , ELMO , and lymphocyte- associated marker IKZF1

summary:
In Homo sapiens, corneal immune cells express PTPRC, CYTIP, FYB1, ELMO, and the lymphocyte-associated marker IKZF1.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:7be77733f708449bfa20
claim_id: claim:7be77733f708449bfa20
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Those with robust KRT12 , KRT3 , and/or KRT24 expression were corneal, whereas those with KRT15 , KRT14 , KRT13 , and/or KRT7 expression were conjunctival or limbal

summary:
In Homo sapiens, corneal epithelial cells express KRT12, KRT3, and KRT24, whereas conjunctival or limbal epithelial cells express KRT15, KRT14, KRT13, and KRT7.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:c188eed1887198d00846
claim_id: claim:c188eed1887198d00846
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
The three conjunctival clusters were all positive for IGFBP3 , previously shown to be specific to conjunctival epithelium; among them, we identified basal (e.g., KRT14 + PDGFC +), superficial (e.g., KRT7 + LCN2 + WFDC2 + ENTPD2 +), and wing clusters (e.g., KRT13 + KRT15 + BCAS1 + RARRES1 +)

summary:
In Homo sapiens, conjunctival epithelial cells are positive for IGFBP3; conjunctival basal cells express KRT14 and PDGFC; conjunctival superficial cells express KRT7, LCN2, WFDC2, and ENTPD2; and conjunctival wing cells express KRT13, KRT15, BCAS1, and RARRES1.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:2281a5dfa1f80950ea74
claim_id: claim:2281a5dfa1f80950ea74
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Superficial limbal epithelial cells were distinguished and confirmed histologically as WFDC2 - ENTPD1 + BCAS1 + RARRES1 +

summary:
In Homo sapiens, superficial limbal epithelial cells are WFDC2 negative and ENTPD1, BCAS1, and RARRES1 positive.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:67df0b6176c268c5c378
claim_id: claim:67df0b6176c268c5c378
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Limbal basal cells were KRT15 + KRT12 − GJB6 −, whereas limbal wing cells were KRT15 + KRT12 + GJB6 +, consistent with prior reports

summary:
In Homo sapiens, limbal basal cells are KRT15 positive, KRT12 negative, and GJB6 negative, whereas limbal wing cells are KRT15 positive, KRT12 positive, and GJB6 positive.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:da83e544f5805023baae
claim_id: claim:da83e544f5805023baae
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
corneal basal epithelial cells were strongly NTRK2 positive, whereas those in the conjunctiva were NTRK2 negative but PDGFC and LGR6 positive

summary:
In Homo sapiens, corneal basal epithelial cells are NTRK2 positive, whereas conjunctival basal epithelial cells are NTRK2 negative but PDGFC and LGR6 positive.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:80baf2f75e93b4bff36f
claim_id: claim:80baf2f75e93b4bff36f
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
corneal basal epithelial cells were strongly NTRK2 positive, whereas those in the conjunctiva were NTRK2 negative but PDGFC and LGR6 positive

summary:
In Homo sapiens, conjunctival basal epithelial cells are NTRK2 negative but PDGFC and LGR6 positive.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:f8591ee2f4f2e6fe7a18
claim_id: claim:f8591ee2f4f2e6fe7a18
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, goblet cells of the ocular surface are identified by enrichment of MUC5AC.
span_literal:
A distinct cluster corresponding to the specialized, mucin-producing goblet cells of the ocular surface was identified based on enrichment of MUC5AC


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:51afd9edf974eedea88e
claim_id: claim:51afd9edf974eedea88e
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, goblet cells in the conjunctival epithelium also express ATP2C2, AGR3, and TFF1.
span_literal:
This cluster was visualized within the conjunctival epithelium and also expressed ATP2C2 , AGR3 , and TFF1 .


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:13de2ff816dc8aa65051
claim_id: claim:13de2ff816dc8aa65051
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, melanocytes share canonical markers PAX3, TYR, and MITF.
span_literal:
They shared canonical melanocyte markers, such as PAX3 , TYR , and MITF , but were transcriptionally distinct


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:8a469a36f8121e0bf73a
claim_id: claim:8a469a36f8121e0bf73a
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, uveal melanocytes selectively express ERBB4, NRG3, and MET.
span_literal:
The uveal type, derived from both the TM and CSW, represented melanocytes in the ciliary muscle and selectively expressed ERBB4 , NRG3 , and MET


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:a456868f326fde3299e4
claim_id: claim:a456868f326fde3299e4
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, conjunctival melanocytes selectively express LEF1, PLPPR4, and KIT.
span_literal:
the conjunctival type, derived exclusively from the CSW, represented melanocytes nestled among the basal epithelial cells of the conjunctiva and selectively expressed LEF1 , PLPPR4 , and KIT


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:89bb74efd81f24ccf83c
claim_id: claim:89bb74efd81f24ccf83c
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
For example, MYOC , CEMIP , CDH23 , SLC4A10 , FAM155A , KCNIP1 , PDE1C , ADAM12 , MICAL2 , and LMX1B were among the top 20 DE genes for the TM cluster

summary:
In Homo sapiens, trabecular meshwork fibroblasts have MYOC, CEMIP, CDH23, SLC4A10, FAM155A, KCNIP1, PDE1C, ADAM12, MICAL2, and LMX1B among their top differentially expressed genes.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:0fd19352cba94f59f7ed
claim_id: claim:0fd19352cba94f59f7ed
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
whereas BMP5 , EYA1 , BICC1 , DCN , APOD , KCNT2 , ABCA8 , IGFBP5 , DYNC1I1 , and MGP were for the uveal cluster

summary:
In Homo sapiens, uveal fibroblasts have BMP5, EYA1, BICC1, DCN, APOD, KCNT2, ABCA8, IGFBP5, DYNC1I1, and MGP among their top differentially expressed genes.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:3d18128b9c15db37254e
claim_id: claim:3d18128b9c15db37254e
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
we identified one as Schlemm canal endothelium expressing FN1 and PLAT and a second as vascular endothelium, expressing ALPL

summary:
In Homo sapiens, Schlemm canal endothelium expresses FN1 and PLAT, and vascular endothelium expresses ALPL.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:554bb2d1b8222f7bf930
claim_id: claim:554bb2d1b8222f7bf930
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, collector channel and venous endothelium expresses ACKR1, AQP1, SELE, and COL15A1.
span_literal:
A third corresponded to endothelium lining the collector channels, aqueous veins, and scleral venous plexuses, expressing ACKR1/DARC , AQP1 , SELE , and COL15A1


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:fe36230db8a6151e5fca
claim_id: claim:fe36230db8a6151e5fca
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
The fourth endothelial cluster selectively expressed lymphatic markers including LYVE1 , PROX1 , CCL21 , and FLT4 and was localized to subepithelial vessels within the conjunctival stroma using immunostaining against PDPN

summary:
In Homo sapiens, conjunctival lymphatic endothelium selectively expresses LYVE1, PROX1, CCL21, and FLT4.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:abd8665fc295d67b5f23
claim_id: claim:abd8665fc295d67b5f23
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Seven additional clusters were identified as pericytes ( NOTCH3 and PDGFRB ), macrophages ( LYVE1 + CD163 +), lymphocytes ( CD69 +), mast cells ( IL1RL1 + CPA3 +), ciliary muscle cells ( DES and CHRM3 ), Schwann cells ( LGI4 and CDH19 ), corneal stromal fibroblasts ( KERA and MME ), and scleral fibroblasts ( TXNB , FBLN1 ).

summary:
In Homo sapiens, pericytes express NOTCH3 and PDGFRB, macrophages express LYVE1 and CD163, lymphocytes express CD69, mast cells express IL1RL1 and CPA3, ciliary muscle cells express DES and CHRM3, Schwann cells express LGI4 and CDH19, corneal stromal fibroblasts express KERA and MME, and scleral fibroblasts express TXNB and FBLN1.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:f08df966982eb0bde2cd
claim_id: claim:f08df966982eb0bde2cd
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, FibroX cells exhibit distinct markers EBF2 and SHISA6.
span_literal:
An eighth cluster, provisionally labeled FibroX, was transcriptomically similar to scleral fibroblasts but exhibited distinct markers such as EBF2 and SHISA6


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:474c7eb1a46f06b4ea67
claim_id: claim:474c7eb1a46f06b4ea67
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, iris stromal fibroblasts express DCN, APOD, MYOC, RARRES1, and PDPN.
span_literal:
Iris stromal fibroblasts, expressing DCN , APOD , MYOC , RARRES1 , and PDPN , were identified in the stroma and anterior border layer of the iris via immunostaining against PDPN


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:93f6fa65bff6db944c35
claim_id: claim:93f6fa65bff6db944c35
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, iris melanocytes selectively express PAX3, EDNRB, MITF, MLANA, MLPH, and TYR.
span_literal:
The melanocytes were identified through their selective expression of melanocyte marker PAX3 , as well as EDNRB , MITF , MLANA , MLPH , and TYR


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:0cfca9605fac9703842c
claim_id: claim:0cfca9605fac9703842c
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Smooth muscle cells comprising the iris sphincter muscle, responsible for constricting the pupil upon cholinergic stimulation, were identified by selective expression of the muscarinic receptor CHRM3 , as well as DES

summary:
In Homo sapiens, iris sphincter smooth muscle cells are identified by selective expression of CHRM3 and DES.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:d24767a2fa20b030b0d5
claim_id: claim:d24767a2fa20b030b0d5
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
The iris dilator muscle, responsible for dilating the pupil upon adrenergic stimulation, selectively expressed the alpha-1a adrenergic receptor ADRA1A

summary:
In Homo sapiens, iris dilator muscle cells selectively express the alpha-1a adrenergic receptor ADRA1A.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:6df3fbf302ff281f3e7b
claim_id: claim:6df3fbf302ff281f3e7b
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
DE genes in the PCE included ATP6V1C2 , encoding the H + vacuolar ATPase; SLC23A2 , encoding a sodium-dependent ascorbate transporter; and SLC4A4 , encoding the sodium-bicarbonate cotransporter (NBC)

summary:
In Homo sapiens, pigmented ciliary epithelium differentially expresses ATP6V1C2, SLC23A2, and SLC4A4.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:35008d7a4b0dc67d2c45
claim_id: claim:35008d7a4b0dc67d2c45
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Other DE genes included MAMDC1 , CCBE1 , DCT , and numerous additional solute transporters ( SLC35G1 , SLC38A11 , SLC24A5 , SLC9B2 , SLC7A2 , and SLC7A6 ), consistent with the PCE’s role alongside the NPCE in secreting aqueous humor.

summary:
In Homo sapiens, pigmented ciliary epithelium differentially expresses MAMDC1, CCBE1, DCT, SLC35G1, SLC38A11, SLC24A5, SLC9B2, SLC7A2, and SLC7A6.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:8085e4ae6ea48df56c78
claim_id: claim:8085e4ae6ea48df56c78
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
DE genes that distinguished NPCE from PCE included the vitreous humor components, COL9A1 , COL9A3 , and OPTC , reflecting the NPCE’s close association with this gel ( 28 ), as well as ATP1A2 , NECTIN3 , CACNA1E , ENPP2 , and the chloride transporter BEST2

summary:
In Homo sapiens, nonpigmented ciliary epithelium is distinguished from pigmented ciliary epithelium by expression of COL9A1, COL9A3, OPTC, ATP1A2, NECTIN3, CACNA1E, ENPP2, and BEST2.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:0d8c86bc4deb2ba8f44a
claim_id: claim:0d8c86bc4deb2ba8f44a
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
They included DES and MYH11 for muscle, DCN and PDPN for fibroblasts ( Fig. 3 K ), LGI4 and SCN7A for Schwann cells, MLANA for melanocytes ( Fig. 3 L ), PECAM1 for vascular endothelium ( Fig. 3 K ), ADCY3 for pericytes, CD163 for macrophages, and CD96 for lymphocytes

summary:
In Homo sapiens ciliary body, muscle cells express DES and MYH11, fibroblasts express DCN and PDPN, Schwann cells express LGI4 and SCN7A, melanocytes express MLANA, vascular endothelium expresses PECAM1, pericytes express ADCY3, macrophages express CD163, and lymphocytes express CD96.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:4cc84cb59557447602dd
claim_id: claim:4cc84cb59557447602dd
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Four clusters of vessel endothelial cells were identified through the expression of the canonical marker PECAM1

summary:
In Homo sapiens, vessel endothelial cells are identified through expression of the canonical marker PECAM1.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:bcd57ac10d1fde355e62
claim_id: claim:bcd57ac10d1fde355e62
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, pericytes are identified by shared expression of PDGFRB, ADCY3, JAG1, and NOTCH3.
span_literal:
Two distinct pericyte clusters were identified by the shared expression of PDGFRB , ADCY3 , JAG1 , and NOTCH3


