# claims

claim_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da:claim:2c6c6537edad49cfda03
claim_id: claim:2c6c6537edad49cfda03
paper_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da
span_literal:
As with the mouse, the human scANVI model also utilised the expression of some traditional markers, such as the surface marker PDGFRA for PrE, the TGF-β ligands NODAL and GDF3 for the EPI and several critical genes in placental development KRT18, CGF and PGF for TE (Suppl. Table 4, S4).

summary:
In Homo sapiens, the human scANVI model identified KRT18, CGF, and PGF as markers for trophectoderm.


claim_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da:claim:a4516f37c090e73fee0d
claim_id: claim:a4516f37c090e73fee0d
paper_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da
span_literal:
Similar analysis in the human model revealed the classification of transcriptomes to prelineage or 8C stages logically relied on the previously identified NLRP family gene NLRP4 and the oocyte factor Oocyte secreted protein 2 (OOSP2).

summary:
In Homo sapiens, the classification of prelineage or eight-cell stage cells relied on NLRP4 and oocyte secreted protein 2 (OOSP2).


claim_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da:claim:b64cfef743e537e7022e
claim_id: claim:b64cfef743e537e7022e
paper_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da
span_literal:
Moreover, while our human classifier also avoided factors like SOX2 and GATA6, it reiterated the importance of PDGFRA as a PrE marker, also highlighting the significance of TGF-β family genes in epiblast (NODAL and GDF3) and NANOG.

summary:
In Homo sapiens, the human classifier reiterated the importance of PDGFRA as a primitive endoderm marker, highlighted NODAL and GDF3 as markers for epiblast, and identified NANOG as a marker for epiblast.


claim_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1:claim:8d23d4ce5409b47d974b
claim_id: claim:8d23d4ce5409b47d974b
paper_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1
summary: In Homo sapiens, tendon-derived stem cells are positive for the markers CD44, CD90, and CD105.
span_literal:
tendon stem cells were successfully isolated from human tissues, which were positive for markers CD44, CD90, and CD105, and exhibited clonality and multilineage differentiation ability.


claim_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1:claim:38ab5fce03f0730dcf3c
claim_id: claim:38ab5fce03f0730dcf3c
paper_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1
span_literal:
The specific surface markers CD44, CD90 and CD105 of hTDSCs were detected, and the positive rates were 99.24% ± 0.15%, 99.52% ± 1.52% and 89.81% ± 2.7%, respectively (Figure 1B).

summary:
In Homo sapiens, human tendon-derived stem cells are positive for the surface markers CD44, CD90, and CD105.


claim_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1:claim:b56642345568be908e06
claim_id: claim:b56642345568be908e06
paper_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1
span_literal:
The primary isolated hTDSC have uniform morphology, stable growth, positive cell surface markers CD44, CD90 and CD105, and can undergo tri-lineage differentiation under corresponding induction conditions, with typical stem cell characteristics.

summary:
In Homo sapiens, primary isolated human tendon-derived stem cells are positive for the cell surface markers CD44, CD90, and CD105.


claim_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1:claim:2a2314eb5ca7ac6b3a0a
claim_id: claim:2a2314eb5ca7ac6b3a0a
paper_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1
span_literal:
The cell surface markers CD44, CD90, and CD105 are positive and can differentiate into three lines under corresponding induction conditions.

summary:
In Homo sapiens, tendon-derived stem cells are positive for the cell surface markers CD44, CD90, and CD105.


claim_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1:claim:21fe5ee7b529928a9bc7
claim_id: claim:21fe5ee7b529928a9bc7
paper_key: biorxiv:e78eaa01-6c93-1014-839e-bb3dc2108ab1
span_literal:
The cell surface markers CD44, CD90 and CD105 are positive, and can differentiate into three lines under corresponding induction conditions.

summary:
In Homo sapiens, human tendon-derived stem cells are positive for the cell surface markers CD44, CD90, and CD105.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:44af250c8f2743adb157
claim_id: claim:44af250c8f2743adb157
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
The FHF, characterized by expression of NKX2.5, TBX5, and HAND1, predominantly generates the left ventricle

summary:
In Homo sapiens, the first heart field is characterized by expression of NKX2.5, TBX5, and HAND1 and predominantly generates the left ventricle.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:036dc2802fddefc7545b
claim_id: claim:036dc2802fddefc7545b
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
while the SHF, marked by NKX2.5 and ISL1 expression, contributes to the right ventricle, OFT, and atrial regions

summary:
In Homo sapiens, the second heart field is marked by NKX2.5 and ISL1 expression and contributes to the right ventricle, outflow tract, and atrial regions.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:2e54bca1320cb2087196
claim_id: claim:2e54bca1320cb2087196
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
Cardiac progenitors of the FHF express HAND1 at low levels, compared to high expression in extraembryonic mesoderm and epicardial progenitors

summary:
In Homo sapiens, cardiac progenitors of the first heart field express HAND1 at low levels, compared to high expression in extraembryonic mesoderm and epicardial progenitor.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:9215b6f9e4b3a380edec
claim_id: claim:9215b6f9e4b3a380edec
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
more than 95% of cTNT-positive CMs expressed HAND1 across all CHIR concentrations, a marker positive in both LV and OFT CMs

summary:
In Homo sapiens, more than 95% of cardiac troponin T-positive cardiomyocytes expressed HAND1, a marker positive in both left ventricular and outflow tract cardiomyocytes.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:a39062650d4344182297
claim_id: claim:a39062650d4344182297
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
Critically, all CMs from both CHIR concentrations exhibited co-expression of FHF-derived and LV markers HAND1 and TBX5, indicating that the MYL2-low population represents immature LV CMs rather than alternative cardiac lineages

summary:
In Homo sapiens, all cardiomyocytes exhibited co-expression of first heart field-derived and left ventricular markers HAND1 and TBX5, indicating that the MYL2-low population represents immature left ventricular cardiomyocytes.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:ac1a58345775fce83014
claim_id: claim:ac1a58345775fce83014
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
multi-marker single-cell analysis revealed that more than 95% of mature CMs co-expressed the chamber-defining combination of MYL2, HAND1, and TBX5

summary:
In Homo sapiens, multi-marker single-cell analysis revealed that more than 95% of mature left ventricular cardiomyocytes co-expressed the chamber-defining combination of MYL2, HAND1, and TBX5.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:5839738219816ec226e5
claim_id: claim:5839738219816ec226e5
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
Mature CMs were negative for the left atrial-specific marker PITX2 and the cardiac conduction system marker TBX3

summary:
In Homo sapiens, mature left ventricular cardiomyocytes were negative for the left atrial-specific marker PITX2 and the cardiac conduction system marker TBX3.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:522a7d8add4db180aab7
claim_id: claim:522a7d8add4db180aab7
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
only approximately 5% of cells expressed the atrial marker NR2F2, with these NR2F2-positive cells largely corresponding to the small MYL2-negative fraction

summary:
In Homo sapiens, only approximately 5% of cardiomyocytes expressed the atrial marker NR2F2, with these NR2F2-positive cells largely corresponding to the small MYL2-negative fraction of atrial cardiomyocytes.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:0638f0466e713436ca7d
claim_id: claim:0638f0466e713436ca7d
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
The transcription factor MESP1, the earliest transcriptional regulator committing hPSCs to cardiovascular lineage, also showed increased expression with higher CHIR concentrations.

summary:
In Homo sapiens, the transcription factor MESP1 is the earliest transcriptional regulator committing human pluripotent stem cells to cardiovascular lineage.


claim_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06:claim:5163a0a9af50a84de532
claim_id: claim:5163a0a9af50a84de532
paper_key: biorxiv:e8350987-7003-1014-ae7a-192d8e5e2a06
span_literal:
The ventricular protein MYL2 (MLC2v) has been the most extensively used marker for subtype identity characterization

summary:
In Homo sapiens, the ventricular protein MYL2 (myosin light chain 2 ventricular) has been the most extensively used marker for ventricular cardiomyocyte subtype identity characterization.


claim_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae:claim:f509d39240f189c8cdf8
claim_id: claim:f509d39240f189c8cdf8
paper_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae
span_literal:
We developed HCR probes for 1 marker of each cell type (AGER for AT1 cells, SFTPC for AT2 cells, and MARCO for alveolar macrophages, Supp. Fig. 6).

summary:
In Homo sapiens lung, AGER is a marker gene for alveolar type 1 cells, SFTPC is a marker gene for alveolar type 2 cells, and MARCO is a marker gene for alveolar macrophages.


claim_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae:claim:7e9ff0561b6bcfd97fd5
claim_id: claim:7e9ff0561b6bcfd97fd5
paper_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae
span_literal:
We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene (SFTPC) and the alveolar macrophage marker gene (MARCO), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene (AGER).

summary:
In Homo sapiens lung, SFTPC is a marker gene for alveolar type 2 cells, MARCO is a marker gene for alveolar macrophages, and AGER is a marker gene for alveolar type 1 cells.


claim_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae:claim:5dd8c5f1bff9fcb7705a
claim_id: claim:5dd8c5f1bff9fcb7705a
paper_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae
span_literal:
We probed FFPE human lung tissue with SARS-CoV-2 probe sets as well as probe sets for cell-type specific marker genes, AGER for AT1 cells and SFTPC for AT2 cells.

summary:
In Homo sapiens lung tissue, AGER is a cell-type specific marker gene for alveolar type 1 cells and SFTPC is a cell-type specific marker gene for alveolar type 2 cells.


claim_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae:claim:f9945f88b00b9c2bdd0d
claim_id: claim:f9945f88b00b9c2bdd0d
paper_key: biorxiv:e890b47f-6ccc-1014-913e-b4bab8edebae
summary: In Homo sapiens, MARCO is a macrophage specific gene used to identify alveolar macrophages.
span_literal:
We multiplexed a probe set for a macrophage specific gene (MARCO) with the SARS-CoV-2 ORF1a probe set (Fig. 4a).


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:515acef750f5c4bf91d3
claim_id: claim:515acef750f5c4bf91d3
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
CDKN1A was enriched in 7 cell types, thus is included in SenSet, while CDKN2A, which was enriched in only alveolar macrophages, is not included.

summary:
In Homo sapiens lung, CDKN2A is a positive marker of senescent alveolar macrophages, being enriched only in that cell type among senescent cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:546db24d84baf6edc37a
claim_id: claim:546db24d84baf6edc37a
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
Additional genes upregulated in most senescent cell types include ZFP36 ring finger protein (ZFP36, 16 cell types), Jun proto-oncogene (JUN, 13), and thioredoxin interacting protein (TXNIP), early growth response 1 (EGR1), Fos proto-oncogene (FOS) (11 each), all of which encode for proteins known to be involved in signaling in transcriptional response to hypoxia and cellular stress29,30.

summary:
In Homo sapiens lung, ZFP36 ring finger protein, Jun proto-oncogene, thioredoxin interacting protein, early growth response 1, and Fos proto-oncogene are upregulated in senescent cells across multiple cell types.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:317b8d31a0ad7e5d310a
claim_id: claim:317b8d31a0ad7e5d310a
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
In contrast, nucleoside diphosphate kinase 2 (NME2), a suppressor of apoptosis, was downregulated in 9 cell types, followed by nucleophosmin 1 (NPM1) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (7 each), involved in DNA replication and cell cycle31–33.

summary:
In Homo sapiens lung, nucleoside diphosphate kinase 2 (NME2), nucleophosmin 1 (NPM1), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are downregulated in senescent cells across multiple cell types.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:53a269a008d7c668fd1e
claim_id: claim:53a269a008d7c668fd1e
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
We found substantial overlap in upregulated genes between basal(−) cells and type II(−) pneumocytes, fibroblasts(−), respectively, with TNFRSF1A, CITED2, and ZFP36 in common across all three.

summary:
In Homo sapiens lung, TNFRSF1A, CITED2, and ZFP36 are upregulated in senescent basal cells, senescent type II pneumocytes, and senescent fibroblasts.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:5cdc5252d19dad586649
claim_id: claim:5cdc5252d19dad586649
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
We found substantial overlap in upregulated genes between basal(−) cells and type II(−) pneumocytes, fibroblasts(−), respectively, with TNFRSF1A, CITED2, and ZFP36 in common across all three.

summary:
In Homo sapiens lung, TNFRSF1A, CITED2, and ZFP36 are upregulated in senescent type II pneumocytes, as well as in senescent basal cells and senescent fibroblasts.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:3cecf99826f341f8ebbf
claim_id: claim:3cecf99826f341f8ebbf
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
We found substantial overlap in upregulated genes between basal(−) cells and type II(−) pneumocytes, fibroblasts(−), respectively, with TNFRSF1A, CITED2, and ZFP36 in common across all three.

summary:
In Homo sapiens lung, TNFRSF1A, CITED2, and ZFP36 are upregulated in senescent fibroblasts, as well as in senescent basal cells and senescent type II pneumocytes.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:6a556e1f2bf9a0884dbf
claim_id: claim:6a556e1f2bf9a0884dbf
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
For instance, LMNA, encoding for lamin A protein, known to be downregulated in more immature/undifferentiated cells40, was downregulated in basal(−) cells, but upregulated in both fibroblasts(−) and type II pneumocytes(−).