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:460067f3202f36b0d747
claim_id: claim:460067f3202f36b0d747
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Pericyte1 ( LAMA2 +, TRPC4 +) was derived mostly from TM and CB, whereas Pericyte2 ( ID4 +, TRPC6 +, RGS6 +) was derived almost exclusively from the CSW

summary:
In Homo sapiens, Pericyte1 expresses LAMA2 and TRPC4, whereas Pericyte2 expresses ID4, TRPC6, and RGS6.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:e21d61fc704b91112da7
claim_id: claim:e21d61fc704b91112da7
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, fibroblasts express diagnostic genes PDGFRA, COL6A3, DCN, PRRX1, and CDH11.
span_literal:
Six transcriptomically related clusters expressed genes diagnostic of fibroblasts (e.g., PDGFRA , COL6A3 , DCN , PRRX1 , CDH11


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:24ece09a6e6b42b772fd
claim_id: claim:24ece09a6e6b42b772fd
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Three of the fibroblast clusters—iris, ciliary, and TM fibroblasts—were closely related and shared numerous markers (e.g., MYOC , PDPN , and RSPO2 ).

summary:
In Homo sapiens, iris, ciliary, and trabecular meshwork fibroblasts share markers MYOC, PDPN, and RSPO2.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:ccb5e6bcd2fc3078aa66
claim_id: claim:ccb5e6bcd2fc3078aa66
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Three of the fibroblast clusters—iris, ciliary, and TM fibroblasts—were closely related and shared numerous markers (e.g., MYOC , PDPN , and RSPO2 ).

summary:
In Homo sapiens, ciliary fibroblasts share markers MYOC, PDPN, and RSPO2 with iris and trabecular meshwork fibroblasts.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:5b420c701fdeddf7b44c
claim_id: claim:5b420c701fdeddf7b44c
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
Three of the fibroblast clusters—iris, ciliary, and TM fibroblasts—were closely related and shared numerous markers (e.g., MYOC , PDPN , and RSPO2 ).

summary:
In Homo sapiens, trabecular meshwork fibroblasts share markers MYOC, PDPN, and RSPO2 with iris and ciliary fibroblasts.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:8b4307a5b74365ac0f41
claim_id: claim:8b4307a5b74365ac0f41
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
WIF1 and ETNPPL for iris fibroblasts; BMP5 , PI16 , and C7 for ciliary fibroblasts; and NEB , NELL2 , UNC5D , and TMEM178A for TM fibroblasts

summary:
In Homo sapiens, iris fibroblasts selectively express WIF1 and ETNPPL, ciliary fibroblasts selectively express BMP5, PI16, and C7, and trabecular meshwork fibroblasts selectively express NEB, NELL2, UNC5D, and TMEM178A.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:913461099b81ad4ba0e5
claim_id: claim:913461099b81ad4ba0e5
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
WIF1 and ETNPPL for iris fibroblasts; BMP5 , PI16 , and C7 for ciliary fibroblasts; and NEB , NELL2 , UNC5D , and TMEM178A for TM fibroblasts

summary:
In Homo sapiens, trabecular meshwork fibroblasts selectively express NEB, NELL2, UNC5D, and TMEM178A.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:79c9bd46e5119072e96e
claim_id: claim:79c9bd46e5119072e96e
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
melanocytes derived from the iris and CB coclustered with the uveal melanocytes ( MET +) identified in the CSW, and these cells remained distinct from the conjunctival melanocytes ( KIT + and LEF1 +)

summary:
In Homo sapiens, uveal melanocytes are MET positive and distinct from conjunctival melanocytes, which are KIT positive and LEF1 positive.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:059c246817fa0a9d1271
claim_id: claim:059c246817fa0a9d1271
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
span_literal:
melanocytes derived from the iris and CB coclustered with the uveal melanocytes ( MET +) identified in the CSW, and these cells remained distinct from the conjunctival melanocytes ( KIT + and LEF1 +)

summary:
In Homo sapiens, conjunctival melanocytes are KIT positive and LEF1 positive, distinct from uveal melanocytes.


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:159204526236664eaf28
claim_id: claim:159204526236664eaf28
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, corneal macrophages express CXCR4 and ITGA4 but not LYVE1 or F13A1.
span_literal:
Macrophages of corneal origin were too few in number to form a distinct cluster but segregated within a discrete zone, demonstrating the expression of CXCR4 and ITGA4 but not LYVE1 or F13A1


claim_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05:claim:eaa1087079ea157128a0
claim_id: claim:eaa1087079ea157128a0
paper_key: hca:0085_10.1073_pnas.2200914119_3dd916fb05
summary: In Homo sapiens, non-corneal macrophages express LYVE1, STAB1, and F13A1.
span_literal:
In contrast, the remainder of the macrophage cluster, which derived from the other tissues, expressed LYVE1 , STAB1 , and F13A1


claim_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189:claim:15831a406b6c94deb854
claim_id: claim:15831a406b6c94deb854
paper_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189
span_literal: GNAT2 is accessible and expressed in developing and mature cones
summary:
In Homo sapiens retina, GNAT2 is accessible and expressed in developing and mature cone photoreceptors.


claim_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189:claim:cc675bda483320641e7d
claim_id: claim:cc675bda483320641e7d
paper_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189
span_literal:
NRL , which is required for rod development, increases drastically in both accessibility and expression over the course of pseudotime during rod development, whereas NOTCH1 , which represses the rod fate, decreases in both accessibility and expression

summary:
In Homo sapiens retina, NRL increases in accessibility and expression during rod photoreceptor development, whereas NOTCH1 decreases in both accessibility and expression in rod photoreceptors.


claim_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189:claim:43d2cf602767abcfab34
claim_id: claim:43d2cf602767abcfab34
paper_key: hca:0088_10.1016_j.devcel.2022.02.018_aeffb1d189
span_literal:
ATOH7 , which is important for RGC survival during development ( Brodie-Kommit et al., 2021 ), exhibits transient increases in accessibility and expression halfway through the course of RGC development

summary:
In Homo sapiens retina, ATOH7 exhibits transient increases in accessibility and expression during retinal ganglion cell development.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:bd3599f2138acda1df7a
claim_id: claim:bd3599f2138acda1df7a
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Cardiomyocytes show high-level expression of genes that encode contractile force-generating sarcomere proteins ( TTN , MYBPC3 and TNNT2 ) and calcium-mediated processes ( RYR2 , PLN and SLC8A1 ).

summary:
In Homo sapiens, cardiomyocytes show high-level expression of TTN, MYBPC3, TNNT2, RYR2, PLN, and SLC8A1.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:1ec712df625fa584a0d2
claim_id: claim:1ec712df625fa584a0d2
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Ventricular cardiomyocytes are enriched in genes encoding sarcomere proteins ( MYH7 and MYL2 ), transcription factors ( IRX3 , IRX5 , IRX6 , MASP1 and HEY2 ), and PRDM16 , mutated in left ventricular non-compaction cardiomyopathy 7 .

summary:
In Homo sapiens, ventricular cardiomyocytes are enriched in MYH7, MYL2, IRX3, IRX5, IRX6, MASP1, HEY2, and PRDM16.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:7875e76b9e4f1452409f
claim_id: claim:7875e76b9e4f1452409f
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, ventricular cardiomyocytes abundantly express PCDH7 and SMYD2.
span_literal:
Other abundant transcripts enable tissue integrity despite high ventricular strain: PCDH7 encodes a calcium-dependent strong adhesive molecule 8 ; SMYD2 encodes a lysine methyltransferase that promotes sarcomere formation and stabilization 9 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:0b0b6074bb0be3242afd
claim_id: claim:0b0b6074bb0be3242afd
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, atrial cardiomyocytes abundantly express ALDH1A2, ROR2, and SYNPR.
span_literal:
Atrial cardiomyocytes abundantly express prototypic genes and also ALDH1A2 , an enzyme required for retinoic acid synthesis, ROR2 , which participates in Wnt signalling during lineage differentiation 10 , and SYNPR , which functions in the mechanosensing of TRP channels by atrial volume receptors 11 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:b5609d41aa94a15f1df0
claim_id: claim:b5609d41aa94a15f1df0
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, ventricular cardiomyocyte 2 shows higher expression of PRELID2.
span_literal:
vCM2 shows higher expression of PRELID2 , a developmental molecule with unknown cardiac function 12 (verified by single-molecule fluorescence in situ hybridization (smFISH) (Fig. 2c , Extended Data Fig. 3c ).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:e3812808e62e4dca5edf
claim_id: claim:e3812808e62e4dca5edf
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Among vCMs, vCM2 has the highest expression of the myosin gene MYH6 and CDH13 , a cell surface T-cadherin receptor for cardioprotective adiponectin and low density lipoproteins, both associated with several cardiometabolic traits 13 .

summary:
In Homo sapiens, ventricular cardiomyocyte 2 has the highest expression of MYH6 and CDH13 among ventricular cardiomyocytes.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:b83c642d49c721e02a43
claim_id: claim:b83c642d49c721e02a43
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, ventricular cardiomyocyte 3 is enriched for MYH9, NEXN, and CNN1.
span_literal:
The vCM3 transcriptional profile resembles a prominent right atrium population (aCM3, discussed below) with retinoic-acid-responsive SMC gene enrichment ( MYH9 , NEXN and CNN1 ) 14 , 15 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:c805be891a38e7cdfdf3
claim_id: claim:c805be891a38e7cdfdf3
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
vCM3 also express stress-response genes including ANKRD1 16 , FHL1 17 (verified by smFISH) (Fig. 2d , Extended Data Fig. 3c ), DUSP27 18 , and XIRP1 and XIRP2 , interacting with intercalated disc ion channel proteins implicated in cardiomyopathy and arrhythmias 19 .

summary:
In Homo sapiens, ventricular cardiomyocyte 3 expresses stress-response genes ANKRD1, FHL1, DUSP27, XIRP1, and XIRP2.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:25c7b1e228d5784de251
claim_id: claim:25c7b1e228d5784de251
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
The small population vCM4 is enriched for nuclear-encoded mitochondrial genes ( NDUFB11 , NDUFA4 , COX7C and COX5B ) and Gene Ontology terms indicative of a high energetic state (Extended Data Fig. 3f ).

summary:
In Homo sapiens, ventricular cardiomyocyte 4 is enriched for nuclear-encoded mitochondrial genes NDUFB11, NDUFA4, COX7C, and COX5B.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:dee563ddf6b16f0de652
claim_id: claim:dee563ddf6b16f0de652
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, ventricular cardiomyocyte 4 demonstrates high levels of CRYAB and PLN.
span_literal:
vCM4 also demonstrates high levels of CRYAB , which encodes a cytoprotective and antioxidant heat shock protein 20 , of sarcomere protein genes and PLN , indicating that these ventricular cardiomyocytes are outfitted to perform higher workload than other ventricular cardiomyocytes.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:4667d62914ba295c44c5
claim_id: claim:4667d62914ba295c44c5
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
vCM5 (approximately 1%) comprises cells with high levels of DLC1 and EBF2 21 , regulating brown adipocyte differentiation and perhaps cardiac pacemaker activity, and transcripts identified in neuronal lineages ( SOX5 , EBF1 and KCNAB1 ).

summary:
In Homo sapiens, ventricular cardiomyocyte 5 expresses high levels of DLC1, EBF2, SOX5, EBF1, and KCNAB1.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:0db9dd8ab02fe81c3220
claim_id: claim:0db9dd8ab02fe81c3220
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
aCM2 predominantly expresses HAMP within the right atrium and is enriched for SLIT3 , the developmental ligand for cardiac ROBO receptors 25 , ALDH1A2 26 and BRINP3 , involved in retinoic acid signalling, and GRXCR2 , supporting cilia involved in mechanosensing 27 .