summary:
In Homo sapiens lung, LMNA is downregulated in senescent basal cells but upregulated in senescent fibroblasts and senescent type II pneumocytes.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:cf9fafd1c455ac50177a
claim_id: claim:cf9fafd1c455ac50177a
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
Notably, 15 genes downregulated in fibroblasts(−) in the HLCA dataset were also downregulated in fibroblasts(−) in the treated PCLS data: CALR, GAPDH, GUK1, IL32, MIF, NME2, NPM1, PKM, PLAUR, RAB13, S100A11, THBS1, TNFAIP3, TXN, YBX1.

summary:
In Homo sapiens lung, CALR, GAPDH, GUK1, IL32, MIF, NME2, NPM1, PKM, PLAUR, RAB13, S100A11, THBS1, TNFAIP3, TXN, and YBX1 are downregulated in senescent fibroblasts.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:0b4fe000f2440d1ee0b6
claim_id: claim:0b4fe000f2440d1ee0b6
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
For AT2(−) cells, 13 SenSet markers were upregulated in both the HLCA (19 total) and the PCLS (73 total), including TNFRSF1A, PKM, PEBP1, ID1, ZFP36, LGALS3, RAC1, LMNA, S100A11, CITED2, B2M, JUN, SELENOH.

summary:
In Homo sapiens lung, TNFRSF1A, PKM, PEBP1, ID1, ZFP36, LGALS3, RAC1, LMNA, S100A11, CITED2, B2M, JUN, and SELENOH are upregulated in senescent alveolar type 2 cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:4ae616f2f509ec15f082
claim_id: claim:4ae616f2f509ec15f082
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
Among the 19 upregulated genes in fibroblasts(−), 8 genes are also upregulated in basal(−) cells and/or in AT2(−) cells such as TNFRSF1A, YPEL3, SPOP, ZFP36, CITED2, and MARCKS (Fig. 3G).

summary:
In Homo sapiens lung, TNFRSF1A, YPEL3, SPOP, ZFP36, CITED2, and MARCKS are upregulated in senescent fibroblasts and also in senescent basal cells and/or senescent alveolar type 2 cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:37a8a66646932453a1eb
claim_id: claim:37a8a66646932453a1eb
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
For instance, PLAUR, involved in fibroblast-to-myofibroblast differentiation74, was downregulated in fibroblasts(−) but upregulated in basal(−) cells.

summary:
In Homo sapiens lung, PLAUR is downregulated in senescent fibroblasts but upregulated in senescent basal cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:c5cc0e5fb45f34aca4d0
claim_id: claim:c5cc0e5fb45f34aca4d0
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
For instance, PLAUR, involved in fibroblast-to-myofibroblast differentiation74, was downregulated in fibroblasts(−) but upregulated in basal(−) cells.

summary:
In Homo sapiens lung, PLAUR is upregulated in senescent basal cells but downregulated in senescent fibroblasts.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:5cd7446755ce5186fc17
claim_id: claim:5cd7446755ce5186fc17
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
IGFBP4 encodes for insulin-like growth factor binding protein 4, and is downregulated in fibroblasts(−) and upregulated in AT2(−) cells.

summary:
In Homo sapiens lung, insulin-like growth factor binding protein 4 (IGFBP4) is downregulated in senescent fibroblasts and upregulated in senescent alveolar type 2 cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:9c699bc97d034812e1dd
claim_id: claim:9c699bc97d034812e1dd
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
IGFBP4 encodes for insulin-like growth factor binding protein 4, and is downregulated in fibroblasts(−) and upregulated in AT2(−) cells.

summary:
In Homo sapiens lung, insulin-like growth factor binding protein 4 (IGFBP4) is upregulated in senescent alveolar type 2 cells and downregulated in senescent fibroblasts.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:815eb3b65241daad1a17
claim_id: claim:815eb3b65241daad1a17
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
TXNIP, associated with oxidative stress responses, was upregulated in both basal(−) cells and AT2(−) cells.

summary:
In Homo sapiens lung, thioredoxin interacting protein (TXNIP) is upregulated in senescent basal cells and senescent alveolar type 2 cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:3716e543bc84ff12840d
claim_id: claim:3716e543bc84ff12840d
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
span_literal:
TXNIP, associated with oxidative stress responses, was upregulated in both basal(−) cells and AT2(−) cells.

summary:
In Homo sapiens lung, thioredoxin interacting protein (TXNIP) is upregulated in senescent alveolar type 2 cells and senescent basal cells.


claim_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15:claim:6f9d3c200e45078b9703
claim_id: claim:6f9d3c200e45078b9703
paper_key: biorxiv:e91c125a-709d-1014-bc43-9d192767cd15
summary: In Homo sapiens lung, CTNNB1 is downregulated in senescent type II pneumocytes.
span_literal:
Type II pneumocytes(−) also show an upregulation of 19 SenSet genes (different set), and 1 downregulated gene, CTNNB1.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:1f7547ad4d78c37fa20a
claim_id: claim:1f7547ad4d78c37fa20a
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
we also examined the primed hESCs cells with several well-characterized primed-specific markers (e.g., CD24, CD57, and CD90) and naïve-specific markers (e.g., CD75, SUSD2, and CD130)

summary:
In Homo sapiens, primed human embryonic stem cells are marked by the primed-specific markers CD24, CD57, and CD90.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:dd45dc0bd299a0abadf5
claim_id: claim:dd45dc0bd299a0abadf5
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
we also examined the primed hESCs cells with several well-characterized primed-specific markers (e.g., CD24, CD57, and CD90) and naïve-specific markers (e.g., CD75, SUSD2, and CD130)

summary:
In Homo sapiens, naïve human embryonic stem cells are marked by the naïve-specific markers CD75, SUSD2, and CD130.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:725133087eec6c6d5ae3
claim_id: claim:725133087eec6c6d5ae3
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
RSeT hESCs did not express naïve surface markers such as CD75, SUSD2, and CD130 at a significant level.

summary:
In Homo sapiens, RSeT human embryonic stem cells do not significantly express the naïve surface markers CD75, SUSD2, and CD130.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:63963710ff74ec711fb8
claim_id: claim:63963710ff74ec711fb8
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
Some of the most notable human naïve signature genes (e.g., DNMT3L, DPPA2, DPPA5, TFCP2L1, XIST, and ZFP42) remained unchanged by microarray assays

summary:
In Homo sapiens, the notable naïve signature genes DNMT3L, DPPA2, DPPA5, TFCP2L1, XIST, and ZFP42 remained unchanged in RSeT human embryonic stem cells compared with primed cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:6e192f08d4abd9b5ebfe
claim_id: claim:6e192f08d4abd9b5ebfe
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal: Notably, only a few naïve pluripotency genes (e.g., KLF4) were upregulated
summary:
In Homo sapiens, the naïve pluripotency gene KLF4 was upregulated in RSeT human embryonic stem cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:a2a3787ebab22456ecf3
claim_id: claim:a2a3787ebab22456ecf3
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
Interestingly, NANOG was downregulated in RSeT cells in both RSeT normoxia (RN) and RSeT hypoxia (RH) conditions

summary:
In Homo sapiens, NANOG was downregulated in RSeT human embryonic stem cells under both normoxia and hypoxia conditions.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:a9577b8f07572e63adc7
claim_id: claim:a9577b8f07572e63adc7
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
POU5F1, another important pluripotency marker gene, was also significantly suppressed in RSeT hESCs as determined by qPCR

summary:
In Homo sapiens, POU5F1, a pluripotency marker gene, was significantly suppressed in RSeT human embryonic stem cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:394b6c0773c5fb765a50
claim_id: claim:394b6c0773c5fb765a50
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
Moreover, the expression of GDF3 and NODAL, which were highly expressed in the naïve epiblast of human embryos (Blakeley et al., 2015; Stirparo et al., 2018), was also significantly reduced in RSeT hESCs

summary:
In Homo sapiens, GDF3 and NODAL are highly expressed in the naïve epiblast and were significantly reduced in RSeT human embryonic stem cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:7b6dd338ffbe26508cfc
claim_id: claim:7b6dd338ffbe26508cfc
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
Moreover, the expression of GDF3 and NODAL, which were highly expressed in the naïve epiblast of human embryos (Blakeley et al., 2015; Stirparo et al., 2018), was also significantly reduced in RSeT hESCs

summary:
In Homo sapiens, GDF3 and NODAL were significantly reduced in RSeT human embryonic stem cells compared with naïve epiblast cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:dc74805865d6dd6ab65b
claim_id: claim:dc74805865d6dd6ab65b
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
several formative pluripotency associated genes (e.g., DNMT3A, DNMT3B, OTX2, SALL2, and SOX3) and imprinted gene clusters (e.g., DLK1, MEG3, and MEST) had no significant alterations

summary:
In Homo sapiens, formative pluripotency associated genes DNMT3A, DNMT3B, OTX2, SALL2, and SOX3 as well as imprinted genes DLK1, MEG3, and MEST had no significant alterations in RSeT human embryonic stem cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:5b991d1e407e7455dd76
claim_id: claim:5b991d1e407e7455dd76
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal: Other down-regulated primed genes include CER1, EGR1, GSC, LEFTY1, NODAL, and ZIC2
summary:
In Homo sapiens, the primed genes CER1, EGR1, GSC, LEFTY1, NODAL, and ZIC2 were down-regulated in RSeT human embryonic stem cells.


claim_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c:claim:a676e1f64d0c52f56455
claim_id: claim:a676e1f64d0c52f56455
paper_key: biorxiv:e9d73630-745a-1014-825d-9281d616c32c
span_literal:
RSeT hESCs highly expressed several primed pluripotency surface markers such as SSEA-4, Tra-1-60, and Tra-1-81

summary:
In Homo sapiens, RSeT human embryonic stem cells highly expressed the primed pluripotency surface markers SSEA-4, Tra-1-60, and Tra-1-81.


claim_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078:claim:5127c484a8d22fabe7d7
claim_id: claim:5127c484a8d22fabe7d7
paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
span_literal:
For the classification of major cell types, we first thresholded the different markers by quantiles, depending on the specificity and overall signal intensity of each marker. We started with the following default values: {PAX5: 0.8, CD3: 0.7, CD11b: 0.8, CD11c: 0.9, CD68: 0.9, CD31: 0.95, CD34: 0.95, CD90: 0.95, Podoplanin: 0.95}.

summary:
In Homo sapiens B cell Non-Hodgkin lymphoma lymph node biopsies, PAX5 is used as a marker for B cell classification.


claim_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078:claim:f50ec7f91f8bcb7cc8c8
claim_id: claim:f50ec7f91f8bcb7cc8c8
paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
span_literal:
For the classification of major cell types, we first thresholded the different markers by quantiles, depending on the specificity and overall signal intensity of each marker. We started with the following default values: {PAX5: 0.8, CD3: 0.7, CD11b: 0.8, CD11c: 0.9, CD68: 0.9, CD31: 0.95, CD34: 0.95, CD90: 0.95, Podoplanin: 0.95}.

summary:
In Homo sapiens B cell Non-Hodgkin lymphoma lymph node biopsies, CD3 is used as a marker for T cell classification.


claim_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078:claim:eb6a7fc2e48c592f3107
claim_id: claim:eb6a7fc2e48c592f3107
paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
span_literal:
For the classification of major cell types, we first thresholded the different markers by quantiles, depending on the specificity and overall signal intensity of each marker. We started with the following default values: {PAX5: 0.8, CD3: 0.7, CD11b: 0.8, CD11c: 0.9, CD68: 0.9, CD31: 0.95, CD34: 0.95, CD90: 0.95, Podoplanin: 0.95}.

summary:
In Homo sapiens B cell Non-Hodgkin lymphoma lymph node biopsies, CD68 is used as a marker for macrophage classification.


claim_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078:claim:f626d63f98bfda95f64f
claim_id: claim:f626d63f98bfda95f64f
paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
summary:
In Homo sapiens B cell Non-Hodgkin lymphoma lymph node biopsies, CD11c is used as a marker for dendritic cell classification.


claim_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078:claim:5cf5bffeb7def14ef038
claim_id: claim:5cf5bffeb7def14ef038
paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
summary: In Homo sapiens, CD68 is used as a marker for macrophage segmentation.
span_literal:
For example, segmentation of macrophages or dendritic cells can be hampered by their large size beyond the imaged tissue’s thickness and irregular shape. To counteract this problem, we can perform independent segmentation on several markers, e.g., DAPI (nuclei), CD68 (macrophages) and CD11c (dendritic cells).


claim_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078:claim:765258bb515d239b6d97
claim_id: claim:765258bb515d239b6d97
paper_key: biorxiv:ea9c1bed-6e40-1014-a65a-d0c254f9e078
span_literal:
Next to single marker positivity or negativity, a cell subtype can also be defined by a combination of both positive and negative expression, or by a set of alternative markers (e. g. a cytotoxic T cell could be predicted to be exhausted if it expresses either PD1 or TIM3).

summary:
In Homo sapiens, a cytotoxic T cell could be predicted to be an exhausted cytotoxic T cell if it expresses either PD1 or TIM3.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:9e818846299c5fa6c950
claim_id: claim:9e818846299c5fa6c950
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
For Ciliated Cells, we examined the distribution of the Interferon-responsive Ciliated Cell subtype, previously reported as expanded in COVID-19 patients. Using the top 5 DEG markers (IFI6, ISG15, IFIT1, IFI27, MX1) for this known subtype, we observed a strong correlation between the subtype signature score and our infection-associated subgroup (Figure 3j).

summary:
In Homo sapiens, the interferon-responsive ciliated cell subtype is marked by positive expression of IFI6, ISG15, IFIT1, IFI27, and MX1.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:9e956fd95622486c85e1
claim_id: claim:9e956fd95622486c85e1
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
All marker genes for this subtype (S100A8, S100A12, S100A9, S100A6, and TSPO) were among the top 15 differentially expressed genes in our Hosp-associated subgroup within the CD14+ monocytes cell type.

summary:
In Homo sapiens, dysfunctional CD14+ monocytes associated with COVID-19 hospitalization are marked by positive expression of S100A8, S100A12, S100A9, S100A6, and TSPO.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:0bde3b2132e722455b3d
claim_id: claim:0bde3b2132e722455b3d
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Cluster 0 exhibited elevated expression of interferon-stimulated genes (ISG15, IRF7, MX2, IFITM1, MX1).

summary:
In Homo sapiens, early antiviral response CD14+ monocytes (Cluster 0) exhibit elevated expression of ISG15, IRF7, MX2, IFITM1, and MX1.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:dc512318cc8ae8216474
claim_id: claim:dc512318cc8ae8216474
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal: Cluster 2 was defined by upregulation of stress response genes (PPIF, KDM6B, CSRNP1, ATP2B1, PLK3).
summary:
In Homo sapiens, stress response CD14+ monocytes (Cluster 2) are defined by upregulation of PPIF, KDM6B, CSRNP1, ATP2B1, and PLK3.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:668965de67b091ba92ff
claim_id: claim:668965de67b091ba92ff
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Cluster 3 showed upregulation of genes associated with platelet activation processes (CAVIN2, PPBP, TUBB1, GP9, PF4, ITGA2B).

summary:
In Homo sapiens, platelet activation-associated CD14+ monocytes (Cluster 3) show upregulation of CAVIN2, PPBP, TUBB1, GP9, PF4, and ITGA2B.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:c9d5f000d3cb1050f729
claim_id: claim:c9d5f000d3cb1050f729
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Direct comparison revealed distinct signatures: ‘LD’ CD14+ monocytes had significantly higher expression of MHC class II-related genes (HLA-DQA1, HLA-DPB1), while ‘Shared’ CD14+ monocytes were characterized by high expression of previously reported dysfunctional monocyte markers from COVID-19 (S100A8/A9/A12, TSPO).

summary:
In Homo sapiens, Lupus-Dominant CD14+ monocytes have significantly higher expression of HLA-DQA1 and HLA-DPB1 compared to Shared CD14+ monocytes.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:d09eca0c481d77fd4ebf
claim_id: claim:d09eca0c481d77fd4ebf
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Direct comparison revealed distinct signatures: ‘LD’ CD14+ monocytes had significantly higher expression of MHC class II-related genes (HLA-DQA1, HLA-DPB1), while ‘Shared’ CD14+ monocytes were characterized by high expression of previously reported dysfunctional monocyte markers from COVID-19 (S100A8/A9/A12, TSPO).

summary:
In Homo sapiens, Shared CD14+ monocytes are characterized by high expression of S100A8, S100A9, S100A12, and TSPO compared to Lupus-Dominant CD14+ monocytes.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:020afdae7d9b81ad668e
claim_id: claim:020afdae7d9b81ad668e
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Differential gene expression (DEG) analysis comparing ‘Shared’, ‘LD’, and ‘Control’ CD14+ monocytes (Figure 6d) showed that interferon-response genes (ISG15, IFI6, IFITM3) were commonly upregulated in both ‘Shared’ and ‘LD’ groups versus ‘Control’ cells, indicating activated interferon-mediated inflammation.

summary:
In Homo sapiens, both Shared and Lupus-Dominant CD14+ monocytes show upregulation of ISG15, IFI6, and IFITM3 compared to Control CD14+ monocytes.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:d13d2a629b28f98e1cea
claim_id: claim:d13d2a629b28f98e1cea
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Differential gene expression (DEG) analysis comparing ‘Shared’, ‘LD’, and ‘Control’ CD14+ monocytes (Figure 6d) showed that interferon-response genes (ISG15, IFI6, IFITM3) were commonly upregulated in both ‘Shared’ and ‘LD’ groups versus ‘Control’ cells, indicating activated interferon-mediated inflammation.

summary:
In Homo sapiens, both Lupus-Dominant and Shared CD14+ monocytes show upregulation of ISG15, IFI6, and IFITM3 compared to Control CD14+ monocytes.


claim_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14:claim:470a099ad093dd8386e9
claim_id: claim:470a099ad093dd8386e9
paper_key: biorxiv:ebaf49e5-7438-1014-8951-c3e925f71d14
span_literal:
Notably, many of these genes, such as LY6E, IFI6, and IFITM3, are known to be involved in the interferon response, further confirming the biological relevance of our identified subgroups.

summary:
In Homo sapiens, infection-associated goblet cells express interferon response genes LY6E, IFI6, and IFITM3.


claim_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4:claim:e5516f7eb5c0c46321e1
claim_id: claim:e5516f7eb5c0c46321e1
paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
span_literal:
the juxta-cardiac field (JCF) which overlaps the FHF and is marked by the basic helix-loop-helix (bHLH) TF, Hand1.

summary:
In Homo sapiens, the juxta-cardiac field is marked by the basic helix-loop-helix transcription factor HAND1.


claim_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4:claim:a76c7277d28c43cdcf01
claim_id: claim:a76c7277d28c43cdcf01
paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
span_literal:
The SHF-like lineage showed prominent ISL1, FGF10, FOXC1/2 and JAG1 expression (Figure 4B), which are well-established SHF markers.

summary:
In Homo sapiens, the second heart field-like lineage shows prominent expression of ISL1, FGF10, FOXC1, FOXC2, and JAG1, which are well-established second heart field markers.


claim_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4:claim:4b38a17080afa150b1f6
claim_id: claim:4b38a17080afa150b1f6
paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
span_literal:
the FHF-like lineage – which at its early stage included a strong JCF-like signature (HAND1, MAB21L2, BNC2 and MSX1/2)8,11,12 – displayed multilineage fate also giving rise to epicardial and fibroblast-like cells.

summary:
In Homo sapiens, the juxta-cardiac field-like progenitor displays a signature including HAND1, MAB21L2, BNC2, MSX1, and MSX2.


claim_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4:claim:51a1fd96c1d6f8a42dd3
claim_id: claim:51a1fd96c1d6f8a42dd3
paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
span_literal:
Additionally, we detected a side branch from the FHF/JCF-like progenitors with high transient CDX2, GATA2, and TBX3 expression and low TBX5, which may represent an extraembryonic mesoderm-like lineage

summary:
In Homo sapiens, the extraembryonic mesoderm-like lineage shows high CDX2, GATA2, and TBX3 expression and low TBX5 expression.


claim_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4:claim:1b2941736a51f61f27e2
claim_id: claim:1b2941736a51f61f27e2
paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
span_literal:
The main lineage of progenitors in the HAND1-null had a SHF-like signature with an equivalent or higher frequency of FGF10+ (51% vs 46%) ISL1+ (43% vs 43%), and TBX1+ (18% vs 10%) cells compared to the wild-type SHF-like lineage

summary:
In Homo sapiens, the second heart field-like lineage is characterized by expression of FGF10, ISL1, and TBX1.


claim_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4:claim:f090d1998082b72f1080
claim_id: claim:f090d1998082b72f1080
paper_key: biorxiv:eceae834-7948-1014-8997-9142ec9c1cd4
span_literal:
with DMH1, emerging GFP+ Tom-neg cells displayed an anterior SHF-like profile with high FGF8 and FGF10 expression and an absence of posterior HOXB1.

summary:
In Homo sapiens, the anterior second heart field-like population displays high FGF8 and FGF10 expression and an absence of HOXB1.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:419dab5999d829dfc579
claim_id: claim:419dab5999d829dfc579
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
The epithelial MYB-expressing cluster was characterized by elevated expression of canonical epithelial markers such as AZGP1 and ITGB4.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, the epithelial MYB-expressing cluster is characterized by elevated expression of AZGP1 and ITGB4.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:e81233cb3f76a6398166
claim_id: claim:e81233cb3f76a6398166
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
In contrast, the basal MYB-expressing cluster was delineated by the high expression of basal-specific markers including KRT5 and KRT17.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, the basal MYB-expressing cluster is delineated by high expression of KRT5 and KRT17.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:bef71a7c23f965f25de0
claim_id: claim:bef71a7c23f965f25de0
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal: Endothelial cell populations were annotated based on the expression of MGP and EGR3.
summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, endothelial cell populations were annotated based on the expression of MGP and EGR3.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:2e3f4d6e9a479460020c
claim_id: claim:2e3f4d6e9a479460020c
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
Non-MYB-expressing epithelial clusters were identified by their ubiquitous expression of markers such as KRT13, SPRR2A, SBSN, and LY6D.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, non-MYB-expressing epithelial clusters were identified by expression of KRT13, SPRR2A, SBSN, and LY6D.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:e03aa9ea1a5083b34d54
claim_id: claim:e03aa9ea1a5083b34d54
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
Fibroblast clusters were annotated by notable expression of extracellular matrix-related genes including COL1A1, COL3A1, and COL1A2.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, fibroblast clusters were annotated by expression of COL1A1, COL3A1, and COL1A2.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:d17b6e5f38f06dfeb29c
claim_id: claim:d17b6e5f38f06dfeb29c
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
The muscle cell population was defined based on the corroborated expression of contractility-associated genes such as TNNT3, CKM, MB, TTN, and STAC3.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, the muscle cell population was defined by expression of TNNT3, CKM, MB, TTN, and STAC3.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:495e94dc9ea98279c984
claim_id: claim:495e94dc9ea98279c984
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
Plasma cell (PC) clusters exhibited strong transcriptional signatures consistent with antibody-producing cells, including IGKC, IGHA2, IGLC2, and JCHAIN.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, plasma cell clusters exhibited strong transcriptional signatures including IGKC, IGHA2, IGLC2, and JCHAIN.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:de8a1bd7943899d9320d
claim_id: claim:de8a1bd7943899d9320d
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
Non-MYB stromal cells were annotated based on the expression of CLEC3B, COL1A1, and HBA2, whereas MYB-expressing stromal cells demonstrated high levels of ALDH1A3, EGR3, and NR4A1.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, non-MYB stromal cells were annotated based on expression of CLEC3B, COL1A1, and HBA2, whereas MYB-expressing stromal cells demonstrated high levels of ALDH1A3, EGR3, and NR4A1.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:8764ec6b79b7a3eceb04
claim_id: claim:8764ec6b79b7a3eceb04
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
Non-MYB stromal cells were annotated based on the expression of CLEC3B, COL1A1, and HBA2, whereas MYB-expressing stromal cells demonstrated high levels of ALDH1A3, EGR3, and NR4A1.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, MYB-expressing stromal cells demonstrated high levels of ALDH1A3, EGR3, and NR4A1.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:710ab8c3473c819cd945
claim_id: claim:710ab8c3473c819cd945
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
We observed expression of tertiary lymphoid structure (TLS)-associated gene signatures including CD79A, CXCL8, and IL7R (interleukin-7 receptor) which supports the presence of well-organized TLS within the tumor microenvironment.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, tertiary lymphoid structures express CD79A, CXCL8, and IL7R (interleukin-7 receptor).


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:cba6656850255de2f464
claim_id: claim:cba6656850255de2f464
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
However, comparative analysis with non-MYB-expressing epithelial populations revealed the retention of epithelial features in the latter, including robust cell-cell adhesion and keratinocyte differentiation. These phenotypes were supported by elevated expression of canonical epithelial markers such as CRNN, CSTA, ANXA9, and DSG3.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, non-MYB-expressing epithelial populations show elevated expression of canonical epithelial markers CRNN, CSTA, ANXA9, and DSG3.


claim_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d:claim:3815d2b6abae6f5f8f9a
claim_id: claim:3815d2b6abae6f5f8f9a
paper_key: biorxiv:eda68d46-7b76-1014-b9f8-bf62f9afae8d
span_literal:
We identified a population of cancer-associated fibroblasts (CAFs), marked by the expression of genes such as COL1A1, COL3A1, COL11A1(Fig. 2D), and ACTA2, which are known to contribute to the activation of EMT programing116,117.

summary:
In Homo sapiens salivary gland adenoid cystic carcinoma, cancer-associated fibroblasts are marked by expression of COL1A1, COL3A1, COL11A1, and ACTA2.


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:53b6072b734185ecd003
claim_id: claim:53b6072b734185ecd003
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
summary: In Homo sapiens, alveolar type 2 cells showed the highest ACE2 expression in the lung.
span_literal:
As expected from prior literature, the AT2 cells showed highest ACE2 expression in the lung both in terms of their CPM values (Fig. 1D, further referred to as ACE2+ cells) and the percentage of positive cells (Supp. Fig. 3).