summary:
In Homo sapiens, atrial cardiomyocyte 2 predominantly expresses HAMP and is enriched for SLIT3, ALDH1A2, BRINP3, and GRXCR2.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:2a7dc23bfdd07792d16d
claim_id: claim:2a7dc23bfdd07792d16d
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, atrial cardiomyocyte 1 shows lower levels of ADGRL2, NFXL1, and ROBO2.
span_literal:
aCM1 shows robust expression of prototypic atrial transcripts, indicative of a basal atrial cardiomyocyte gene program, and lower levels of molecules with neuronal functions ( ADGRL2 , NFXL1 and ROBO2 ).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:330aa18622a8e83f1ebf
claim_id: claim:330aa18622a8e83f1ebf
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Endothelial cells, identified by pan-EC markers PECAM1 , CDH5 and VWF , comprise 10 populations (Extended Data Fig. 4a–c, g ).

summary:
In Homo sapiens, endothelial cells are identified by pan-endothelial cell markers PECAM1, CDH5, and VWF.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:cdd0512440a6b68e2af8
claim_id: claim:cdd0512440a6b68e2af8
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Capillary-like EC4_immune ECs express transcripts related to antigen presentation and immune regulation ( CX3CL1 , CCL2 , IL6 and ICAM1 ) 30 .

summary:
In Homo sapiens, immune-related capillary-like endothelial cells express CX3CL1, CCL2, IL6, and ICAM1.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:13fbf1f5f5e9565c66b3
claim_id: claim:13fbf1f5f5e9565c66b3
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Arterial EC5_art ECs are enriched for SEMA3G , EFNB2 and DLL4 , whereas EC6_ven ECs express venous markers NR2F2 31 and ACKR1 32 , which we confirmed by smFISH (Fig. 3c ).

summary:
In Homo sapiens, arterial endothelial cells are enriched for SEMA3G, EFNB2, and DLL4, whereas venous endothelial cells express NR2F2 and ACKR1.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:a56a40ca2dc427529b90
claim_id: claim:a56a40ca2dc427529b90
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Mainly atrial EC7_atria ECs express the angiogenesis regulator SMOC1 33 and NPR3 , detected in mouse endocardium 34 , suggestive of endocardial cells.

summary:
In Homo sapiens, atria-enriched endothelial cells express the angiogenesis regulator SMOC1 and NPR3.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:a1ea18655ef8159b9657
claim_id: claim:a1ea18655ef8159b9657
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, lymphatic endothelial cells are enriched for PROX1, TBX1, and PDPN.
span_literal:
Lymphatic EC8_ln ECs, enriched for PROX1 , TBX1 and PDPN , represent approximately 1% of the captured ECs 29 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:802dc7a8243a1dcedf44
claim_id: claim:802dc7a8243a1dcedf44
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, pericytes express ABCC9 and KCNJ8.
span_literal:
Pericytes express ABCC9 and KCNJ8 and segregate into four clusters, with PC1_vent cells enriched in ventricles and PC2_atria cells in atria.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:4f89fee4cf9f65cfe822
claim_id: claim:4f89fee4cf9f65cfe822
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, ventricle-enriched pericytes express NCAM2, CD38, and CSPG4.
span_literal:
PC1_vent cells express adhesion molecules ( NCAM2 and CD38 ), and CSPG4 , which is involved in microvascular morphogenesis and EC cross-talk 35 (Extended Data Fig. 4d–f ).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:9dbe208f31bb89569f16
claim_id: claim:9dbe208f31bb89569f16
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
SMC1_basic cells express transcripts that indicate immaturity, including the stem-cell marker LGR6 37 and proliferation-associated RGS5 38 .

summary:
In Homo sapiens, basic smooth muscle cells express the stem-cell marker LGR6 and proliferation-associated RGS5.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:e3ba945042a6eec2872a
claim_id: claim:e3ba945042a6eec2872a
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
SMC2_art cells express considerably higher levels of CNN1 , ACTA2 and TAGLN , indicating arterial origin, whereas SMC1_basic cells may be venous-derived 39 (Extended Data Fig. 4d–f ).

summary:
In Homo sapiens, arterial smooth muscle cells express considerably higher levels of CNN1, ACTA2, and TAGLN.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:564e2c3715efbc01bbf7
claim_id: claim:564e2c3715efbc01bbf7
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, mesothelial cells are enriched for MSLN, WT1, and BNC1.
span_literal:
We define a distinct small population as mesothelial cells that enrich for MSLN , WT1 and BNC1 41 but lack EC, FB or mural genes.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:1c980cb7e58317a69285
claim_id: claim:1c980cb7e58317a69285
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, fibroblasts show enriched expression of DCN, GSN, and PDGFRA.
span_literal:
Cells of the FB compartment show enriched expression of DCN , GSN and PDGFRA within seven populations (Fig. 3g ) with regional enrichment in ventricles (FB1) and atria (FB2).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:64c00b6cf3a97213d6c9
claim_id: claim:64c00b6cf3a97213d6c9
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal: FB4 cells express genes responsive to TGFβ signalling (for example, POSTN and TNC ) (Fig. 3e ).
summary:
In Homo sapiens, fibroblast 4 cells express genes responsive to transforming growth factor beta signalling such as POSTN and TNC.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:6afbbc123390e6e052dc
claim_id: claim:6afbbc123390e6e052dc
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, fibroblast 3 cells have higher expression of cytokine receptors OSMR and IL6ST.
span_literal:
By contrast, FB3 cells have lower expression of ECM-related genes but higher expression of cytokine receptors such as OSMR and ILST6 43 (Fig. 3f , Extended Data Fig. 6b , Supplementary Table 12 ).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:5016fe2a58573207b43b
claim_id: claim:5016fe2a58573207b43b
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, LYVE1-positive macrophage 3 is enriched for HLA-DOA, HLA-DQA1/2, and HLA-DQB1.
span_literal:
Macrophages include three LYVE1 + macrophage populations: LYVE1 + MP1–2 enrich for clathrin and cathepsin genes, and LYVE1 + MP3 for HLA-DOA , HLA-DQA1/2 and HLA-DQB1 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:99abd12f169292a7ea56
claim_id: claim:99abd12f169292a7ea56
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Monocyte-derived macrophages express LYVE1 and FOLR2 , monocyte-like markers CEBPB and S100A8 , and chemoattractant cytokine genes CCL13 and CCL18 .

summary:
In Homo sapiens, monocyte-derived macrophages express LYVE1, FOLR2, CEBPB, S100A8, CCL13, and CCL18.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:f9e7fd174f22c654c485
claim_id: claim:f9e7fd174f22c654c485
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Antigen-presenting macrophages are FOLR2 − , LYVE1 − and MERTK − , and enrich for HLA-DRA , HLA-DMA , HLA-DMB , HLA-DPA1 and TREM2 (described in lipid-associated macrophages) 46 .

summary:
In Homo sapiens, antigen-presenting macrophages are negative for FOLR2, LYVE1, and MERTK, and enriched for HLA-DRA, HLA-DMA, HLA-DMB, HLA-DPA1, and TREM2.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:adfeedf9438f2cb6e3ad
claim_id: claim:adfeedf9438f2cb6e3ad
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Among 3,961 cells expressing prototypic electrophysiologic transcripts ( NRXN1 , NRXN3 and KCNMB4 ), we identify six neuronal cell subclusters (Extended Data Fig. 9a–c ).

summary:
In Homo sapiens, neuronal cells express prototypic electrophysiologic transcripts NRXN1, NRXN3, and KCNMB4.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:3612b3a0899760cc78e6
claim_id: claim:3612b3a0899760cc78e6
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, neuronal cell 1 exhibits a basal gene program including LGI4.
span_literal:
NC1 constitutes 75–80% of neuronal cells and exhibits a basal gene program including LGI4 , required for glia development and axon myelination 52 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:ae732b32e366bdf6daaa
claim_id: claim:ae732b32e366bdf6daaa
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, neuronal cell 2 shows strong expression of PRKG1.
span_literal:
NC2 and NC4 show strong expression of the central nervous system marker, PRKG1 53 , and co-express typical fibroblast and cardiomyocyte genes, respectively.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:07b6797c342c12a21ff6
claim_id: claim:07b6797c342c12a21ff6
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
NC5 expresses LGR5 , a Wnt signalling, G-protein-coupled receptor and stem-cell marker that promotes cardiomyocyte differentiation in the outflow tract 54 , an arrhythmogenic area 55 .

summary:
In Homo sapiens, neuronal cell 5 expresses LGR5, a Wnt signalling G-protein-coupled receptor and stem-cell marker.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:36c2d06cdc1794384d67
claim_id: claim:36c2d06cdc1794384d67
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, neuronal cell 5 expresses PPP2R2B, LSAMP, and LPL.
span_literal:
This cluster also expresses the neurodegenerative disease gene PPP2R2B 56 (verified by smFISH) (Extended Data Fig. 9d , Supplementary Table 20 ); LSAMP , which guides the development of specific patterns of neuronal connections 57 ; and the lipoprotein transport enzyme LPL that remyelinates damaged neurons 58 .


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:64df9ad999f46d15aba4
claim_id: claim:64df9ad999f46d15aba4
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, cardiac adipocytes uniformly express GPAM, FASN, ADIPOQ, and at lower levels LEP.
span_literal:
Cardiac adipocytes uniformly express GPAM , FASN and ADIPOQ and at lower levels, LEP 60 (Extended Data Fig. 9e–h ).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:7b9a9a754e3e6e3f5631
claim_id: claim:7b9a9a754e3e6e3f5631
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, adipocyte 2 expresses extracellular matrix genes LAMA2, IGFBP7, and FBN1.
span_literal:
ADIP2 expresses ECM genes such as LAMA2 , IGFBP7 and FBN1 , which encodes both the glycoprotein fibrillin1 and asprosin, a white adipose tissue secreted hormone involved in glucose homeostasis (Supplementary Table 21 ).


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:6cc19fdbe93022eb1339
claim_id: claim:6cc19fdbe93022eb1339
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
span_literal:
Naive T cells (CD4+T_naive) identified expressed CCR7 and SELL , indicative of their naive and tissue-resident nature 95 .

summary:
In Homo sapiens, naive CD4-positive T cells express CCR7 and SELL, indicative of their naive and tissue-resident nature.


claim_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d:claim:12507315f30a5c1bb776
claim_id: claim:12507315f30a5c1bb776
paper_key: hca:0089_10.1038_s41586-020-2797-4_6e65d21b5d
summary: In Homo sapiens, CD8-positive effector-memory T cells express BACH2, STAT4, and IL7R.
span_literal:
Memory T cells (CD8+T_tem) expressed BACH2 , STAT4 and IL7R , associated with long-term immune memory 96 , 97 .