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:ee6f12b9292b148abf9e
claim_id: claim:ee6f12b9292b148abf9e
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
summary: In Homo sapiens, TMPRSS2 expression in the lung showed specificity for alveolar type 2 cells.
span_literal:
The expression of TMPRSS2 across cell types of the lung (further referred to as TMPRSS2+ cells) was much stronger with a certain specificity for AT2 cells (Fig. 1E), which is in agreement with previous studies.


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:9ac3f51897d770209485
claim_id: claim:9ac3f51897d770209485
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
span_literal:
ACE2 were comparable but slightly elevated compared to the lung tissue samples, with the strongest expression being observed in a subset of secretory cells (‘secretory3

summary:
In Homo sapiens, ACE2 expression was strongest in the transient secretory cell (secretory3) subset among human bronchial epithelial cells.


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:0dee1053c742ae15208b
claim_id: claim:0dee1053c742ae15208b
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
span_literal:
In this dataset, we identified all expected cell types, including recently described and rare cell types such as FOXN4-positive cells and ionocytes (Fig. 1F, Supp. Fig. 1, 2).

summary:
In Homo sapiens, FOXN4-positive cells were identified among human bronchial epithelial cells, marked by FOXN4 expression.


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:386060d06c9e8f095f35
claim_id: claim:386060d06c9e8f095f35
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
span_literal:
In lung tissue, AT2, endothelial, and immune cells were most strongly positive for FURIN expression (Fig. 3A).

summary:
In Homo sapiens, alveolar type 2 cells in lung tissue were most strongly positive for FURIN expression.


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:70946ede8c8f7760bf5d
claim_id: claim:70946ede8c8f7760bf5d
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
span_literal:
Interestingly, also transient secretory cells in the HBECs showed an intermediate expression of FURIN (Fig. 3C).

summary:
In Homo sapiens, transient secretory cells in human bronchial epithelial cells showed an intermediate expression of FURIN.


claim_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4:claim:4ccdc762438cbe8a53be
claim_id: claim:4ccdc762438cbe8a53be
paper_key: biorxiv:ede8f8d0-6d2d-1014-a8e8-fbbc8a92dcf4
summary: In Homo sapiens, about 40% of ACE2-positive transient secretory cells co-express TMPRSS2.
span_literal:
Interestingly, about 40% of the ACE2+ transient secretory cells are co-expressing the protease TMPRSS2 that is known to be involved in S protein priming, making this cell type potentially highly vulnerable for SARS-CoV-2 infection.


claim_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8:claim:576e072b2fbd95d1a313
claim_id: claim:576e072b2fbd95d1a313
paper_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8
span_literal:
Cluster 2 genes were expressed in mammary epithelial and luminal secretory precursor cells, and encompassed genes associated with hormone-responsive differentiation and developmental control, such as ESR1, GATA3, and TBX3.

summary:
In Homo sapiens, luminal secretory precursor cells of the mammary gland express ESR1, GATA3, and TBX3, which are associated with hormone-responsive differentiation and developmental control.


claim_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8:claim:83b02304723340ab6417
claim_id: claim:83b02304723340ab6417
paper_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8
span_literal:
Cluster 1 showed broad expression, and included estrogen-driven epithelial proliferation genes and stromal signaling genes, including ESR1, PGR and IGF1.

summary:
In Homo sapiens, female-biased genes ESR1, PGR, and IGF1 show broad expression across mammary cell types, associated with estrogen-driven epithelial proliferation and stromal signaling.


claim_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8:claim:ed74b345115d76761eb4
claim_id: claim:ed74b345115d76761eb4
paper_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8
span_literal:
Cluster 2 genes were expressed in mammary epithelial and luminal secretory precursor cells, and associated with hormone-linked inflammatory and oxidative stress regulation, including SAA1, HMOX1 and IL6.

summary:
In Homo sapiens, luminal secretory precursor cells of the mammary gland express SAA1, HMOX1, and IL6, which are associated with hormone-linked inflammatory and oxidative stress regulation.


claim_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8:claim:00f86db391ab7e82b05e
claim_id: claim:00f86db391ab7e82b05e
paper_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8
span_literal:
Finally, the “Female-biased genes” category was dominated by immunoglobulin genes, including IGHV, IGKJ, IGLJ, and IGKC family members, together with POU2AF1 and CD27.

summary:
In Homo sapiens, female-biased mammary tissue expression includes immunoglobulin genes IGHV, IGKJ, IGLJ, and IGKC, together with POU2AF1 and CD27, which are associated with B cell and T cell immune functions.


claim_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8:claim:a2273623ed1586ae1e15
claim_id: claim:a2273623ed1586ae1e15
paper_key: biorxiv:ee1031b0-6c51-1014-b641-cbb0196af9f8
span_literal:
Genes exhibiting female-biased expression were dominated by B cell-related immunoglobulin genes, including IGKC, IGHM, IGHV, and IGKJ family members, which are well characterized as components of B cell and antibody-mediated immune responses

summary:
In Homo sapiens, B cells in female mammary tissue are marked by immunoglobulin genes IGKC, IGHM, IGHV, and IGKJ, which are components of B cell and antibody-mediated immune responses.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:f9328d1e66501cf06bce
claim_id: claim:f9328d1e66501cf06bce
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
The cell surface marker panel CD54+/PSA-NCAM- was identified to enrich for an RPE subpopulation with high potential for monolayer formation following transplantation.

summary:
In Homo sapiens, the cell surface marker panel CD54-positive/polysialic acid-neural cell adhesion molecule-negative identifies a retinal pigment epithelium subpopulation with high potential for monolayer formation following transplantation.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:9b18fbeea00146fc5ff0
claim_id: claim:9b18fbeea00146fc5ff0
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
After validation of several initial hits the combination of CD54 (ICAM) positivity and PSA-NCAM negativity proved to be the most robust combination allowing identification (Figs. 4B and 4C) and reproducible isolation of highly pigmented target cells (Fig. 4D).

summary:
In Homo sapiens, the combination of CD54 (intercellular adhesion molecule 1) positivity and polysialic acid-neural cell adhesion molecule negativity allows identification and reproducible isolation of highly pigmented retinal pigment epithelium cells.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:7a871420e19cb08e81c0
claim_id: claim:7a871420e19cb08e81c0
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
The epitope PSA-NCAM, derived from the posttranslational modification of the neural cell adhesion molecule (NCAM) with polysialic acid, is considered a marker for immature neural precursors (Nguyen et al, 2003) and can be used to isolate primitive, proliferative neural progenitors derived from pluripotent stem cells (Barral et al, 2013; Kim et al, 2012).

summary:
In Homo sapiens, polysialic acid-neural cell adhesion molecule is considered a marker for immature neural precursor cells and can be used to isolate primitive, proliferative neural progenitor cells derived from pluripotent stem cells.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:379511fa74332bf14569
claim_id: claim:379511fa74332bf14569
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
As such, removal of unwanted, non-RPE cells using CD56+ and CD24+ cell depletion has been introduced for the generation of RPE monolayers and patches in vitro for transplantation purposes (Sharma et al, 2022).

summary:
In Homo sapiens, CD56 and CD24 are positive markers of non-retinal pigment epithelium cells, and their depletion is used to purify retinal pigment epithelium cultures for transplantation.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:94f582631fec0a8aa5b9
claim_id: claim:94f582631fec0a8aa5b9
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
Reyes et al identified CD140b+/CD184− sorting for improving RPE cultures that also have the capacity for monolayer formation after transplantation in rabbits (Plaza Reyes et al, 2020)

summary:
In Homo sapiens, CD140b-positive and CD184-negative sorting identifies retinal pigment epithelium cells with the capacity for monolayer formation after transplantation.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:4685fb4f111e498ca15a
claim_id: claim:4685fb4f111e498ca15a
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
both P1 and P2 cells exhibited high expression levels of typical RPE genes characteristic for the visual cycle (e.g. BEST1, SFRP5, RLBP1), phagocytosis (e.g. LAMP2, ERMN, GULP1), or pigmentation (e.g. DCT, PMEL, MITF) and others (Fig. 1F and Doc. S2 sheet 1).

summary:
In Homo sapiens, retinal pigment epithelium cells exhibit high expression levels of typical retinal pigment epithelium genes including BEST1, SFRP5, RLBP1 (visual cycle), LAMP2, ERMN, GULP1 (phagocytosis), and DCT, PMEL, MITF (pigmentation).


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:fb99797a86bc112c33c8
claim_id: claim:fb99797a86bc112c33c8
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
Additionally, in P2 RPE-transplanted retinas a striking increase of cells positive for IBA1 (Ionized calcium-binding adapter molecule 1), a marker for microglia and macrophages, was observed both in the retina and the choroid (Fig. 3F).

summary:
In Homo sapiens, ionized calcium-binding adapter molecule 1 (IBA1) is a positive marker for microglia and macrophages in the retina and choroid.


claim_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c:claim:53c6c4e799861e742087
claim_id: claim:53c6c4e799861e742087
paper_key: biorxiv:ef286bb1-6ccb-1014-ab06-ecd5927e269c
span_literal:
Additionally, in P2 RPE-transplanted retinas a striking increase of cells positive for IBA1 (Ionized calcium-binding adapter molecule 1), a marker for microglia and macrophages, was observed both in the retina and the choroid (Fig. 3F).

summary:
In Homo sapiens, ionized calcium-binding adapter molecule 1 (IBA1) is a positive marker for macrophages in the retina and choroid.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:4f13b64dda3cd1c19800
claim_id: claim:4f13b64dda3cd1c19800
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
Clustering of these nuclei identified 8 major brain cell types based on the expression profile of literature-based cell-type specific markers15: 39% excitatory neurons (SLC17A7), 28% mature oligodendrocytes (MOBP, MAG), 10% inhibitory neurons (GAD1, GAD2), 9.4% astrocytes (AQP4, GJA1), 5.3% microglia (CSF1R, P2RY12), 4.6% oligodendrocyte progenitor cells (OPCs; VCAN, PDGFRA), 1.8% pericytes (STEAP4, JAG1) and 1.2% endothelial cells (FLT1, CLDN5).

summary:
In Homo sapiens entorhinal cortex, excitatory neurons are marked by SLC17A7, mature oligodendrocytes by MOBP and MAG, inhibitory neurons by GAD1 and GAD2, astrocytes by AQP4 and GJA1, microglia by CSF1R and P2RY12, oligodendrocyte progenitor cells by VCAN and PDGFRA, pericytes by STEAP4 and JAG1, and endothelial cells by FLT1 and CLDN5.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:63637a5b4a82193893d4
claim_id: claim:63637a5b4a82193893d4
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
Since marker genes for this microglia subtype included genes characteristic of disease-associated microglia (DAM) (e.g. TYROBP, APOE, CLEC7A, CTSZ or CD63)

summary:
In Homo sapiens entorhinal cortex, disease-associated microglia are characterized by marker genes TYROBP, APOE, CLEC7A, CTSZ, and CD63.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:081ae9c4a81bac8902e8
claim_id: claim:081ae9c4a81bac8902e8
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal: Astro_s2, characterized by higher expression of homeostatic genes (e.g. SLC1A2, NRXN1 and GPC5)
summary:
In Homo sapiens entorhinal cortex, homeostatic astrocyte subcluster Astro_s2 is characterized by higher expression of SLC1A2, NRXN1, and GPC5.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:8f6925977954b70a0c3f
claim_id: claim:8f6925977954b70a0c3f
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
RELN is known to be expressed at high levels in perforant path-forming layer II neurons (stellate/fan) across species, including humans36-38, in addition to several inhibitory neuron subpopulations36-38.

summary:
In Homo sapiens, RELN is expressed at high levels in layer II excitatory neurons (stellate/fan) of the entorhinal cortex.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:6fbef31e559a0dd76a91
claim_id: claim:6fbef31e559a0dd76a91
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
Besides RELN, Exc_s4 was also enriched in CALB1, a marker for pyramidal neurons from layer II/III in non-human primates and mouse39, 40, and in BMPR1B, previously suggested to be enriched in layer II neurons41.

summary:
In Homo sapiens entorhinal cortex, excitatory neuron subpopulation Exc_s4 is enriched in RELN, CALB1, and BMPR1B.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:1092fe4792daff58c42c
claim_id: claim:1092fe4792daff58c42c
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
As shown in Fig. 4c, neurons stained for both RELN and GPC5 were large neurons of polygonal shape in layer II, displaying dark hematoxylin counterstain and forming islands42, consistently reported as early sites of NFT deposition.

summary:
In Homo sapiens entorhinal cortex, layer II neurons of polygonal shape are positive for RELN and GPC5.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:283e92145e713a151028
claim_id: claim:283e92145e713a151028
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
As expected, LHX6 and SP9, transcription factors necessary for the specification of MGE-derived interneurons44-48, were enriched in NeuN+/RBFOX1+ nuclei (log2FC = 3.24, Padj = 2.3 x 10-12 and log2FC = 1.70, Padj = 0.031 respectively).

summary:
In Homo sapiens entorhinal cortex, medial ganglionic eminence-derived interneurons in the NeuN+/RBFOX1+ fraction are enriched in LHX6 and SP9.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:85ea92f8969f2f0f4377
claim_id: claim:85ea92f8969f2f0f4377
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
SST and PVALB were also among the top enriched genes in this population (log2FC = 3.07, Padj = 3.2 x 10-3 and log2FC = 2.94, Padj = 1.6 x 10-4, respectively).

summary:
In Homo sapiens entorhinal cortex, the NeuN+/RBFOX1+ neuronal population is enriched in SST and PVALB.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:b0432661543ad5e71c57
claim_id: claim:b0432661543ad5e71c57
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
On the other hand, the NeuN+/RBFOX1- population was enriched for SP8 (log2FC = 2.08, Padj = 0.015) and NR2F2 (log2FC = 1.79, Padj = 1.1 x 10-4), transcription factors necessary for CGE interneuron specification49-51

summary:
In Homo sapiens entorhinal cortex, the NeuN+/RBFOX1- neuronal population is enriched for SP8 and NR2F2, transcription factors necessary for caudal ganglionic eminence interneuron specification.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:504731e1d05811522939
claim_id: claim:504731e1d05811522939
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
Instead, we found an enrichment in markers of more specific subsets of CGE-derived interneurons like CHRNA7 (log2FC = -2.0, Padj = 4.8 x 10-15), a marker for a subset of NDNF-positive neurons from layer I52 and CALB2 (log2FC = -2.10, Padj = 2.0 x 10-4), a marker for a subset of VIP-positive interneurons49

summary:
In Homo sapiens entorhinal cortex, CHRNA7 is a marker for a subset of NDNF-positive neurons from layer I, and CALB2 is a marker for a subset of VIP-positive interneurons.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:a21bdbb3befb67726ff9
claim_id: claim:a21bdbb3befb67726ff9
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
span_literal:
Interestingly, according to our snRNAseq data, NPTX2 is enriched in two subpopulations of excitatory neurons: Exc_s0 and Exc_s9, both sorted in the NeuN+/RBFOX1- fraction and enriched in LAMP5

summary:
In Homo sapiens entorhinal cortex, NPTX2 is enriched in excitatory neuron subpopulations Exc_s0 and Exc_s9, which are also enriched in LAMP5.


claim_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd:claim:3767ad49a100ad2a707b
claim_id: claim:3767ad49a100ad2a707b
paper_key: biorxiv:efe4cabd-770f-1014-96d7-8e75af964dbd
summary: In Homo sapiens entorhinal cortex, CBLN4 is enriched in excitatory neuron subpopulation Exc_s9.
span_literal:
Interestingly, CBLN4 is also enriched in Exc_s9 neurons in our snRNAseq dataset (log2FC = 1.44, Padj = 0.0089).


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:ffe053e143edad9a9e6d
claim_id: claim:ffe053e143edad9a9e6d
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
Unexpanded HSCs were characterized by expression of THY1 and AVP, known markers of HSCs in single cell transcriptomics (Figure 5C)33,34.

summary:
In Homo sapiens, hematopoietic stem cells are characterized by expression of THY1 and AVP, known markers of hematopoietic stem cells in single cell transcriptomics.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:069af6f526fa28a31ce7
claim_id: claim:069af6f526fa28a31ce7
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
summary: In Homo sapiens, unexpanded hematopoietic stem cells exhibit high expression of PRSS2.
span_literal:
Interestingly, these cells also exhibited high expression of PRSS2, which is associated with pancreatic functions and does not have a well characterized hematopoietic function35,36.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:e2eca36cd12098fdb06a
claim_id: claim:e2eca36cd12098fdb06a
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
This primitive HSC/HPC subpopulation showed oxygen-dependent expression of genes associated with regulating metabolism, mitochondrial function, and proliferation. Some of these genes are associated with the mTORc pathway including BNIP3, DDIT4, ENO1, and LDHA (Figure 5D)37–41.

summary:
In Homo sapiens, the expanded early hematopoietic stem cell and multipotent progenitor subpopulation shows oxygen-dependent expression of BNIP3, DDIT4, ENO1, and LDHA, genes associated with the mechanistic target of rapamycin complex pathway.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:2317925636792eb04736
claim_id: claim:2317925636792eb04736
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
Others are a core group of mitochondrial genes including MT-ATP6, MT-ND1/2/3, and MT-CO2 (Figure 5D).

summary:
In Homo sapiens, the expanded early hematopoietic stem cell and multipotent progenitor subpopulation shows oxygen-dependent expression of mitochondrial genes MT-ATP6, MT-ND1, MT-ND2, MT-ND3, and MT-CO2.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:4bdafa3614c4ed8546f7
claim_id: claim:4bdafa3614c4ed8546f7
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
We examined PRSS2 expression in HSC/HPC populations by sequencing immunophenotypically defined HSC/HPC subpopulations from freshly isolated CBUs and found that PRSS2 is most highly expressed in MLPs followed by HSCs (Figure 7C, Table S3).

summary:
In Homo sapiens, PRSS2 is most highly expressed in multilymphoid progenitors followed by hematopoietic stem cells among hematopoietic stem and progenitor cell subpopulations.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:b8af92479947bfcf53ab
claim_id: claim:b8af92479947bfcf53ab
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
We examined PRSS2 expression in HSC/HPC populations by sequencing immunophenotypically defined HSC/HPC subpopulations from freshly isolated CBUs and found that PRSS2 is most highly expressed in MLPs followed by HSCs (Figure 7C, Table S3).

summary:
In Homo sapiens, PRSS2 is highly expressed in hematopoietic stem cells, second to multilymphoid progenitors among hematopoietic stem and progenitor cell subpopulations.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:0d5107e0c5acb58abf07
claim_id: claim:0d5107e0c5acb58abf07
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
In independently published data, HSCs exhibit significantly higher expression of PRSS2 compared to mature HPC populations (Figure 7D).

summary:
In Homo sapiens, hematopoietic stem cells exhibit significantly higher expression of PRSS2 compared to mature hematopoietic progenitor cell populations.


claim_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b:claim:fad8ff957d5140e607c6
claim_id: claim:fad8ff957d5140e607c6
paper_key: biorxiv:f1a588ac-746e-1014-a4d0-f5cc921ee68b
span_literal:
Here we have identified O2 dependent genes that mark potent HSCs/HPCs, including PRSS2 and DDIT4, which could aid in the selection of the optimal donor units that are most likely to achieve favorable outcomes.

summary:
In Homo sapiens, PRSS2 and DDIT4 are oxygen-dependent genes that mark potent hematopoietic stem and progenitor cells.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:dc3162a81c3d82d9e242
claim_id: claim:dc3162a81c3d82d9e242
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
two main cell type populations at day 11: proliferating and non-proliferating midbrain floorplate progenitors (both expressing LMX1A, FOXA2 and expressing MIK67, TOP2A when proliferating17)

summary:
In Homo sapiens iPSC-derived midbrain differentiation, proliferating midbrain floorplate progenitors express LMX1A, FOXA2, MKI67, and TOP2A.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:a130dee67de912b698ff
claim_id: claim:a130dee67de912b698ff
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
two main cell type populations at day 11: proliferating and non-proliferating midbrain floorplate progenitors (both expressing LMX1A, FOXA2 and expressing MIK67, TOP2A when proliferating17)

summary:
In Homo sapiens iPSC-derived midbrain differentiation, non-proliferating midbrain floorplate progenitors express LMX1A and FOXA2.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:aa096b53093d60ea57a1
claim_id: claim:aa096b53093d60ea57a1
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
Two of these additional cell types appeared neuronal and two were non-neuronal (characterised by expression and lack of the pan-neuronal markers SNAP25 and SYT1 respectively).

summary:
In Homo sapiens iPSC-derived midbrain differentiation, neuronal cells are characterized by expression of the pan-neuronal markers SNAP25 and SYT1.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:2aa08cef7d52c6b06129
claim_id: claim:2aa08cef7d52c6b06129
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
Two of these additional cell types appeared neuronal and two were non-neuronal (characterised by expression and lack of the pan-neuronal markers SNAP25 and SYT1 respectively).

summary:
In Homo sapiens iPSC-derived midbrain differentiation, non-neuronal cells are characterized by lack of the pan-neuronal markers SNAP25 and SYT1.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:822fadc39191c4b31d75
claim_id: claim:822fadc39191c4b31d75
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
The two neuronal populations could be further divided into midbrain dopaminergic neurons, which expressed NR4A2, PBX1, TMCC317–19 and serotonergic neurons (Sert), which expressed TPH1, TPH2, GATA220.

summary:
In Homo sapiens iPSC-derived midbrain differentiation, midbrain dopaminergic neurons express NR4A2, PBX1, and TMCC3.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:fe52e5185c664a0a3f50
claim_id: claim:fe52e5185c664a0a3f50
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
The two neuronal populations could be further divided into midbrain dopaminergic neurons, which expressed NR4A2, PBX1, TMCC317–19 and serotonergic neurons (Sert), which expressed TPH1, TPH2, GATA220.

summary:
In Homo sapiens iPSC-derived midbrain differentiation, serotonergic neurons express TPH1, TPH2, and GATA2.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:eb080b26f7f7ed987665
claim_id: claim:eb080b26f7f7ed987665
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
We also identified a neuroblast population, specific to day 11 (4% of all cells at day 11) expressing pro-neuronal genes (NEUROD1, NEUROG2, NHLH124,25)

summary:
In Homo sapiens iPSC-derived midbrain differentiation, neuroblasts express the pro-neuronal genes NEUROD1, NEUROG2, and NHLH1.


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:15c08e4c4eebf35bf5b0
claim_id: claim:15c08e4c4eebf35bf5b0
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
summary: In Homo sapiens iPSC-derived midbrain differentiation, unknown neurons 1 express SNAP25 and SYT1.
span_literal:
an additional neuronal population (expressing SNAP25 and SYT1) that could not be assigned to a specific neuronal identity (Unknown neurons 1, present at Day 30 and Day 52 at around 7%)


claim_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f:claim:879b14d45ac6329773b7
claim_id: claim:879b14d45ac6329773b7
paper_key: biorxiv:f29672cc-6d87-1014-b915-87fbd4bb053f
span_literal:
all but one of which expressed similarly high levels of core pluripotency markers (NANOG, SOX2, POU5F1, Supplementary Fig. 6a,b; Methods)

summary:
In Homo sapiens, induced pluripotent stem cell clusters express high levels of the core pluripotency markers NANOG, SOX2, and POU5F1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:eb361e26a070b67ff940
claim_id: claim:eb361e26a070b67ff940
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: T_NK cells, comprising both T and NK cells, identified by markers such as CD3D/G and NCAM1
summary:
In Homo sapiens glioblastoma, T and natural killer cells are identified by markers such as CD3D, CD3G, and NCAM1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:09011c9b8b6acac7ab0f
claim_id: claim:09011c9b8b6acac7ab0f
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: myeloid cells, expressing LYZ, ITGAM, and CD14
summary:
In Homo sapiens glioblastoma, myeloid cells are characterized by expression of LYZ, ITGAM, and CD14.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:d12e22865dd39543d91b
claim_id: claim:d12e22865dd39543d91b
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: malignant glioma cells were characterized by the expression of SOX2, OLIG1, GFAP, and S100B
summary:
In Homo sapiens glioblastoma, malignant glioma cells are characterized by the expression of SOX2, OLIG1, GFAP, and S100B.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:c2ee7fb6b210d2c71e5c
claim_id: claim:c2ee7fb6b210d2c71e5c
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
TAM was noted for expressing well-known microglia markers such as P2RY12, TMEM119, BHLHE41, SORL1, SPRY1, and SRGAP28, alongside classical macrophage markers including C1AC, C1QA, and APOE.

summary:
In Homo sapiens glioblastoma, tumor-associated macrophages express microglia markers P2RY12, TMEM119, BHLHE41, SORL1, SPRY1, and SRGAP28, alongside classical macrophage markers C1AC, C1QA, and APOE.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:82fc652d9dcc461eee26
claim_id: claim:82fc652d9dcc461eee26
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
the cDC cell type marked by expression of traditional dendritic cell markers including CD1C, CLEC9A, CLEC10A, and LAMP3.

summary:
In Homo sapiens glioblastoma, conventional dendritic cells are marked by expression of CD1C, CLEC9A, CLEC10A, and LAMP3.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:ab85d51002b7fa988f3b
claim_id: claim:ab85d51002b7fa988f3b
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: monocyte-derived cells were distinguished by high levels of S100A8, S100A9, and VCAN
summary:
In Homo sapiens glioblastoma, monocyte-derived cells are distinguished by high levels of S100A8, S100A9, and VCAN.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:2b5ce0cc2a367db05b74
claim_id: claim:2b5ce0cc2a367db05b74
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The TAM_MRC1 subtype was defined by high levels of MRC1, an established M2 polarization marker, as well as other M2-associated markers like CD163 and CD204/MSR1.

summary:
In Homo sapiens glioblastoma, the TAM_MRC1 tumor-associated macrophage subtype is defined by high levels of MRC1, CD163, and MSR1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:a412303407226af37b98
claim_id: claim:a412303407226af37b98
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
the TAM_ISG15 subset exhibited increased levels of ISG15, along with markers linked to M1 polarization such as CD86, CXCL9, CXCL10, IRF1, and CD40.