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:053cc9e117f6b635229f
claim_id: claim:053cc9e117f6b635229f
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
small-intestinal BEST4 cells were marked by high expression of the gene CFTR , which encodes a chloride channel and is mutated in cystic fibrosis

summary:
In Homo sapiens, small-intestinal BEST4 epithelial cells are marked by high expression of CFTR, which encodes a chloride channel.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:46c78d3b16ea0b22b7f3
claim_id: claim:46c78d3b16ea0b22b7f3
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, enteroendocrine precursor cells express NEUROG3.
span_literal:
Subclustering of enteroendocrine cells (EECs) revealed NEUROG3 -expressing precursor cells enriched in the first-trimester fetal gut


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:fdf8f35afe4d23fe81e2
claim_id: claim:fdf8f35afe4d23fe81e2
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, a subpopulation of enterochromaffin cells expresses NPW, PRAC1, and RXFP4.
span_literal:
we found a subpopulation of NPW -expressing enterochromaffin cells that are also specific for PRAC1 and RXFP4


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:c7b095566e996b3d2b58
claim_id: claim:c7b095566e996b3d2b58
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, FCGR2A is specifically expressed by approximately 2.75% of tuft cells.
span_literal:
FCGR2A, which is activated in response to IgG and expressed by selected epithelial cells in immunized mice 21 , was specifically expressed by approximately 2.75% of tuft cells


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:0aa527f87dea9096942e
claim_id: claim:0aa527f87dea9096942e
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, enteric neuron branch A is marked by ETV1 and branch B is marked by BNC2.
span_literal:
In early development, ENCCs differentiated primarily to neurons via neuroblasts, giving rise to two distinct branches: branch A ( ETV1 ) and branch B ( BNC2 )


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:29fdf1b09aedc23c88d9
claim_id: claim:29fdf1b09aedc23c88d9
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, enteric interneurons of branch A express NEUROD6.
span_literal:
At later development, branch A differentiated into NEUROD6 -expressing interneurons (resembling ENC10 22 )


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:d234deb748f6e0e1a442
claim_id: claim:d234deb748f6e0e1a442
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
This included high expression of RORC , KIT , TNF , LTA , LTB , IL7R and ITGB7 (beta chain of gut-specific α4β7 integrin) as well as the absence of productive αβ TCR

summary:
In Homo sapiens, lymphoid tissue inducer-like cells are characterized by high expression of RORC, KIT, TNF, LTA, LTB, IL7R, and ITGB7.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:535fdddc2be8e2308801
claim_id: claim:535fdddc2be8e2308801
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
we observed a stromal population—marked by the expression of CCL19 , CCL21 and CXCL13 as well as adhesion and NF-κB pathway molecules

summary:
In Homo sapiens, mesenchymal lymphoid tissue organizer cells are marked by expression of CCL19, CCL21, and CXCL13.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:5c2cb066a21f1d73289a
claim_id: claim:5c2cb066a21f1d73289a
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
shared between fetal, paediatric and adult datasets were stem cells ( LGR5 , ASCL2 , SMOC2 , RGMB , OLFM4 )

summary:
In Homo sapiens, intestinal stem cells are marked by expression of LGR5, ASCL2, SMOC2, RGMB, and OLFM4.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:648aa8d41dbff0e94fdd
claim_id: claim:648aa8d41dbff0e94fdd
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: Tuft cells ( POU2F3 , LRMP (also known as IRAG2 ), TRPM5 )
summary:
In Homo sapiens, tuft cells are marked by expression of POU2F3, LRMP (also known as IRAG2), and TRPM5.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:66ebd2c5ad16e70d9640
claim_id: claim:66ebd2c5ad16e70d9640
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, BEST2 goblet cells are enriched for KLK15, KLK3, WFDC2, and WFDC3.
span_literal:
Amongst the genes enriched in BEST2 goblet cells were Kallikreins KLK15 and KLK3 , as well as protease inhibitors WFDC2 and WFDC3


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:32d0f71caac6012ef150
claim_id: claim:32d0f71caac6012ef150
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
( PECAM1 , CDH5 ) were subdivided into arterial ( GJA4 , HEY1 , HEY2 , EFNB2 ), venous ( ACKR1 , VWF ) and lymphatic endothelium ( PROX1 , LYVE1 , CCL21 )

summary:
In Homo sapiens, arterial endothelial cells are marked by GJA4, HEY1, HEY2, and EFNB2; venous endothelial cells by ACKR1 and VWF; and lymphatic endothelial cells by PROX1, LYVE1, and CCL21.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:ce69c96a3332f69c1654
claim_id: claim:ce69c96a3332f69c1654
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
LEC2 ( GP1BA, UBD, ANO9, FIBIN, PAPLN ) and only LEC expressing MADCAM1 and reassembled LECs lining subcapsular sinus floor in human lymph nodes

summary:
In Homo sapiens, lymphatic endothelial cell 2 (LEC2) is marked by expression of GP1BA, UBD, ANO9, FIBIN, PAPLN, and MADCAM1.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:22b354ebbc9950c86283
claim_id: claim:22b354ebbc9950c86283
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
LEC5 ( CLDN11 , DEGS2 , SBSPON , ANGPT2 hi , GJA4 hi ) reassembled collecting lymphatic valves in lymph nodes

summary:
In Homo sapiens, lymphatic endothelial cell 5 (LEC5) is marked by expression of CLDN11, DEGS2, SBSPON, ANGPT2, and GJA4.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:b0a1f538a696a08af8c6
claim_id: claim:b0a1f538a696a08af8c6
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
Branch A1 was functionally named inhibitory motor neurons (iMN) based on expression of GAL, NOS1 and VIP

summary:
In Homo sapiens, inhibitory motor neurons (branch A1) are marked by expression of GAL, NOS1, and VIP.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:f693af0fcb180b51731f
claim_id: claim:f693af0fcb180b51731f
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: branch A2 was a mixed IPAN/IN population based on NTNG1 and NXPH2
summary:
In Homo sapiens, enteric neuron branch A2 (a mixed intrinsic primary afferent neuron/interneuron population) is marked by NTNG1 and NXPH2.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:9b35dfe054b9cc2c07a0
claim_id: claim:9b35dfe054b9cc2c07a0
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: Branch B1 were annotated as immature excitatory motor neurons (eMN) based on NXPH4 and NDUFA4L2
summary:
In Homo sapiens, enteric neuron branch B1 immature excitatory motor neurons are marked by NXPH4 and NDUFA4L2.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:a90ef9875fb3ae0639e1
claim_id: claim:a90ef9875fb3ae0639e1
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: branch B3 (IPAN) was assigned the IPAN label based on DLX3 , ANO2 , NOG and NTRK3
summary:
In Homo sapiens, enteric neuron branch B3 intrinsic primary afferent neurons are marked by DLX3, ANO2, NOG, and NTRK3.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:3e65975800d9c0092781
claim_id: claim:3e65975800d9c0092781
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
All terminal glial cells expressed high levels of ENCC progenitor/terminal glial marker genes including FOXD3, MPZ, CDH19, PLP1, SOX10, S100B and ERBB3 , but lacked RET

summary:
In Homo sapiens, terminal glial cells express FOXD3, MPZ, CDH19, PLP1, SOX10, S100B, and ERBB3, but lack RET.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:7545c82d099345e4b909
claim_id: claim:7545c82d099345e4b909
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: glia 3 ( BCAN , APOE , CALCA , HES5 , FRZB )
summary:
In Homo sapiens, enteric glia 3 cells are marked by expression of BCAN, APOE, CALCA, HES5, and FRZB.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:22fc094342856667272c
claim_id: claim:22fc094342856667272c
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: stromal 1 ( ADAMDEC1 ) subset either highly expressing ADAM28 or CCL11, CCL8, CCL13
summary:
In Homo sapiens, stromal 1 cells are marked by ADAMDEC1 and subsets express ADAM28 or CCL11, CCL8, CCL13.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:c7b01c8fc72a7ac8f150
claim_id: claim:c7b01c8fc72a7ac8f150
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: stromal 2 ( PDGFRA , BMP4 ) either enriched for F3, NPY or CH25H, MMP1 expression
summary:
In Homo sapiens, stromal 2 cells are marked by PDGFRA and BMP4, with subsets enriched for F3, NPY, or CH25H and MMP1.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:34c6a9e9adb3604c86a5
claim_id: claim:34c6a9e9adb3604c86a5
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
Myofibroblasts were identified on the basis of expression of actin ( ACTA2 ) and transgelin ( TAGLN ), fibroblast characteristic decorin ( DCN ), but lacked smooth muscle marker desmin ( DES )

summary:
In Homo sapiens, myofibroblasts are identified by expression of ACTA2, TAGLN, and DCN, but lack the smooth muscle marker DES.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:a26555dc99c8ec59ee31
claim_id: claim:a26555dc99c8ec59ee31
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
Smooth muscle cells were annotated on the basis of high expression of DES , calponin ( CNN1 ) 58 and actin/myosin chain expression ( ACTA2, MYH11 )

summary:
In Homo sapiens, smooth muscle cells are annotated based on high expression of DES, CNN1, ACTA2, and MYH11.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:1497200cb210fe05f15b
claim_id: claim:1497200cb210fe05f15b
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, immature pericytes are marked by high expression of PDGFRB, CSPG4, and NDUFA4L2.
span_literal:
Immature pericytes were annotated based on high expression of PDGFRB , CSPG4 (encoding NG2) 58 and was marked by high NDUFA4L2 expression


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:355ba75e61b1d39b242a
claim_id: claim:355ba75e61b1d39b242a
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
Pro-B cells had specific expression of DNTT (TdT), recombination-activating genes (RAG) 1 and 2, high expression of B lymphocyte antigen receptor CD79B , V-set pre-B cell surrogate light chains ( VPREB1, VPREB3 ) and expression of immunoglobulin-lambda chain IGLL1

summary:
In Homo sapiens, pro-B cells specifically express DNTT, RAG1, RAG2, CD79B, VPREB1, VPREB3, and IGLL1.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:d59f5b762960d290430a
claim_id: claim:d59f5b762960d290430a
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: Pre-B cells specifically expressed CD38 and had higher expression of CD19 than pro-B cells
summary:
In Homo sapiens, pre-B cells specifically express CD38 and have higher expression of CD19 compared to pro-B cells.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:fdee1c396840919ae71c
claim_id: claim:fdee1c396840919ae71c
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, immature B cells have the highest expression of MS4A1 among B lineage cells.
span_literal:
Immature B cells had the highest expression of MS4A1 among B lineage cells and expression of immunoglobulin heavy chains M and D


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:226e150b8899f10c2826
claim_id: claim:226e150b8899f10c2826
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, naive B cells are marked by FCMR and memory B cells are marked by SELL.
span_literal:
Adult B lineage cells had distinct clusters of naive B cells (Fc fragment of IgM receptor- FCMR), memory B cells ( SELL (encodes CD62L))


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:27cad18e63af153c99c3
claim_id: claim:27cad18e63af153c99c3
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, a tissue-restricted memory B cell population specifically expresses FCRL4.
span_literal:
a population of memory B cells that specifically expressed transmembrane immunoregulatory molecule FCRL4 (encodes protein also known as FcRH4) that has been suggested to be tissue-restricted


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:d28f150c87645289f768
claim_id: claim:d28f150c87645289f768
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
summary: In Homo sapiens, class-switched plasma cells express SDC1.
span_literal:
Class switch IgA and IgG plasma cells showed expression of the syndecan, SDC1 , and immunoglobulin heavy chains A and G, respectively


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:ef606ede9488f14552c1
claim_id: claim:ef606ede9488f14552c1
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: Adult ILC3s were defined based on the expression of RORC , IL1R1, IL23R, KIT
summary:
In Homo sapiens, adult type 3 innate lymphoid cells (ILC3) are defined by expression of RORC, IL1R1, IL23R, and KIT.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:63f1c5e6bb301c734388
claim_id: claim:63f1c5e6bb301c734388
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
LTi-like NCR + ILC3 cells had highest expression of TNFRSF11A (RANK) and its ligand TNFSF11 (RANKL), as well as NCR1 (NKp46) and NCR2 (NKp44)

summary:
In Homo sapiens, lymphoid tissue inducer-like NCR-positive type 3 innate lymphoid cells have highest expression of TNFRSF11A, TNFSF11, NCR1, and NCR2.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:7934453d16b9ee3e0e5c
claim_id: claim:7934453d16b9ee3e0e5c
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
LTi-like NCR- ILC3s lacked NCR2 (NKp44) and expressed IL17A , ITGAE and CCR9 , and NK-associated genes including NKG7 , PRF1 and GZMA

summary:
In Homo sapiens, lymphoid tissue inducer-like NCR-negative type 3 innate lymphoid cells lack NCR2 and express IL17A, ITGAE, CCR9, NKG7, PRF1, and GZMA.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:1b2618bc9636f38b84a2
claim_id: claim:1b2618bc9636f38b84a2
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal: cDC1 ( CLEC9A ) and cDC2 ( CLEC10A )
summary:
In Homo sapiens, conventional dendritic cell type 1 (cDC1) is marked by CLEC9A and conventional dendritic cell type 2 (cDC2) is marked by CLEC10A.


claim_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36:claim:7da921031bf4cb9250c0
claim_id: claim:7da921031bf4cb9250c0
paper_key: hca:0090_10.1038_s41586-021-03852-1_eec89a5e36
span_literal:
common lymphoid progenitor (CLP) cells were classified on the basis of minimal expression of the lineage markers and specific expression of CD34, SPINK2 and FLT3

summary:
In Homo sapiens, common lymphoid progenitor cells are classified by specific expression of CD34, SPINK2, and FLT3.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:ea9835a48e6ab605fc01
claim_id: claim:ea9835a48e6ab605fc01
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
Beyond the well-characterised COL1A1+TNMD+MKX+intrafascicular tenocytes responsible for ECM production and fibre alignment,

summary:
In Homo sapiens, intrafascicular tenocytes are characterized by positive expression of COL1A1, TNMD, and MKX.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:422516633beb62a7ef2f
claim_id: claim:422516633beb62a7ef2f
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal: NOTCH3+ mural or ACTA2+ smooth muscle cells,
summary:
In Homo sapiens, tendon mural cells are marked by positive expression of NOTCH3, and smooth muscle cells are marked by positive expression of ACTA2.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:b9456d4600ab1581145a
claim_id: claim:b9456d4600ab1581145a
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
The largest, ABI3BP GAS2 Fibroblasts, were defined by high levels of COL11A1[48](https://doi.org/10.1007/978-3-642-16555-9_3) alongside ECM- and cytoskeletal-regulators ABI3BP, GAS2, SOX5, EXT1 and PLEKHH2, consistent with roles in matrix assembly and cellular adhesion

summary:
In Homo sapiens, ABI3BP GAS2 Fibroblasts in foetal tendon are defined by high expression of COL11A1, ABI3BP, GAS2, SOX5, EXT1, and PLEKHH2.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:28bd88d89cecf3edb2bd
claim_id: claim:28bd88d89cecf3edb2bd
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
KERA TNMD Fibroblasts were enriched for collagens (COL1A1, COL1A2, COL6A3, COL6A1, COL12A1) and matrix-associated genes (SPARC, POSTN, FMOD, KERA), with low MKX and high TNMD expression

summary:
In Homo sapiens, KERA TNMD Fibroblasts in foetal tendon are enriched for COL1A1, COL1A2, COL6A3, COL6A1, COL12A1, SPARC, POSTN, FMOD, KERA, and TNMD, with low MKX expression.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:c18ec1f9ae2ed4b9888e
claim_id: claim:c18ec1f9ae2ed4b9888e
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
CHSY3 MECOM Fibroblasts, in contrast, expressed ECM-hydration regulator CHSY3, transcriptional regulators MECOM and FOXP2, and mineralisation-associated COL24A1,56 SMOC1,57 and ENPP1,58 as well as chondrogenic and enthesis markers SOX630 and COL27A131

summary:
In Homo sapiens, CHSY3 MECOM Fibroblasts in foetal tendon express CHSY3, MECOM, FOXP2, COL24A1, SMOC1, ENPP1, SOX6, and COL27A1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:65daf30505e4cd5492f7
claim_id: claim:65daf30505e4cd5492f7
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
The most abundant, COL3A1 PI16 Fibroblasts, exhibited high expression of COL3A1, PI16, EBF1, DCLK1, LUM, MFAP5 and FBN1

summary:
In Homo sapiens, COL3A1 PI16 Fibroblasts in foetal tendon exhibit high expression of COL3A1, PI16, EBF1, DCLK1, LUM, MFAP5, and FBN1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:70ab871a2c0b75abc16c
claim_id: claim:70ab871a2c0b75abc16c
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
A transcriptionally similar population, COL6A6 FNDC1 Fibroblasts, was distinguished by elevated expression of COL6A6, FNDC1, and regulators of chondrogenesis and mineralisation SFRP2,61 GNAS,62 and ASPN63–65

summary:
In Homo sapiens, COL6A6 FNDC1 Fibroblasts in foetal tendon are distinguished by elevated expression of COL6A6, FNDC1, SFRP2, GNAS, and ASPN.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:bf4c257ecbb1533156ba
claim_id: claim:bf4c257ecbb1533156ba
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
NEGR1 SCN7A Fibroblasts were characterised by high expression of NEGR1, SCN7A, EBF2, NRK, and KCNMB2, suggesting involvement in fibroblast mechanosensitivity.

summary:
In Homo sapiens, NEGR1 SCN7A Fibroblasts in foetal tendon are characterized by high expression of NEGR1, SCN7A, EBF2, NRK, and KCNMB2.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:ac4f334f127aaedb636f
claim_id: claim:ac4f334f127aaedb636f
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
FGF14 THBS4 Fibroblasts, occupied the tendon–muscle boundaries ([Figure 1F](660575v1_fig1.tif)) and expressed MTJ-associated genes COL22A166,67 and THBS4, alongside high levels of FGF14, SLIT3, TSHZ2, CDH12, BMP5, RGS6, EGFR, and FSTL5

summary:
In Homo sapiens, FGF14 THBS4 Fibroblasts in foetal tendon express COL22A1, THBS4, FGF14, SLIT3, TSHZ2, CDH12, BMP5, RGS6, EGFR, and FSTL5.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:d49aa61dc7ce2dbd43ec
claim_id: claim:d49aa61dc7ce2dbd43ec
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
a small CREB5 PRG4 Fibroblast population localised within LCT regions ([Figures 1F](660575v1_fig1.tif), [2E](660575v1_fig2.tif)) expressed synovium- and cartilage-associated CREB5,68,69 alongside lubricating PRG4.70–75 These cells also showed high levels of TIMP3, TNXB, and NOVA1

summary:
In Homo sapiens, CREB5 PRG4 Fibroblasts in foetal tendon express CREB5, PRG4, TIMP3, TNXB, and NOVA1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:fd80fb2e74e67171c599
claim_id: claim:fd80fb2e74e67171c599
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
Vascular endothelial cells expressed PECAM1, CD34, and VWF, while lymphatic endothelial cells were marked by LYVE1, PROX1, and FLT4

summary:
In Homo sapiens, vascular endothelial cells in foetal tendon express PECAM1, CD34, and VWF, while lymphatic endothelial cells are marked by LYVE1, PROX1, and FLT4.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:8e868e37c8989daad265
claim_id: claim:8e868e37c8989daad265
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal: Smooth muscle cells showed high expression of ACTA2, MYH11, CALD1, NOTCH3, and PDGFRB
summary:
In Homo sapiens, smooth muscle cells in foetal tendon show high expression of ACTA2, MYH11, CALD1, NOTCH3, and PDGFRB.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:8de905033245aa20d993
claim_id: claim:8de905033245aa20d993
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
Nervous system-associated cells were distinguished by NRXN1, NCAM2, and SOX10 expression, displaying transcriptomic features consistent with glial cells

summary:
In Homo sapiens, nervous system-associated cells in foetal tendon are distinguished by NRXN1, NCAM2, and SOX10 expression, consistent with glial cells.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:cc21a9df07c2479675cd
claim_id: claim:cc21a9df07c2479675cd
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal: Immune cells broadly expressed PTPRC, CD44, IKZF1, RUNX1, DOCK2, and INPP5D.
summary:
In Homo sapiens, immune cells in foetal tendon broadly express PTPRC, CD44, IKZF1, RUNX1, DOCK2, and INPP5D.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:fedf3c7cb31b9e15154e
claim_id: claim:fedf3c7cb31b9e15154e
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
The predominant subset expressed F13A1, CD163, MRC1 (CD206), CSF1R, CD36, and LGMN, consistent with macrophage identity

summary:
In Homo sapiens, macrophages in foetal tendon express F13A1, CD163, MRC1 (CD206), CSF1R, CD36, and LGMN.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:28839b9f89c948c097a2
claim_id: claim:28839b9f89c948c097a2
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
summary: In Homo sapiens, foetal tendon monocytes express FCN1, LYZ, and IRAK3.
span_literal:
Additional immune subsets included monocytes (FCN1, LYZ, IRAK3), mast cells (KIT, CPA3, GATA2) and T cells (SKAP1, CD247, CD96, CD38)


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:f88c6c29ed4f885eef8d
claim_id: claim:f88c6c29ed4f885eef8d
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
One cluster expressed PAX7, marking satellite cells, while a second expressed markers of differentiated skeletal myocytes including DES, NES, TNNT3, TTN, MYH3, COL22A1, and TNNC1

summary:
In Homo sapiens, satellite cells in foetal tendon express PAX7, while differentiated skeletal myocytes express DES, NES, TNNT3, TTN, MYH3, COL22A1, and TNNC1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:b8a7e509e59960364a5c
claim_id: claim:b8a7e509e59960364a5c
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
One cluster expressed PAX7, marking satellite cells, while a second expressed markers of differentiated skeletal myocytes including DES, NES, TNNT3, TTN, MYH3, COL22A1, and TNNC1

summary:
In Homo sapiens, differentiated skeletal myocytes in foetal tendon express DES, NES, TNNT3, TTN, MYH3, COL22A1, and TNNC1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:8e97ad2401ce254564db
claim_id: claim:8e97ad2401ce254564db
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
A third small cluster, expressing MYOG, FNDC5, EMC10, MEGF10, and overlapping markers from both satellite and skeletal myocytes, likely represented a transitional state

summary:
In Homo sapiens, a transitional myocyte state in foetal tendon expresses MYOG, FNDC5, EMC10, and MEGF10.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:5b82df5f9eb5e7037739
claim_id: claim:5b82df5f9eb5e7037739
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
a discrete population expressing COL2A1, COL9A1, ACAN, COMP, MATN1, and HAPLN1 was detected, consistent with a chondrocyte identity

summary:
In Homo sapiens, chondrocytes in foetal tendon express COL2A1, COL9A1, ACAN, COMP, MATN1, and HAPLN1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:79c6f1ac96c36dfcb280
claim_id: claim:79c6f1ac96c36dfcb280
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
By 8.4 pcw, a distinct COL6A6 Progenitor population emerged, expressing canonical MSC markers (CD73/NT5E, CD90/THY1, CD44, TWIST2), along with tendon-associated matrisomal genes (FSTL1, DCLK1, COL1A1, COL3A1, COL5A1, COL6A1, COL12A1, ELN, DCN, ASPN, OGN, FNDC1, LUM, VCAN, EMILIN2, MFAP5, TNXB, POSTN)

summary:
In Homo sapiens, COL6A6 Progenitors in embryonic tendon express canonical mesenchymal stem cell markers NT5E, THY1, CD44, and TWIST2, along with tendon-associated matrisomal genes FSTL1, DCLK1, COL1A1, COL3A1, COL5A1, COL6A1, COL12A1, ELN, DCN, ASPN, OGN, FNDC1, LUM, VCAN, EMILIN2, MFAP5, TNXB, and POSTN.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:a18584a19ce7890258ba
claim_id: claim:a18584a19ce7890258ba
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
SCX Progenitors were characterised by high expression of FGF14, THBS4, FSTL5, CHODL, TSHZ2, CDH12, KERA, POSTN, DCN, OGN, and a broad array of fibrillar (COL1A1, COL3A1, COL5A1, COL6A1, COL12A1, COL14A1), basement membrane (COL18A1, COL4A1, COL4A2), and MTJ-associated (COL22A1) collagens

summary:
In Homo sapiens, SCX Progenitors in embryonic tendon are characterized by high expression of FGF14, THBS4, FSTL5, CHODL, TSHZ2, CDH12, KERA, POSTN, DCN, OGN, COL1A1, COL3A1, COL5A1, COL6A1, COL12A1, COL14A1, COL18A1, COL4A1, COL4A2, and COL22A1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:37429a0ae331ee9999e4
claim_id: claim:37429a0ae331ee9999e4
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
MKX Progenitors exhibited even higher expression of matrisomal genes, along with LOX, MKX, TNMD, ABI3BP, and GAS2, marking a more differentiated tenogenic state

summary:
In Homo sapiens, MKX Progenitors in embryonic tendon express LOX, MKX, TNMD, ABI3BP, and GAS2, marking a more differentiated tenogenic state.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:51dc3e9ca2b55a722a71
claim_id: claim:51dc3e9ca2b55a722a71
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
A multipotent RUNX2-expressing population exhibited a hybrid transcriptomic profile, co-expressing collagens linked to tendon (COL1A1, COL3A1), cartilage (COL2A1, COL9A1–COL9A3), and endothelial basement membranes (COL8A1)

summary:
In Homo sapiens, RUNX2-expressing progenitors in embryonic tendon co-express COL1A1, COL3A1, COL2A1, and COL8A1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:a66645b272a06d439cc0
claim_id: claim:a66645b272a06d439cc0
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
Two more differentiated clusters expressed classic cartilage markers (SOX5, SOX6, SOX9, ACAN, CILP2, HAPLN1, COMP, COL2A1, COL9A1–COL9A3)

summary:
In Homo sapiens, differentiated chondrogenic clusters in embryonic tendon express classic cartilage markers SOX5, SOX6, SOX9, ACAN, CILP2, HAPLN1, COMP, and COL2A1.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:8b9eedbab337c77542d9
claim_id: claim:8b9eedbab337c77542d9
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
The less mature SOX5 Progenitors additionally expressed CREB5 and PRG4, while the more differentiated Chondrocyte cluster was enriched for MATN1, MATN3, and MATN4

summary:
In Homo sapiens, SOX5 Progenitors in embryonic tendon additionally express CREB5 and PRG4, while the more differentiated Chondrocyte cluster is enriched for MATN1, MATN3, and MATN4.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:3c0d7fa5c753cf37e298
claim_id: claim:3c0d7fa5c753cf37e298
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
The less mature SOX5 Progenitors additionally expressed CREB5 and PRG4, while the more differentiated Chondrocyte cluster was enriched for MATN1, MATN3, and MATN4

summary:
In Homo sapiens, the more differentiated Chondrocyte cluster in embryonic tendon is enriched for MATN1, MATN3, and MATN4.