summary:
In Homo sapiens glioblastoma, the TAM_ISG15 tumor-associated macrophage subtype exhibits increased levels of ISG15, CD86, CXCL9, CXCL10, IRF1, and CD40.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:286ca29843298af846e9
claim_id: claim:286ca29843298af846e9
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
two NK subtypes, NK_CD56dim (n = 1,345) and NK_CD56bright (n = 993), identified by the relative expression levels of NCAM1 (CD56) and FCGR3A (CD16)

summary:
In Homo sapiens glioblastoma, NK_CD56dim natural killer cells are identified by relative expression levels of NCAM1 and FCGR3A.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:383e044416de56e9b1da
claim_id: claim:383e044416de56e9b1da
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
two NK subtypes, NK_CD56dim (n = 1,345) and NK_CD56bright (n = 993), identified by the relative expression levels of NCAM1 (CD56) and FCGR3A (CD16)

summary:
In Homo sapiens glioblastoma, NK_CD56bright natural killer cells are identified by relative expression levels of NCAM1 and FCGR3A.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:b5ae77045407ab392e97
claim_id: claim:b5ae77045407ab392e97
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The CD4T_FOXP3 cells, characterized by elevated expression of FOXP3, CTLA4, and TIGHT, were identified as regulatory T (Treg) cells.

summary:
In Homo sapiens glioblastoma, CD4T_FOXP3 regulatory T cells are characterized by elevated expression of FOXP3, CTLA4, and TIGIT.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:351b886ef86a95a22830
claim_id: claim:351b886ef86a95a22830
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: The CD4T_CCR7 subset, with high levels of CCR7 and SELL, was classified as Naive T cells.
summary:
In Homo sapiens glioblastoma, CD4T_CCR7 naive T cells are characterized by high levels of CCR7 and SELL.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:6d45d11ad06586a4f1ab
claim_id: claim:6d45d11ad06586a4f1ab
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: The CD4T_IL21 subset, known for significant IL21 expression, was recognized as helper T cells
summary:
In Homo sapiens glioblastoma, CD4T_IL21 helper T cells are characterized by significant IL21 expression.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:1ba88b73c16a5ae32047
claim_id: claim:1ba88b73c16a5ae32047
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The CD8T_LAG3 subset, distinguished by high expression of LAG3, PDCD1, and TIGHT, was identified as exhausted T (Trex) cells.

summary:
In Homo sapiens glioblastoma, CD8T_LAG3 exhausted T cells are distinguished by high expression of LAG3, PDCD1, and TIGIT.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:510d2efc7120e2fa0e8f
claim_id: claim:510d2efc7120e2fa0e8f
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The CD8T_GZMB subset, with robust expression of GZMB, GZMA, and PRF1, was classified as effector T (Teff) cells.

summary:
In Homo sapiens glioblastoma, CD8T_GZMB effector T cells are characterized by robust expression of GZMB, GZMA, and PRF1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:b96ee3b3465cf45c07fd
claim_id: claim:b96ee3b3465cf45c07fd
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: The CD8T_GZMK subset, showing high levels of GZMK, was identified as effector memory (Tem) T cells
summary:
In Homo sapiens glioblastoma, CD8T_GZMK effector memory T cells are characterized by high levels of GZMK.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:508e3f6b6e0c93b3d446
claim_id: claim:508e3f6b6e0c93b3d446
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal: The NK_CD56bri_KLRK1 subtype, distinguished by elevated levels of KLRK1, also known as NKG2D.
summary:
In Homo sapiens glioblastoma, the NK_CD56bri_KLRK1 natural killer cell subtype is distinguished by elevated levels of KLRK1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:94f0ad00689682767e80
claim_id: claim:94f0ad00689682767e80
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The NK_CD56bri_CXCR6 subtype is notable for its expression of cytokine genes such as CXCR6, CCL4, CCL4L2, CCL3, and CCL3L1.

summary:
In Homo sapiens glioblastoma, the NK_CD56bri_CXCR6 natural killer cell subtype is notable for expression of CXCR6, CCL4, CCL4L2, CCL3, and CCL3L1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:afcb3efcc1fe98a69594
claim_id: claim:afcb3efcc1fe98a69594
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The CD56dim_DNAJB1 subset was particularly noted for expressing stress response genes such as DNAJB1, HSPA1A, and HSP90AA1.

summary:
In Homo sapiens glioblastoma, the CD56dim_DNAJB1 natural killer cell subset is noted for expressing stress response genes DNAJB1, HSPA1A, and HSP90AA1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:3cd75d0f2f5f55d2d638
claim_id: claim:3cd75d0f2f5f55d2d638
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
This subset also showed elevated levels of NR4A1, identified as a key mediator of T cell dysfunction, aligning with characteristics of the recently described TaNK population

summary:
In Homo sapiens glioblastoma, the CD56dim_DNAJB1 natural killer cell subset shows elevated levels of NR4A1.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:d53b4da21e0ffafd6ef6
claim_id: claim:d53b4da21e0ffafd6ef6
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
these cells exhibited low expression of immune checkpoint genes such as PDCD1 and CTLA4, suggesting they may not respond to anti-PD-1/CTLA-4 therapies.

summary:
In Homo sapiens glioblastoma, CD56dim_DNAJB1 natural killer cells exhibit low expression of PDCD1 and CTLA4.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:7eb31448db8b57627650
claim_id: claim:7eb31448db8b57627650
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
These NK subtypes exhibited low expression of B3GAT1 (CD57) and the killer immunoglobulin-like receptor (KIR) family, indicating immaturity and reduced killing capacity.

summary:
In Homo sapiens glioblastoma, tumor-infiltrating natural killer cells exhibit low expression of B3GAT1 and killer immunoglobulin-like receptor family genes, indicating immaturity.


claim_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e:claim:ccc0dc0ed03d920ab40b
claim_id: claim:ccc0dc0ed03d920ab40b
paper_key: biorxiv:f3be1d12-72db-1014-a9a0-ac8d78e3151e
span_literal:
The NK_CD56dim_CCL3 subtype, characterized by high levels of CCL3, likely enhances antitumor immunity by promoting the recruitment of NK cells and other immune cells, such as DC and CD8+ T cells, thereby facilitating increased IFNγ production.

summary:
In Homo sapiens glioblastoma, the NK_CD56dim_CCL3 natural killer cell subtype is characterized by high levels of CCL3.


claim_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23:claim:2e204d82915ea06b7501
claim_id: claim:2e204d82915ea06b7501
paper_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23
span_literal:
All imaged cells exhibited strong CD14 expression and a single, clearly delineated nucleus, confirming their monocyte identity and morphological integrity.

summary:
In Homo sapiens, monocytes are identified by strong CD14 expression, confirming their monocyte identity.


claim_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23:claim:2c9fb1b9833dfab312ad
claim_id: claim:2c9fb1b9833dfab312ad
paper_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23
summary: In Homo sapiens, HLA-DR expression on monocytes correlates with immune suppression and prognosis.
span_literal:
One promising marker is the expression of HLA-DR on monocytes (mHLA-DR), which correlates with immune suppression and prognosis 16-19.


claim_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23:claim:262f213ebcc8931ee86d
claim_id: claim:262f213ebcc8931ee86d
paper_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23
span_literal:
While our monocyte population was enriched based on CD14 expression, it likely included a mixture of classical, intermediate, and non-classical subtypes 43.

summary:
In Homo sapiens, the monocyte population was enriched based on CD14 expression, encompassing classical, intermediate, and non-classical subtypes.


claim_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23:claim:32f3f2936f8e7deb232c
claim_id: claim:32f3f2936f8e7deb232c
paper_key: biorxiv:f61157f2-6f2c-1014-b8b0-8537883fcb23
summary: In Homo sapiens, monocyte subsets can be defined by subset-specific markers CD14 and CD16.
span_literal:
Future work incorporating subset-specific markers (e.g., CD14/CD16) could refine the interpretation of HT-derived features.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:ee905f5a192e5fa75d61
claim_id: claim:ee905f5a192e5fa75d61
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
summary: In Homo sapiens, macrophages and monocytes express MAFB as a marker gene.
span_literal:
As anticipated, most of the macrophage/monocyte genes such as MAFB, Fc gamma receptors, lysosomal proteases and associated membrane proteins were most strongly expressed in human MP subtypes putatively labeled as macrophages or monocytes


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:671378f18fa9da987250
claim_id: claim:671378f18fa9da987250
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
Conversely, classical DC genes such as HLA-DR, CD1C, CCR7, CD40, CD80, LAMP3, IRF4, IRF8, FLT3 and ZBTB46 were strongly expressed in human pulmonary and LN MPs, putatively labeled as DCs

summary:
In Homo sapiens, dendritic cells from lung and lymph node strongly express HLA-DR, CD1C, CCR7, CD40, CD80, LAMP3, IRF4, IRF8, FLT3, and ZBTB46.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:eaef572b99e21dec72f4
claim_id: claim:eaef572b99e21dec72f4
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
summary: In Homo sapiens, alveolar macrophages are defined by the signature genes FABP4, MARCO, and PPARG.
span_literal:
As anticipated, signature genes that define these well-defined cell types are present such as FABP4, MARCO and PPARG for AMs


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:81a6dde622a520d91cc5
claim_id: claim:81a6dde622a520d91cc5
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
and XCR1, CADM1, and CLEC9A, along with a recently identified gene, WDFY4, required for cross-presentation for human blood Clec9a+ DCs and murine splenic CD8+ DCs

summary:
In Homo sapiens, blood Clec9a-positive dendritic cell type 1 expresses XCR1, CADM1, CLEC9A, and WDFY4 as marker genes.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:feefe365e0f3ab7c9a81
claim_id: claim:feefe365e0f3ab7c9a81
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
differences in gene expression for human-mouse AMs include SERPING1, CES1, MME, IL17RB, and C1Q (not shown), which are solely expressed in human AMs and not mouse AMs

summary:
In Homo sapiens, alveolar macrophages solely express SERPING1, CES1, MME, and IL17RB, which are not expressed in mouse alveolar macrophages.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:1d32111001183fd73dc5
claim_id: claim:1d32111001183fd73dc5
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
Human and mouse DC1, blood Clec9a+ and splenic CD8+ DCs, differentially express IDO1 or IDO, CD207 (langerin) and CCR7

summary:
In Homo sapiens, blood Clec9a-positive dendritic cell type 1 differentially expresses IDO1, CD207, and CCR7.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:311c1338c98650e50415
claim_id: claim:311c1338c98650e50415
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
The two murine IMs have a classical IM signature and share gene expression for FOLR2, SEPP1, LYVE1, APOE, C1Q (not shown), CCL7, and CCL2

summary:
In Homo sapiens, interstitial macrophage type 1 and interstitial macrophage type 2 share expression of FOLR2, SEPP1, LYVE1, APOE, CCL7, and CCL2 with their murine counterparts.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:4713e2fb75dc6a54f87a
claim_id: claim:4713e2fb75dc6a54f87a
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
An example gene not shared is SPP1, highly expressed in human IMs (and murine AMs), but not murine IMs

summary:
In Homo sapiens, interstitial macrophages highly express SPP1, which is not expressed in murine interstitial macrophages.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:695a639da5ca28480175
claim_id: claim:695a639da5ca28480175
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
Human LN monocytes share classical murine monocyte genes such as S100A8, S100A9 and CD14 (not shown), as well as mature IM genes such as LYVE1, FOLR2, MMP9, F13A1, C1Q, MAFB, MAF, TIMD4, and STAB1

summary:
In Homo sapiens, lymph node monocytes express S100A8, S100A9, CD14, LYVE1, FOLR2, MMP9, F13A1, MAFB, MAF, TIMD4, and STAB1.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:d014874a580280a15fa9
claim_id: claim:d014874a580280a15fa9
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
However, human IM CD1c matches best with murine splenic CD4+ DCs (Figure 6A), based on their shared non-classical DC genes i.e., cytoskeletal genes, chemokine receptor 6, and cell cycle genes, CD1K1 and CDC20

summary:
In Homo sapiens, interstitial macrophage CD1c-positive expresses chemokine receptor 6 (CCR6) and cell cycle genes CDC20, shared with murine splenic CD4-positive dendritic cell type 2.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:59cf7906f5a72a44895d
claim_id: claim:59cf7906f5a72a44895d
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
summary: In Homo sapiens, lung dendritic cells express CCR6, CD80, CD207, and AXL.
span_literal:
human lung DCs align best with murine splenic CD4+ DCs compared to LN DCs (Figure 7B and Figure 3 and 7C, Group-5 DC2), expressing genes such as CCR6, CD80, CD207, and AXL