claim_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76:claim:7baf19d31ea7bd76ba40
claim_id: claim:7baf19d31ea7bd76ba40
paper_key: hca:0091_10.1101_2025.06.19.660575_df9b499d76
span_literal:
The earliest state, MSC Precursors, was identified at 6.5-7.2 pcw and lacked classical MSC markers, but expressed a combination of non-myogenic (HMGA2, FOXP2, RUNX1T1)78,79 and myogenic (SIX1)78,80,81 connective tissue fate regulators.

summary:
In Homo sapiens, mesenchymal stem cell Precursors in embryonic tendon express HMGA2, FOXP2, RUNX1T1, and SIX1.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:d5252522584480a94692
claim_id: claim:d5252522584480a94692
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
The 11 cluster 9 samples, when compared with the other 8 clusters, showed higher expression of previously reported oocyte markers, such as TUBB8 , ZP3 , LHX8 , and OOSP2

summary:
In Homo sapiens, oocytes show higher expression of previously reported markers TUBB8, ZP3, LHX8, and OOSP2.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:95ce3b11a9946cfab171
claim_id: claim:95ce3b11a9946cfab171
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
In all, we identified 76 markers for human primordial and primary oocytes ( Fig. 2D and data S5), many of which are involved in meiosis ( HSP90A1 , UBB , RALB , ESRP1 , EIF4ENIF1 , CDK7 , and ZAR1 ).

summary:
In Homo sapiens, primordial and primary oocytes express markers involved in meiosis including HSP90A1, UBB, RALB, ESRP1, EIF4ENIF1, CDK7, and ZAR1.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:d28ce2d0be726faac99c
claim_id: claim:d28ce2d0be726faac99c
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
Endothelial cells showed high expression of their canonical markers VWF , PECAM1 , CD34 , and CLDN5 ( 9 , 13 ), as well as NOTCH4 , which is typically confined to arterial and sprouting endothelial cells ( 28 ).

summary:
In Homo sapiens, endothelial cells show high expression of canonical markers VWF, PECAM1, CD34, CLDN5, and NOTCH4.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:5820d71d2338b893d3d4
claim_id: claim:5820d71d2338b893d3d4
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal: Pericytes were identified by their characteristic expression of RGS5 , NOTCH3 , ACTA2 , and MUSTN1
summary:
In Homo sapiens, pericytes were identified by their characteristic expression of RGS5, NOTCH3, ACTA2, and MUSTN1.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:8a00f1c1ce0edb669401
claim_id: claim:8a00f1c1ce0edb669401
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
Pericytes in our data showed high expression of PDGFRB , which has been reported in other organ systems for platelet-derived growth factor (PDGF) signaling between pericytes and endothelial cells, and it is also essential to proper theca cell development and steroidogenesis ( 29 ).

summary:
In Homo sapiens, pericytes show high expression of PDGFRB, which is involved in platelet-derived growth factor signaling.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:7609eba84d07c8dd5714
claim_id: claim:7609eba84d07c8dd5714
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
summary: In Homo sapiens, T cells in the ovary are annotated by markers CD3D, CD3G, and IL7R.
span_literal:
Focused clustering of the immune cells from all three donors revealed four immune cell subtypes ( Fig. 5B ), which were annotated as T cells ( CD3D , CD3G , and IL7R ) ( 9 , 13 ), natural killer (NK) cells ( KLRD1 , TRCD , and GNLY ) ( 24 , 30 ), macrophages ( CD68 , CD14 , and FOLR2 ) ( 9 , 13 ), and mast cells ( KIT , TPSB2 , and TPSAB1 ) ( 31 , 32 )


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:24ac90746c77daf72042
claim_id: claim:24ac90746c77daf72042
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
Stromal cells had by far the largest number, reflecting the dominance of this cell population in the ovary. As a group, they were characterized by mesenchymal cell markers DCN and PDGFRA and the more recently reported ovarian stromal cell markers APOE , LUM , ARX , and FHL2

summary:
In Homo sapiens, ovarian stromal cells are characterized by mesenchymal cell markers DCN and PDGFRA and the more recently reported markers APOE, LUM, ARX, and FHL2.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:c560d7ca59aacfeefc24
claim_id: claim:c560d7ca59aacfeefc24
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
The list of theca-specific genes included canonical theca cell markers CYP17A1 , PTCH2 , APOE , DHCR24 , INSL3 , BGN , and CYP11A1 ( 33 , 34 ) and the more recently reported ANPEP ( 35 )

summary:
In Homo sapiens, theca cells express canonical markers CYP17A1, PTCH2, APOE, DHCR24, INSL3, BGN, CYP11A1, and the more recently reported ANPEP.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:eb6e251dbbe8f346a6ff
claim_id: claim:eb6e251dbbe8f346a6ff
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
summary: In Homo sapiens, theca cells express previously unreported markers S100A13, ALAS1, FDX1, and DLK1.
span_literal:
as well as those not previously reported for theca, but having notable biological relevance, such as S100A13 , ALAS1 , FDX1 , and DLK1 (data S5).


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:9abb5d99bb32a049626d
claim_id: claim:9abb5d99bb32a049626d
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
Likewise, the list of granulosa-specific genes included canonical marker genes HSD17B1 , INHBB , FOXL2 , and AMH and the recently reported TNNI3 , MAGED2 , CD99 , SERPINE2 , CDH2 , and BEX1 ( 9 , 13 )

summary:
In Homo sapiens, granulosa cells express canonical markers HSD17B1, INHBB, FOXL2, and AMH, and the recently reported TNNI3, MAGED2, CD99, SERPINE2, CDH2, and BEX1.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:733243c7da8d46721154
claim_id: claim:733243c7da8d46721154
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
The list also included genes involved in granulosa cell–oocyte signaling, such as the transzonal projection–related genes FSCN1 and MYO10 , and the tetraspanin protein gene TSPAN7 , which is involved in extracellular vesicle–mediated signaling between granulosa cells and the oocyte ( 44 , 45 ).

summary:
In Homo sapiens, granulosa cells express FSCN1, MYO10, and TSPAN7, which are involved in granulosa cell–oocyte signaling.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:ca740e2bcf481d6248ed
claim_id: claim:ca740e2bcf481d6248ed
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
span_literal:
The list confirmed many of the genes previously reported as up-regulated in granulosa cells in RNA-based comparisons: LIMS2 , CORO2A , LAMA1 , FAM78A , ST6GAL2 , and MFAP2 ( 20 , 46 , 47 )

summary:
In Homo sapiens, granulosa cells show up-regulation of LIMS2, CORO2A, LAMA1, FAM78A, ST6GAL2, and MFAP2.


claim_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0:claim:b6f868ec1277f42c860a
claim_id: claim:b6f868ec1277f42c860a
paper_key: hca:0092_10.1126_sciadv.adm7506_67b90b1dc0
summary: In Homo sapiens, granulosa cells are marked by canonical markers FOXL2, AMH, and INHBB.
span_literal:
which included canonical markers like FOXL2 , AMH , and INHBB for granulosa; CYP17A1 , CYP11A1 , and PTCH2 for theca; and dozens of previously unreported markers


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:d3f07a200cdf2c77636c
claim_id: claim:d3f07a200cdf2c77636c
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
The RL/EGL trajectory includes granule cells (GCs) and unipolar brush cells (UBCs) transitioning from progenitors (ATOH1) and differentiating cells (PAX6) towards defined GC (GABRA6) and UBC (LMX1A) states

summary:
In Homo sapiens, granule cell progenitors are marked by ATOH1, differentiating granule cells by PAX6, and defined granule cells by GABRA6.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:35e7f1400c55427d52f1
claim_id: claim:35e7f1400c55427d52f1
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
The oligodendrocyte lineage splits into proliferating oligodendrocyte progenitor cells (OPCs, PDGFRA), committed oligodendrocyte precursors (TNR), and postmitotic oligodendrocytes (MAG

summary:
In Homo sapiens, oligodendrocyte progenitor cells are marked by PDGFRA, committed oligodendrocyte precursors by TNR, and postmitotic oligodendrocytes by MAG.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:4a9a90cd4acadd8759b4
claim_id: claim:4a9a90cd4acadd8759b4
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
summary: In Homo sapiens, pre-oligodendrocyte progenitor cells are marked by EGFR expression.
span_literal:
we detected cells intermediate between astroglial progenitors and OPCs that likely represent the preOPC state (EGFR)18


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:88a490e894e684668068
claim_id: claim:88a490e894e684668068
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal: a group of midbrain-originating cells (LEF1) to the cerebellar primordia12
summary:
In Homo sapiens, midbrain-originating cells migrating to the cerebellar primordia are marked by LEF1 expression.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:3a9638dcdd40b4d58f3a
claim_id: claim:3a9638dcdd40b4d58f3a
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
summary: In Homo sapiens, PAX3 is a conserved marker of progenitors in the cerebellum.
span_literal:
e.g., PAX3 in progenitors, HOPX in astrocytes, ESRRB and FOXP2 in Purkinje cells, PAX2 in interneurons, and PAX6 and ETV1 in granule cells


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:16deb08ee65737faecd6
claim_id: claim:16deb08ee65737faecd6
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
interneuron-enriched PRDM8 and BHLHE22, which have previously been shown to form a repressor complex involved in pallial circuit formation34

summary:
In Homo sapiens, PRDM8 and BHLHE22 are conserved markers enriched in interneurons of the cerebellum.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:8bcc0c358fb6a33fdca6
claim_id: claim:8bcc0c358fb6a33fdca6
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
SATB2, which is transiently upregulated in differentiating granule cells and mainly known as a determinant of neocortical upper-layer neurons35

summary:
In Homo sapiens, SATB2 is transiently upregulated in differentiating granule cells of the cerebellum.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:c9f8a6961254e6a49512
claim_id: claim:c9f8a6961254e6a49512
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
We classified UBCs into two subsets: one expresses the canonical pan-UBC marker EOMES and is co-labeled by markers of known UBC subtypes6,7 (TRPC3, GRM1, CALB2), whereas the other is a so far uncharacterized EOMES-low UBC-like subset that is positive for HCRTR2

summary:
In Homo sapiens, unipolar brush cells express the canonical pan-unipolar brush cell marker EOMES and are co-labeled by TRPC3, GRM1, and CALB2, whereas an EOMES-low unipolar brush cell-like subset is positive for HCRTR2.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:a615f62d223e485d38ef
claim_id: claim:a615f62d223e485d38ef
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
We classified UBCs into two subsets: one expresses the canonical pan-UBC marker EOMES and is co-labeled by markers of known UBC subtypes6,7 (TRPC3, GRM1, CALB2), whereas the other is a so far uncharacterized EOMES-low UBC-like subset that is positive for HCRTR2

summary:
In Homo sapiens, the EOMES-low unipolar brush cell-like subset is positive for HCRTR2 and has low expression of EOMES.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:5203996817be923b9650
claim_id: claim:5203996817be923b9650
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
isthmic nuclei neurons include subsets that express marker genes related to dopaminergic (NR4A2), cholinergic (SLC5A7; subtype not detected in human), or somatostatin (SST) identities

summary:
In Homo sapiens, isthmic nuclei neurons include subsets expressing NR4A2 (dopaminergic identity) and SST (somatostatin identity).


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:30aa7adebb9e7d9e6366
claim_id: claim:30aa7adebb9e7d9e6366
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
We detected ZP2 expression in mature granule cells and glutamatergic deep nuclei neurons, and CPLX4 in granule cell layer interneurons, patterns that are supported by human immunohistochemistry data45

summary:
In Homo sapiens, ZP2 is expressed in mature granule cells and glutamatergic deep nuclei neurons, and CPLX4 is expressed in granule cell layer interneurons.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:06854f63d3c84334ca4d
claim_id: claim:06854f63d3c84334ca4d
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
autism and Down syndrome-associated DSCAM gained expression in human astroglia, and FGF2, implicated in pilocytic astrocytoma, gained expression in human astroglia and oligodendrocytes

summary:
In Homo sapiens, DSCAM gained expression in astroglia of the cerebellum. In Homo sapiens, FGF2 gained expression in astroglia and oligodendrocytes of the cerebellum.


claim_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea:claim:4bafaeb094c4184d7449
claim_id: claim:4bafaeb094c4184d7449
paper_key: hca:0093_10.1101_2021.12.20.473443_1d1224d1ea
span_literal:
include the mechanosensitive ion channel PIEZO2 and the phospholipase PLCZ1 expressed in human posterior ventricular zone or rhombic lip progenitors, respectively

summary:
In Homo sapiens, PIEZO2 is expressed in posterior ventricular zone progenitors and PLCZ1 is expressed in rhombic lip progenitors of the cerebellum.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:4cf9d4c95d413592075a
claim_id: claim:4cf9d4c95d413592075a
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
we annotated the five major clusters as lymphatic endothelial (PROX1, NRP2, PDPN, FXYD6, CD36, CAVIN2), blood endothelial (VWF, PECAM1), stromal (MYH11, ACTA2, COL1A1, THY1, PDGFRB, DES), epithelial (consisting of both ciliated epithelial—Epithelial Cell Adhesion Molecule (EPCAM), CAPS, FOXJ1, and nonciliated epithelial cells—EPCAM, PAX8), and immune (KIT, PTPRC, CD3, RUNX3, S100A9, FOLR2, CD86) cells.

summary:
In Homo sapiens uterus, lymphatic endothelial cells are marked by PROX1, NRP2, PDPN, FXYD6, CD36, and CAVIN2.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:df2f55f54a21b2a26730
claim_id: claim:df2f55f54a21b2a26730
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
summary:
In Homo sapiens uterus, ciliated epithelial cells are marked by Epithelial Cell Adhesion Molecule (EPCAM), CAPS, and FOXJ1.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:901766ac92e66612f3f4
claim_id: claim:901766ac92e66612f3f4
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
While all three express PV markers (MYH11, PDGFRB, MCAM, RGS5, SUSD2; Fig. 2 C and Datasets S6 and S7 ), each has its unique distinguishing markers.

summary:
In Homo sapiens uterus, perivascular cells express MYH11, PDGFRB, MCAM, RGS5, and SUSD2 as perivascular markers.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:5de847c9b7be51a718ea
claim_id: claim:5de847c9b7be51a718ea
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
For example, Stro-1 expresses higher levels of FOXC1, DEPP1, and CDKN1A; Stro-2 expresses higher levels of CTGF, HOPX, PRKCDBP (CAVIN3), and ATP5L; and Stro-3 has the highest expression of STEAP4 ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, perivascular cell subtype 1 (Stro-1) expresses higher levels of FOXC1, DEPP1, and CDKN1A.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:f9b268e5a7cb77419d16
claim_id: claim:f9b268e5a7cb77419d16
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
For example, Stro-1 expresses higher levels of FOXC1, DEPP1, and CDKN1A; Stro-2 expresses higher levels of CTGF, HOPX, PRKCDBP (CAVIN3), and ATP5L; and Stro-3 has the highest expression of STEAP4 ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, perivascular cell subtype 2 (Stro-2) expresses higher levels of CTGF, HOPX, PRKCDBP (CAVIN3), and ATP5L.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:22460fed63ea9ea709fe
claim_id: claim:22460fed63ea9ea709fe
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
These cells express some endothelial markers such as VWF and PECAM1 ( Fig. 2 C and Datasets S6 and S7 ) but lack HEG1 and FLI1.

summary:
In Homo sapiens uterus, tissue-resident vascular progenitor cells (Stro-4) express VWF and PECAM1 but lack HEG1 and FLI1.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:a6bb834f934d9a4ff4ce
claim_id: claim:a6bb834f934d9a4ff4ce
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Additionally, they express CD141 (THBD), CD144 (CDH5), CD105 (ENG), MCAM ( Fig. 2 C and Datasets S6 and S7 ), markers for tissue-resident vascular progenitor cells, which are known to reside in the intima of the vessels in individual organs ( 17 ).

summary:
In Homo sapiens uterus, tissue-resident vascular progenitor cells express THBD, CDH5, ENG, and MCAM.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:d448c6ce5c6cc36c89d8
claim_id: claim:d448c6ce5c6cc36c89d8
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
summary: In Homo sapiens uterus, RUNX3+ fibroblast (Stro-5) expresses RUNX3 and CD3E.
span_literal:
Stro-5, RUNX3+ fibroblast, expresses immune markers RUNX3 and CD3E, and has similarities with Imm-2: Fibrocytes (see Fig. 3 A below).


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:b2040eef48ef5ec4044b
claim_id: claim:b2040eef48ef5ec4044b
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
we performed gene–gene correlations in individual Stro-5 cells and show that these cells coexpress both stromal markers (THY1, PDGFRA, COL1A1) and immune markers (RUNX3, PTPRC, GNLY, CD3E)

summary:
In Homo sapiens uterus, RUNX3+ fibroblast (Stro-5) coexpresses stromal markers THY1, PDGFRA, COL1A1 and immune markers RUNX3, PTPRC, GNLY, CD3E.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:dfd90a667c5dbb4daa31
claim_id: claim:dfd90a667c5dbb4daa31
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Stro-6, uterine smooth muscle cells (uSMC) , specifically expresses SMC markers ACTA2 and DES and has moderate expression of MYH11; note that MYH11 is highest in Stro-1/2 ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, uterine smooth muscle cells (Stro-6) specifically express ACTA2 and DES and have moderate expression of MYH11.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:00443094a28caf4135be
claim_id: claim:00443094a28caf4135be
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal: Unlike the PV cells (Stro-1/2), Stro-6 has much lower expression of MCAM and PDGFRB.
summary:
In Homo sapiens uterus, uterine smooth muscle cells (Stro-6) have much lower expression of MCAM and PDGFRB compared to perivascular cells.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:b31328e527a1e75af292
claim_id: claim:b31328e527a1e75af292
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
These cells express varying levels of downstream targets of the cyclic Adenosine Monophosphate (cAMP) and insulin signaling, such as FOXO1, WNT4, PRL, IRS2, IGFBP1, and IGFBP3 ( 21 – 25 ) ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, decidualized fibroblast cells express FOXO1, WNT4, PRL, IRS2, IGFBP1, and IGFBP3.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:0f57949ce97e4d758d5b
claim_id: claim:0f57949ce97e4d758d5b
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Stro-11, stromal progenitor, is notable for its uniquely high expressions of cell cycle regulator MKI67 and the cyclins CCNB1-2 ( Fig. 2 C and Datasets S6 and S7 ) and is more prevalent in proliferative-stage endometrium samples ( Fig. 2 D ).

summary:
In Homo sapiens uterus, stromal progenitor (Stro-11) is notable for its uniquely high expression of MKI67, CCNB1, and CCNB2.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:5e1e269fe54c56531f23
claim_id: claim:5e1e269fe54c56531f23
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Epi-1 is Ciliated population as it expresses classic ciliated markers i.e. FOXJ1, CAPS, and PIFO ( Fig. 2 C and Dataset S7 ).

summary:
In Homo sapiens uterus, the ciliated epithelial cell population (Epi-1) expresses classic ciliated markers FOXJ1, CAPS, and PIFO.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:fbfa2184367f436c6022
claim_id: claim:fbfa2184367f436c6022
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Epi-2, Glandular Secretory, expresses MUC16, SOX5, PAX8, RIMKLB, DENND2C, and LMO7 ( Fig. 2 C and Datasets S6 and S7 ); many of which are previously described glandular secretory cell markers ( 31 ).

summary:
In Homo sapiens uterus, glandular secretory cells (Epi-2) express MUC16, SOX5, PAX8, RIMKLB, DENND2C, and LMO7.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:ebc35b1c392c982e01ac
claim_id: claim:ebc35b1c392c982e01ac
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
summary: In Homo sapiens uterus, SOX9 glandular cells (Epi-3) specifically express FOXA2, MMP26, and SOX9.
span_literal:
Epi-3, Sox9 Glandular, specifically expresses FOXA2 and MMP26, two known glandular markers ( 7 , 32 ), as well as SOX9.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:4f5c2d9f14f364dad91a
claim_id: claim:4f5c2d9f14f364dad91a
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Epi-4 is named Luminal, as it expresses LPAR3, LGR5, WNT7A, SAA1, and LCN2 ( Fig. 2 C and Datasets S6 and S7 ), which are implicated in luminal epithelial cell function ( 33 – 35 ).

summary:
In Homo sapiens uterus, luminal epithelial cells (Epi-4) express LPAR3, LGR5, WNT7A, SAA1, and LCN2.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:7d5f03c165cf31650ded
claim_id: claim:7d5f03c165cf31650ded
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
They both highly express PAEP, GPX3, and SCGB2A2, known glandular secretory markers; yet Epi-5 expresses higher levels of S100P, while Epi-6 expresses higher levels of TSPAN8, DPP4, as well as a moderate level of ciliate cell markers: FOXJ1, PIFO, and CAPS ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, glandular secretory-progenitor A (Epi-5) and glandular secretory-progenitor B (Epi-6) both highly express PAEP, GPX3, and SCGB2A2; Epi-5 expresses higher levels of S100P.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:8c88459a06c2d439d37c
claim_id: claim:8c88459a06c2d439d37c
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
They both highly express PAEP, GPX3, and SCGB2A2, known glandular secretory markers; yet Epi-5 expresses higher levels of S100P, while Epi-6 expresses higher levels of TSPAN8, DPP4, as well as a moderate level of ciliate cell markers: FOXJ1, PIFO, and CAPS ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, glandular secretory-progenitor B (Epi-6) highly expresses PAEP, GPX3, SCGB2A2, TSPAN8, DPP4, and moderately expresses FOXJ1, PIFO, and CAPS.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:340e31cf7ae5ff6e1121
claim_id: claim:340e31cf7ae5ff6e1121
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Epi-7 specifically expresses EPCAM along with WT1, TWIST2, TAGLN, SNAI2, ZEB1, VIM, suggesting that this is a Myoepithelial cell population ( Fig. 2 C and Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, myoepithelial cells (Epi-7) specifically express EPCAM, WT1, TWIST2, TAGLN, SNAI2, ZEB1, and VIM.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:ee2089d155c0e659ca23
claim_id: claim:ee2089d155c0e659ca23
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Epi-7 is the only epithelial cell population that expresses AR, while ESR1 is broadly expressed in all epithelial subtypes, and PGR is specifically high in Epi-3 and Epi-7,8,9

summary:
In Homo sapiens uterus, myoepithelial cell (Epi-7) is the only epithelial cell population that expresses AR.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:f83e792457286b154d61
claim_id: claim:f83e792457286b154d61
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
Epi-8, OLFM4_proliferative , expresses specifically high levels of TF HMGB2, OLFM4, and cell cycle genes TOP2A, MKI67, BIRC5, and CCNB.

summary:
In Homo sapiens uterus, OLFM4 proliferative cells (Epi-8) express specifically high levels of HMGB2, OLFM4, TOP2A, MKI67, BIRC5, and CCNB.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:21cecca80d29f2bed433
claim_id: claim:21cecca80d29f2bed433
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
summary: In Homo sapiens uterus, tissue-resident memory T cells (Epi-9) highly express RUNX3 and CD69.
span_literal:
Epi-9 is named tissue-resident memory T cell and highly expresses RUNX3 and CD69, two tissue-resident T cell markers ( Fig. 2 C and Datasets S6 and S7 ).