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:a7b01f44c8086c964801
claim_id: claim:a7b01f44c8086c964801
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
human LN DCs align best with murine LN DCs (Figure 3 and 7C, Group-4 LN DCs) and express classical DC genes such as ZEB1, CCL22, CCL17, and CCR7, but not the human classical DC gene, LAMP3

summary:
In Homo sapiens, lymph node dendritic cells express ZEB1, CCL22, CCL17, and CCR7, but do not express LAMP3.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:bfa28aa89deaa178a121
claim_id: claim:bfa28aa89deaa178a121
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
Analysis of our RNA-seq data identifies CD88 as a viable cell surface marker that can distinguish macrophages and monocytes from DCs in the tissue of humans and mice

summary:
In Homo sapiens, CD88 is a cell surface marker that distinguishes macrophages and monocytes from dendritic cells.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:491bc15906aca9263d76
claim_id: claim:491bc15906aca9263d76
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
histogram plots demonstrated that human and mouse AMs, IMs, and tissue monocytes express higher levels of CD88 compared to DCs

summary:
In Homo sapiens, alveolar macrophages, interstitial macrophages, and tissue monocytes express higher levels of CD88 compared to dendritic cells.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:17e531a49b6ea986e632
claim_id: claim:17e531a49b6ea986e632
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
histogram plots demonstrated that human and mouse AMs, IMs, and tissue monocytes express higher levels of CD88 compared to DCs

summary:
In Homo sapiens, interstitial macrophages express higher levels of CD88 compared to dendritic cells.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:14df54bce4084d7fd8b4
claim_id: claim:14df54bce4084d7fd8b4
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
summary: In Homo sapiens, blood dendritic cells lack CCR7 expression.
span_literal:
Human blood DCs lack CCR7, a receptor required for lymphatic migration and localization in the T cell zone of LNs


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:c5cc53a97fb549635ef0
claim_id: claim:c5cc53a97fb549635ef0
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
summary: In Homo sapiens, blood dendritic cells highly express CD62L, in contrast to tissue dendritic cells.
span_literal:
CD62L is highly expressed in human blood DCs, but not in tissue DCs, suggesting that once in tissue this gene is no longer required


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:1fb80062dfa5ddd6ae27
claim_id: claim:1fb80062dfa5ddd6ae27
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
CCL17 and CCL22 expression is restricted to DC populations in lung and LNs, and is not expressed in human blood DCs

summary:
In Homo sapiens, lung and lymph node dendritic cells express CCL17 and CCL22, which are not expressed in blood dendritic cells.


claim_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571:claim:c8a8b94fd0da5a59696a
claim_id: claim:c8a8b94fd0da5a59696a
paper_key: biorxiv:f787a6d9-6ce3-1014-a3f6-a662a1333571
span_literal:
murine IM3 matches best with human IM CD1c, where both MPs express inflammatory monocyte genes IL1B, C1QB, C1QC, and F13A1

summary:
In Homo sapiens, interstitial macrophage CD1c-positive expresses inflammatory monocyte genes IL1B, C1QB, C1QC, and F13A1.


claim_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f:claim:eac9ca51dd667a21a6f9
claim_id: claim:eac9ca51dd667a21a6f9
paper_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f
span_literal:
MSCs found in the periapical region were positive for typical stem cell markers, such as STRO-1, CD90, CD73, CD105, CD146 and Sox2

summary:
In Homo sapiens, mesenchymal stem cells found in the periapical region are positive for typical stem cell markers STRO-1, CD90, CD73, CD105, CD146, and SOX2.


claim_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f:claim:64c37df0056397939cb0
claim_id: claim:64c37df0056397939cb0
paper_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f
span_literal:
MSC markers such as CD44, CD73, CD90, CD106 and STRO-1 have been observed in human periapical inflammatory tissues

summary:
In Homo sapiens, mesenchymal stem cell markers CD44, CD73, CD90, CD106, and STRO-1 have been observed in human periapical inflammatory tissues.


claim_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f:claim:b45a71d26eb0d29316b0
claim_id: claim:b45a71d26eb0d29316b0
paper_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f
summary: In Homo sapiens, periodontal mesenchymal stem cells express high levels of SPARC.
span_literal:
Recent research using scRNA-seq revealed high levels of SPARC expression in human periodontal MSCs, highlighting the potential role of SPARC in oral MSC populations


claim_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f:claim:fddcac6faa34720d2149
claim_id: claim:fddcac6faa34720d2149
paper_key: biorxiv:f8386e3b-6c81-1014-8f76-ea7139bf473f
span_literal:
The expressions of SPARC and COL3α1 were significantly enhanced in alveolar bone from patients with AP, accompanied by increases in SPP1 and OCN

summary:
In Homo sapiens, mesenchymal stem cells in alveolar bone from patients with apical periodontitis show significantly enhanced expression of SPARC, COL3A1, SPP1, and osteocalcin.


claim_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668:claim:9fd6b1e3ba3cdbdd412a
claim_id: claim:9fd6b1e3ba3cdbdd412a
paper_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668
span_literal:
SPIB targets include B-cell markers like CD19 and CXCR5, supporting its function in immune lineage commitment (39, 40).

summary:
In Homo sapiens, B cell is marked by positive expression of CD19 and CXCR5, which are targets of the transcription factor SPIB.


claim_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668:claim:0b616db74c376abc5324
claim_id: claim:0b616db74c376abc5324
paper_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668
span_literal:
we did recover several key transcription factors and broad cell types associations mentioned in (30), including IKZF1 and IKZF3 for T-cells, CDX1 for stem cells, SOX30 and TCFL5 for male germ cells, and HEY1, ERG, and LHX6 for endothelial cells.

summary:
In Homo sapiens, T cell is marked by positive expression of IKZF1 and IKZF3, as recovered by TranscriptFormer from the Tabula Sapiens 2.0 dataset.


claim_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668:claim:c1677d112376f9f71a2c
claim_id: claim:c1677d112376f9f71a2c
paper_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668
span_literal:
we did recover several key transcription factors and broad cell types associations mentioned in (30), including IKZF1 and IKZF3 for T-cells, CDX1 for stem cells, SOX30 and TCFL5 for male germ cells, and HEY1, ERG, and LHX6 for endothelial cells.

summary:
In Homo sapiens, stem cell is marked by positive expression of CDX1, as recovered by TranscriptFormer from the Tabula Sapiens 2.0 dataset.


claim_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668:claim:17e0c7c48e8ac04355fe
claim_id: claim:17e0c7c48e8ac04355fe
paper_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668
span_literal:
we did recover several key transcription factors and broad cell types associations mentioned in (30), including IKZF1 and IKZF3 for T-cells, CDX1 for stem cells, SOX30 and TCFL5 for male germ cells, and HEY1, ERG, and LHX6 for endothelial cells.

summary:
In Homo sapiens, male germ cell is marked by positive expression of SOX30 and TCFL5, as recovered by TranscriptFormer from the Tabula Sapiens 2.0 dataset.


claim_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668:claim:7219b11b41c5c43f2626
claim_id: claim:7219b11b41c5c43f2626
paper_key: biorxiv:f96f23ec-83f2-1014-ad76-8d430e749668
summary:
In Homo sapiens, endothelial cell is marked by positive expression of HEY1, ERG, and LHX6, as recovered by TranscriptFormer from the Tabula Sapiens 2.0 dataset.


claim_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461:claim:bb8ad0b97cdf790349ef
claim_id: claim:bb8ad0b97cdf790349ef
paper_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461
summary: In Homo sapiens, plasmacytoid dendritic cells are identified by BDCA2 expression.
span_literal:
plasmacytoid dendritic cells (pDCs: BDCA2), type-1 and type-2 conventional dendritic cells (cDC1: CD141+CD1c–; cDC2: CD141–CD1c+), sinusoidal macrophages (CD169), non-sinusoidal macrophages (CD169–CD68+), NK cells (CD56) and granulocytes (CD66b).


claim_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461:claim:640d8a71523831b7b62e
claim_id: claim:640d8a71523831b7b62e
paper_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461
span_literal:
plasmacytoid dendritic cells (pDCs: BDCA2), type-1 and type-2 conventional dendritic cells (cDC1: CD141+CD1c–; cDC2: CD141–CD1c+), sinusoidal macrophages (CD169), non-sinusoidal macrophages (CD169–CD68+), NK cells (CD56) and granulocytes (CD66b).

summary:
In Homo sapiens, type-1 conventional dendritic cells are identified by positive CD141 expression and negative CD1c expression.


claim_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461:claim:ed8e4c2a0830cfa2f56e
claim_id: claim:ed8e4c2a0830cfa2f56e
paper_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461
span_literal:
plasmacytoid dendritic cells (pDCs: BDCA2), type-1 and type-2 conventional dendritic cells (cDC1: CD141+CD1c–; cDC2: CD141–CD1c+), sinusoidal macrophages (CD169), non-sinusoidal macrophages (CD169–CD68+), NK cells (CD56) and granulocytes (CD66b).

summary:
In Homo sapiens, type-2 conventional dendritic cells are identified by negative CD141 expression and positive CD1c expression.


claim_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461:claim:6d140b9855ce9aca49cb
claim_id: claim:6d140b9855ce9aca49cb
paper_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461
summary:
In Homo sapiens, non-sinusoidal macrophages are identified by negative CD169 expression and positive CD68 expression.


claim_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461:claim:ceb97ab8652dd801ad86
claim_id: claim:ceb97ab8652dd801ad86
paper_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461
span_literal: CD141, which labels both cDC1 and endothelial cells
summary:
In Homo sapiens, CD141 is expressed in both type-1 conventional dendritic cells and endothelial cells.


claim_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461:claim:3975e95ac2335ed02400
claim_id: claim:3975e95ac2335ed02400
paper_key: biorxiv:fa006caa-6c3b-1014-ad2f-9ca3be029461
summary: In Homo sapiens, toll-like receptors are highly expressed in plasmacytoid dendritic cells.
span_literal:
Given the role of TLR receptors (highly expressed in plasmacytoid dendritic cells) in vaccine efficacy


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:0c9ca4a40d7a700f08b3
claim_id: claim:0c9ca4a40d7a700f08b3
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
span_literal:
Samples were annotated as cDC1 if the original study had provided FACS data using current benchmarks of cDC1, including CD141, CLEC9A and CADM1 (Figure 1B, Supplementary Figure 1C).

summary:
In Homo sapiens, conventional dendritic cell 1 is identified by the markers CD141, CLEC9A, and CADM1.


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:c1e5b57eb89f1c176a21
claim_id: claim:c1e5b57eb89f1c176a21
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
summary: In Homo sapiens, CD1C is a common marker of conventional dendritic cell 2 population.
span_literal:
CD1C is a common marker of cDC2 population and is widely used to isolate this cell type from blood and other tissues.


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:659882165f5ef7d72fbe
claim_id: claim:659882165f5ef7d72fbe
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
span_literal:
For example, cDC1 significant markers CLEC9A and TLR3 and cDC2 markers CLEC10A and CD1D were downregulated by bacterial or viral activation (Figure 1C-D, Supplementary Figure 2A-B).

summary:
In Homo sapiens, CLEC9A and TLR3 are significant markers of conventional dendritic cell 1, and CLEC10A and CD1D are markers of conventional dendritic cell 2, all downregulated by bacterial or viral activation.


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:559c50f876c76434cf34
claim_id: claim:559c50f876c76434cf34
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
span_literal:
For example, cDC1 significant markers CLEC9A and TLR3 and cDC2 markers CLEC10A and CD1D were downregulated by bacterial or viral activation (Figure 1C-D, Supplementary Figure 2A-B).

summary:
In Homo sapiens, CLEC10A and CD1D are markers of conventional dendritic cell 2, downregulated by bacterial or viral activation.


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:bc52a12761f7553a3f2d
claim_id: claim:bc52a12761f7553a3f2d
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
span_literal:
viral adjuvant receptor, TLR3, is highly expressed by cDC1 while bacterial adjuvant receptor, TLR4, is highly expressed by cDC2 (Leal Rojas et al., 2017).

summary:
In Homo sapiens, toll-like receptor 3 (TLR3) is highly expressed by conventional dendritic cell 1, while toll-like receptor 4 (TLR4) is highly expressed by conventional dendritic cell 2.


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:c4e06cbfcb62963a0004
claim_id: claim:c4e06cbfcb62963a0004
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
span_literal:
Most isolation methods rely on specific markers to isolate DC subsets from varied tissue types. For example, CLEC9A, XCR1 and CADM1 are the most common markers for isolating blood and tissue-resident cDC1.

summary:
In Homo sapiens, CLEC9A, XCR1, and CADM1 are the most common markers for isolating conventional dendritic cell 1 from blood and tissues.


claim_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e:claim:20e90517d54a880c7ca0
claim_id: claim:20e90517d54a880c7ca0
paper_key: biorxiv:fa200037-7001-1014-b4a8-b2d1b5dda72e
span_literal:
For example, B- and T-lymphocyte attenuator (BTLA), a significant marker of human cDC1 mediating immune regulation (Jones et al., 2016), is missing from the cDC1s differentiated from cord blood CD34+ progenitors, but its expression is rescued in cDC1s differentiated in the HuMouse models (Figure 3B).

summary:
In Homo sapiens, B- and T-lymphocyte attenuator (BTLA) is a significant marker of conventional dendritic cell 1 mediating immune regulation.


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:f40feb10779ce97e1224
claim_id: claim:f40feb10779ce97e1224
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
summary: In Homo sapiens, plasma cells specifically express high levels of CD138 (SDC1).
span_literal:
In Fig 1D, 7 clusters (3, 8, 10, 14, 15, 18 and 21) specifically expressing high levels of CD138 were classified into plasma cells.


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:18be3a8323e6751a14cc
claim_id: claim:18be3a8323e6751a14cc
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
span_literal:
NKG7, GZMA, and GNLY and the chemokines CCL5 and CCL4 were exclusively expressed in C21 cells and were defined as “cytotoxic plasma cells

summary:
In Homo sapiens, cytotoxic plasma cells exclusively express the cytotoxic genes NKG7, GZMA, and GNLY and the chemokines CCL5 and CCL4.