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:59714c8564dbdee94b79
claim_id: claim:59714c8564dbdee94b79
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal:
They are characterized by high expression of mesenchymal markers such as CD44, ACTA2, ZEB2, MYH11, STEAP4, and Col1A1/2 ( Fig. 2 C ), and reduced expression of classic endothelial markers [PECAM1 (CD31), TIE1, and VWF] ( Datasets S6 and S7 ).

summary:
In Homo sapiens uterus, endothelial-to-mesenchymal transition cells are characterized by high expression of CD44, ACTA2, ZEB2, MYH11, STEAP4, and COL1A1, and reduced expression of PECAM1, TIE1, and VWF.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:531218637a26ba5ceac3
claim_id: claim:531218637a26ba5ceac3
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
span_literal: Notably, EndoMT cells are the only endothelial cell subtype that expresses both ESR1 and PGR
summary:
In Homo sapiens uterus, endothelial-to-mesenchymal transition cells are the only endothelial cell subtype that expresses both ESR1 and PGR.


claim_key: hca:0094_10.1073_pnas.2404775121_07bae216d2:claim:f4c1b9c671e191a5dc42
claim_id: claim:f4c1b9c671e191a5dc42
paper_key: hca:0094_10.1073_pnas.2404775121_07bae216d2
summary: In Homo sapiens uterus, RUNX3+ fibroblast (Stro-5) expresses the highest level of HLA-A and HLA-C.
span_literal:
Stro-5 expresses the highest level of HLA-A and C ( Fig. 2 C and Datasets S6 and S7 ), which are class-I histocompatibility antigens that present antigen peptides to cytotoxic T cells; we therefore postulate that Stro-5 may be a dedicated antigen-presenting fibroblast population.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:98286b1904f761f42fe5
claim_id: claim:98286b1904f761f42fe5
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens, ciliated cells of the fallopian tube are positive for FOXJ1 and CAPS.
span_literal:
The ciliated cells (FOXJ1+/CAPS+), the most abundant and well defined, control gamete and embryo movement during fertilization and implantation


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:db261276b3c41565dc99
claim_id: claim:db261276b3c41565dc99
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens, secretory cells of the fallopian tube are positive for PAX8 and KRT7.
span_literal:
The secretory cells (PAX8+/KRT7+) produce and secrete factors required for fertilization and early embryo development.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:be5ff22695ad78d31244
claim_id: claim:be5ff22695ad78d31244
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
Although peg cells are often defined by EPCAM+/CD44+/ITGA6+, their biological functions are poorly understood

summary:
In Homo sapiens, peg cells of the fallopian tube are defined by expression of EPCAM, CD44, and ITGA6.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:06b654f0c7204080c069
claim_id: claim:06b654f0c7204080c069
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens, basal cells of the fallopian tube are defined by expression of EPCAM.
span_literal:
Basal cells are defined histologically by their round morphology with a cytoplasmic ring, and by expression of epithelial (EPCAM) and T-cell or resident T-cell markers, indicative of potential immune function


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:14c5b5d6a5c6a3288233
claim_id: claim:14c5b5d6a5c6a3288233
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens fallopian tube, ciliated cells are positive for EPCAM, FOXJ1, and CAPS.
span_literal:
we identified two major epithelial cell types (EPCAM), consisting of ciliated cells (FOXJ1, CAPS) and non-ciliated cells (PAX8, KRT7, OVGP1).


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:15639f1faaac23805fe9
claim_id: claim:15639f1faaac23805fe9
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens fallopian tube, fibroblasts are positive for DCN, COL1A1, and PDGFRA.
span_literal:
Within the stromal compartment we assigned 6 cell types: fibroblast (DCN, COL1A1, PDGFRA), myofibroblast (POSTN, PDGFRB, ACTA2), smooth muscle (DES, MYH11, ACTA2), pericyte (MCAM, CSPG4), blood endothelial (VWF, KDR, PECAM1), and lymphatic endothelial (PDPN, SCD1).


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:124b8b9eabdebb04ba72
claim_id: claim:124b8b9eabdebb04ba72
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens fallopian tube, B cells are positive for JCHAIN and SDC1.
span_literal:
Lastly, we identified 4 immune cell types: B cell (JCHAIN, SDC1), T/NK cell (RUNX3, CD3E, KLRC1), mast cell (KIT, MS4A2, TPSB2), and macrophage (CD68, ITGAX, CD163).


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:3d8ecd08e93adf8230da
claim_id: claim:3d8ecd08e93adf8230da
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
Based on subtype-specific RNA markers, CE1-1 cells are likely mature, multi-ciliated cells, as they express genes encoding proteins associated with motile cilia and flagella (CFAP157, CFAP73, CFAP52, and CFAP126), dyneins (DYNLL1, DNAI1, DNAI2, DNAH11, KIF21A), radial spike proteins (RSPH1, 4a, and 9), intraflagellar transport proteins (IFT57), and calcium sensing and binding proteins (CAPS, CALM1)

summary:
In Homo sapiens fallopian tube, ciliated epithelial subtype 1-1 cells express CFAP157, CFAP73, CFAP52, CFAP126, DYNLL1, DNAI1, DNAI2, DNAH11, KIF21A, RSPH1, IFT57, CAPS, and CALM1, consistent with mature multi-ciliated cells.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:ae01f035ba0ec6681ec5
claim_id: claim:ae01f035ba0ec6681ec5
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
CE1-3 cells express genes involved in antigen processing (CD74), presentation (HLA-DMA, HLA-DRB1), and chemokine/cytokines (CCL20, CXCL1-3)

summary:
In Homo sapiens fallopian tube, ciliated epithelial subtype 1-3 cells express CD74, HLA-DMA, HLA-DRB1, and CCL20.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:4fe77a87dd3d7e5547e2
claim_id: claim:4fe77a87dd3d7e5547e2
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal: CE1-4 cells express extracellular matrix genes COL1A1, TAGLN, LGALS
summary:
In Homo sapiens fallopian tube, ciliated epithelial subtype 1-4 cells express COL1A1, TAGLN, and LGALS.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:5437d9322de56f481312
claim_id: claim:5437d9322de56f481312
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal: All six subtypes express classic secretory cell markers EPCAM, PAX8, and KRT7
summary:
In Homo sapiens fallopian tube, all six non-ciliated secretory epithelial subtypes express classic secretory cell markers EPCAM, PAX8, and KRT7.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:deff23555987ea1235a7
claim_id: claim:deff23555987ea1235a7
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
NCSE2-1cells account for 1.6-2% of the NCSEs (Supplemental Figure 3B), and express EMT markers ACTA2, ZEB1, SNAI, LGALS1, SPARC, and endothelial cell markers CAVIN2, PECAM, VWF

summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-1 cells express ACTA2, ZEB1, SNAI, LGALS1, SPARC, CAVIN2, PECAM, and VWF.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:4c50f33aef027d8cd8bc
claim_id: claim:4c50f33aef027d8cd8bc
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
Like NCSE2-1, NCSE2-2 cells express EMT markers ACTA2, COL1A1, MMP2, PRRX1, TWIST2, DES, DCN, FN1, ZEB1, TIMP3, LGALS1, SPARC

summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-2 cells express epithelial-mesenchymal transition markers ACTA2, COL1A1, MMP2, PRRX1, TWIST2, DES, DCN, FN1, ZEB1, TIMP3, LGALS1, and SPARC.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:6b7da3d70dafecd4ccf3
claim_id: claim:6b7da3d70dafecd4ccf3
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
In addition to expressing PAX8, KRT7 and OVGP1, NCSE2-3 cells can be distinguished by expression of SOX17 and WNT-signaling regulator RSPO1

summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-3 cells express PAX8, KRT7, OVGP1, SOX17, and RSPO1.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:262d7dea4304e640cbdd
claim_id: claim:262d7dea4304e640cbdd
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal: NCSE2-4 cells express genes related to ovarian cancer (LAMB3, MSLN), and LIF
summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-4 cells express LAMB3, MSLN, and LIF.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:e423f0fe95ddaa2cfcee
claim_id: claim:e423f0fe95ddaa2cfcee
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal: Notably, NCSE2-5 cells express stem/progenitor markers such as LGR5, CD24, and TNFRSF19
summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-5 cells express stem/progenitor markers LGR5, CD24, and TNFRSF19.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:2212e23eca5464c4dee0
claim_id: claim:2212e23eca5464c4dee0
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal: Finally, NCSE2-6 cells express lymphoid lineage markers RUNX3, CD3E, PTPRC
summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-6 cells express lymphoid lineage markers RUNX3, CD3E, and PTPRC, consistent with a basal or resident memory T-cell identity.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:7145a8abd0e2186ec3a2
claim_id: claim:7145a8abd0e2186ec3a2
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
Cluster-specific genes ([Figure 4B](460628v1_fig4.tif)) allowed annotation of fibroblast (DCN, PDGFRA), myofibroblast (PRRX1, POSTN), and smooth muscle cell (ACTA2, MYH11)

summary:
In Homo sapiens fallopian tube, fibroblasts are marked by DCN and PDGFRA, myofibroblasts by PRRX1 and POSTN, and smooth muscle cells by ACTA2 and MYH11.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:aadecc9bec112226f1f4
claim_id: claim:aadecc9bec112226f1f4
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
summary: In Homo sapiens fallopian tube, pericytes are marked by MCAM, PDGFRB, and CSPG4.
span_literal:
The next three cell types are pericyte (MCAM, PDGFRB, CSPG4), blood endothelial (VWF, SELE), and lymphatic endothelial (PPROX1, LYVE1, CAVIN2) cells


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:af021e2d893f6aacf918
claim_id: claim:af021e2d893f6aacf918
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
The next three cell types are pericyte (MCAM, PDGFRB, CSPG4), blood endothelial (VWF, SELE), and lymphatic endothelial (PPROX1, LYVE1, CAVIN2) cells

summary:
In Homo sapiens fallopian tube, lymphatic endothelial cells are marked by PPROX1, LYVE1, and CAVIN2.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:e4d4244ce43cb9832b11
claim_id: claim:e4d4244ce43cb9832b11
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
we identified two secretory cell progenitors: (1) an epithelial progenitor (LGR5/PGR) population, NCSE2-5, predicted to give rise to mature secretory cells (i.e., NCSE2-4), and (2) a bipotential progenitor population, NCSE2-2, expressing several EMT markers, predicted to generate ciliated epithelial cells CE1-4 on one hand, and the blood endothelial cells in the stromal compartment on the other

summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-5 is an epithelial progenitor population marked by LGR5 and PGR.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:d24a3afd839dee5f322c
claim_id: claim:d24a3afd839dee5f322c
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
NCSE2-5 cells express stem/progenitor markers such as LGR5, CD24, and TNFRSF19 ([Figure 3B, G](460628v1_fig3.tif)) (Ng et al. 2014; La Manno et al. 2018; Lamouille, Xu, Jian, and Derynck, Rik 2014; Mabbott et al. 2013; Blanpain, Horsley, and Fuchs 2007), as well as CD44 and ITGA6

summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-5 cells express stem/progenitor markers LGR5, CD24, TNFRSF19, CD44, and ITGA6.


claim_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f:claim:90faf4c990d5408560f6
claim_id: claim:90faf4c990d5408560f6
paper_key: hca:0095_10.1101_2021.09.16.460628_23a839e09f
span_literal:
This population may be hormonally regulated, due to its high expression levels of hormone receptors ESR, PGR, and AR (Supplemental Figure 3G), and CYP1B1

summary:
In Homo sapiens fallopian tube, non-ciliated secretory epithelial subtype 2-5 cells express high levels of estrogen receptor, progesterone receptor, androgen receptor, and CYP1B1.


claim_key: hca:0096_10.1126_sciadv.abo2467_05989af98e:claim:6d287a312210dafc9d9f
claim_id: claim:6d287a312210dafc9d9f
paper_key: hca:0096_10.1126_sciadv.abo2467_05989af98e
summary: In Homo sapiens substantia nigra, neurons are marked by SYT1.
span_literal:
On the basis of known marker genes, we profiled all major cell types in the SN, including neurons ( SYT1 ), oligodendrocytes (Oligo; MAG and MOBP ), oligodendrocyte precursor cells (OPCs; PDGFRA ), astrocytes (Ast; AQP4 and GFAP ), microglia (Micro; CD74 and RUNX1 ), endothelial cells (Endo; CLDN5 ), and pericytes (Peri; PDGFRB )