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:f0053edeb4983c4ed571
claim_id: claim:f0053edeb4983c4ed571
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
span_literal:
Expression of cell proliferation, cell cycle related oncogenic markers MKI67, TOP2A and CDK1 also showed similar pattern with overall cell cycle, suggesting a high proliferation potential of C8 and C10 in MM (Fig 3B).

summary:
In Homo sapiens, proliferating plasma cells (clusters C8 and C10) express cell proliferation and cell cycle related markers MKI67, TOP2A, and CDK1.


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:86b437f62937da47651e
claim_id: claim:86b437f62937da47651e
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
span_literal:
Ribonucleotide Reductase Regulatory Subunit M2 (RRM2), a specific marker of proliferating PCs, was shown to induce MM cell line proliferation and serve as a detrimental marker in MM.

summary:
In Homo sapiens, Ribonucleotide Reductase Regulatory Subunit M2 (RRM2) is a specific marker of proliferating plasma cells in multiple myeloma.


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:0b92f0c3b2fef6f8033d
claim_id: claim:0b92f0c3b2fef6f8033d
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
span_literal:
T2 was marked by high expression of CD8A and no expression of NKG7 and was identified as CD8+ T cells.

summary:
In Homo sapiens, CD8+ T cells (cluster T2) are marked by high expression of CD8A and no expression of NKG7.


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:ad748c7212d2cf440d55
claim_id: claim:ad748c7212d2cf440d55
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
summary: In Homo sapiens, activated neutrophils are characterized by CXCR2 expression.
span_literal:
Significantly, the proportion of activated neutrophils characterized by CXCR2 expression [47-49] (C5 in Fig 1B) decreased with R-ISS stage (C5 in Fig 1F).


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:617377bd3e5ab28c12e7
claim_id: claim:617377bd3e5ab28c12e7
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
summary: In Homo sapiens, CD48 is expressed on more than 90% of multiple myeloma plasma cells.
span_literal:
CD48 was expressed on more than 90% of MM plasma cells, and administration of the anti-CD48 mAb significantly inhibited MM growth [75].


claim_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20:claim:6409f1f97c9e193de65a
claim_id: claim:6409f1f97c9e193de65a
paper_key: biorxiv:fbd95004-6cf9-1014-bead-f9f2e4a06d20
summary: In Homo sapiens, CD74 is predominantly expressed in malignant plasma cells.
span_literal:
CD74 is predominantly expressed in malignant plasma cells, and anti-CD74 mAbs internalize very rapidly and have shown efficacy in B-lymphoma models [76] [77].


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:3373e796c360226dc3d6
claim_id: claim:3373e796c360226dc3d6
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
summary: In Homo sapiens, type 3 innate lymphoid cell is demarcated by expression of IL7R, KIT, and NRP1.
span_literal:
A population of ILC3 was demarcated by expression of IL7R, KIT, and NRP1 (Fig. 5c and Extended Data Fig. 10a).


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:fe06291af90c2e78e74d
claim_id: claim:fe06291af90c2e78e74d
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
summary: In Homo sapiens, type 1 innate lymphoid cell expresses NCR1 and TBX21.
span_literal:
This was juxtaposed by an ILC1 cluster expressing NCR1 and TBX21, as well as NK cells expressing EOMES, all consistent with prior literature36.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:0f6e2756fe990f1b9f9d
claim_id: claim:0f6e2756fe990f1b9f9d
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
summary: In Homo sapiens, conventional dendritic cell type 2 is marked by expression of SIRPA and CD1C.
span_literal:
Nevertheless, we could identify a SIRPA+ population overlapping with CD1C expression, as would be expected for human cDC237.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:ce164af4f5afa0581b22
claim_id: claim:ce164af4f5afa0581b22
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
span_literal:
We annotated a plasmacytoid DC cluster adjacent to this, as these cells were negative for CD1C while positive for IL3RA (CD123) and included rare cells positive for TLR7 and TLR9 expression38.

summary:
In Homo sapiens, plasmacytoid dendritic cell is negative for CD1C and positive for IL3RA, TLR7, and TLR9.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:a38f6d3405ee4ab36d32
claim_id: claim:a38f6d3405ee4ab36d32
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
span_literal:
On querying for RORC in this human dataset, we observed non-ILC3 expression in a single set of cells clustering at the extremity of the cDC2 annotation (arrow, Fig. 5b,c).

summary:
In Homo sapiens, tolerogenic dendritic cell expresses RORC and is distinct from type 3 innate lymphoid cell.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:0cffe168f2946a3212d9
claim_id: claim:0cffe168f2946a3212d9
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
span_literal:
This human cluster was also positive for ZBTB46, CD40, CCR7, and ITGAX, although AIRE was not detected in it or any other HLA-DR+ mLN population.

summary:
In Homo sapiens, tolerogenic dendritic cell is positive for ZBTB46, CD40, CCR7, and ITGAX, and negative for AIRE.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:9c9f6f28e928b0bc0c22
claim_id: claim:9c9f6f28e928b0bc0c22
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
span_literal:
This same analysis revealed 8 candidates conserved as differentially expressed genes across human and mouse tDC (Extended Data Fig. 10b,c), notably including PRDM16, PIGR, IDO2, DLGAP1, MACC1, and CDH1, largely corroborated by broader cross-species analyses of RORγt+ APCs41,42.

summary:
In Homo sapiens, tolerogenic dendritic cell differentially expresses PRDM16, PIGR, IDO2, DLGAP1, MACC1, and CDH1, conserved across species.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:3815974ee7abf70f487c
claim_id: claim:3815974ee7abf70f487c
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
span_literal:
Conserved genes (Extended Data Fig. 10b, Supplemental Table 1) included mostly expected results for cDC1 (such as CLEC9A, CADM1, and XCR1) and ILC3 (such as IL23R, IL22, and RORC).

summary:
In Homo sapiens, conventional dendritic cell type 1 differentially expresses conserved genes CLEC9A, CADM1, and XCR1.


claim_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a:claim:2e583e3c15e45fcbd3c2
claim_id: claim:2e583e3c15e45fcbd3c2
paper_key: biorxiv:fc7595eb-733c-1014-9892-ed444a916a2a
span_literal:
Conserved genes (Extended Data Fig. 10b, Supplemental Table 1) included mostly expected results for cDC1 (such as CLEC9A, CADM1, and XCR1) and ILC3 (such as IL23R, IL22, and RORC).

summary:
In Homo sapiens, type 3 innate lymphoid cell differentially expresses conserved genes IL23R, IL22, and RORC.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:3961dd9ecb12c06ec9b8
claim_id: claim:3961dd9ecb12c06ec9b8
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: NK cells identified by NKG7 expression (N=25,248)
summary:
In Homo sapiens hepatocellular carcinoma tissue, natural killer cells are identified by positive expression of NKG7.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:e613ee03d95a532a8fe4
claim_id: claim:e613ee03d95a532a8fe4
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: Mast cells identified by HPGDS expression (N=2,877)
summary:
In Homo sapiens hepatocellular carcinoma tissue, mast cells are identified by positive expression of HPGDS.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:0ef9b4a7472ca8e6fd08
claim_id: claim:0ef9b4a7472ca8e6fd08
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: T cells identified by CD3D expression (N=6,576)
summary:
In Homo sapiens hepatocellular carcinoma tissue, T cells are identified by positive expression of CD3D.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:3f19fae83035ef6a5dbe
claim_id: claim:3f19fae83035ef6a5dbe
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: Endothelial cells identified by PECAM1 expression (N=1,467)
summary:
In Homo sapiens hepatocellular carcinoma tissue, endothelial cells are identified by positive expression of PECAM1.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:d7ae88b31f2f049f24b6
claim_id: claim:d7ae88b31f2f049f24b6
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: Plasma cells identified by MZB1 expression (N=994)
summary:
In Homo sapiens hepatocellular carcinoma tissue, plasma cells are identified by positive expression of MZB1.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:35f3e0937c65f2dff0a9
claim_id: claim:35f3e0937c65f2dff0a9
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: B cells identified by MS4A1 expression (N=543)
summary:
In Homo sapiens hepatocellular carcinoma tissue, B cells are identified by positive expression of MS4A1.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:666b904c9e95a9e9d1aa
claim_id: claim:666b904c9e95a9e9d1aa
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: Myeloid dendritic cells identified by CLEC9A expression (N=269)
summary:
In Homo sapiens hepatocellular carcinoma tissue, myeloid dendritic cells are identified by positive expression of CLEC9A.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:4249b0825e096c8c0565
claim_id: claim:4249b0825e096c8c0565
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: Macrophages identified by C1QB expression (N=194)
summary:
In Homo sapiens hepatocellular carcinoma tissue, macrophages are identified by positive expression of C1QB.


claim_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509:claim:7e6c6ab72c1f8b3cac36
claim_id: claim:7e6c6ab72c1f8b3cac36
paper_key: biorxiv:fcd07962-6c85-1014-af85-cbe176e26509
span_literal: Hepatocytes identified by ALB expression (N=143)
summary:
In Homo sapiens hepatocellular carcinoma tissue, hepatocytes are identified by positive expression of ALB.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:0b32ab3ea8e7aae37f23
claim_id: claim:0b32ab3ea8e7aae37f23
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
Single-cell transcriptomics has revealed significant diversity within mDA neurons in the adult human SNpc, categorizing them into three major subtypes based on the expression of SOX6, CALB1, and GAD2, establishing that the SOX6 subpopulation is the most susceptible to degeneration

summary:
In Homo sapiens, midbrain dopaminergic neurons in the adult substantia nigra pars compacta are categorized into three major subtypes based on expression of SOX6, CALB1, and GAD2.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:ee1e36c697f225731ff0
claim_id: claim:ee1e36c697f225731ff0
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
DA clusters exhibited high expression of canonical dopaminergic markers (TH, DDC, NR4A2, LMX1A, PBX1, SLC18A2 [VMAT2], SLC6A3 [DAT], PITX3, KCNJ6 [GIRK2]), whereas GABA and glutamatergic clusters lacked these but expressed GAD1 and GAD2 and SLC17A6 [VGLUT2], respectively.

summary:
In Homo sapiens, dopaminergic neurons exhibit high expression of canonical markers TH, DDC, NR4A2, LMX1A, PBX1, SLC18A2, SLC6A3, PITX3, and KCNJ6, whereas GABAergic neurons and glutamatergic neurons lack these markers.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:e325d6fd4e07cd8d0974
claim_id: claim:e325d6fd4e07cd8d0974
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
DA clusters exhibited high expression of canonical dopaminergic markers (TH, DDC, NR4A2, LMX1A, PBX1, SLC18A2 [VMAT2], SLC6A3 [DAT], PITX3, KCNJ6 [GIRK2]), whereas GABA and glutamatergic clusters lacked these but expressed GAD1 and GAD2 and SLC17A6 [VGLUT2], respectively.

summary:
In Homo sapiens, GABAergic neurons express GAD1 and GAD2, distinguishing them from dopaminergic neurons.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:fac4924779e774a248f7
claim_id: claim:fac4924779e774a248f7
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
DA clusters exhibited high expression of canonical dopaminergic markers (TH, DDC, NR4A2, LMX1A, PBX1, SLC18A2 [VMAT2], SLC6A3 [DAT], PITX3, KCNJ6 [GIRK2]), whereas GABA and glutamatergic clusters lacked these but expressed GAD1 and GAD2 and SLC17A6 [VGLUT2], respectively.

summary:
In Homo sapiens, glutamatergic neurons express SLC17A6, distinguishing them from dopaminergic neurons.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:7cbf60b9147855d4ef07
claim_id: claim:7cbf60b9147855d4ef07
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
Within the DA lineage, subclusters were resolved by differential expression of SOX6, CALB1 and ONECUT2 (Fig. 5c,d).

summary:
In Homo sapiens, dopaminergic neuron subclusters within the dopaminergic lineage are resolved by differential expression of SOX6, CALB1, and ONECUT2.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:fbb72e0b8dee0a7cdab7
claim_id: claim:fbb72e0b8dee0a7cdab7
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
INA clusters were distinguished from glutamatergic clusters by elevated SLC17A6, STMN2 and INA expression (Extended Fig. 8b,c, Extended Fig. 9b,c)

summary:
In Homo sapiens, immature neuron clusters are distinguished from glutamatergic neuron clusters by elevated expression of SLC17A6, STMN2, and INA.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:6f4c4a71965137654ddb
claim_id: claim:6f4c4a71965137654ddb
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
Further analysis of the neuronal clusters (defined by RBFOX3) resolved into four distinct populations: dopaminergic (DAergic), glutamatergic, GABAergic,and a small cluster of neural progenitors (defined by high expression of INA)

summary:
In Homo sapiens, neuronal clusters are defined by RBFOX3 expression, and neural progenitors are defined by high expression of INA.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:f2959e31f429fda66e3d
claim_id: claim:f2959e31f429fda66e3d
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
Moreover, the DA_SOX6 is differentially highly enriched in SOX6 (score >0.8) and CUX2 (score >0.6) within the DA clusters.

summary:
In Homo sapiens, the DA_SOX6 dopaminergic neuron subtype is differentially enriched in SOX6 and CUX2 regulon activity compared to other dopaminergic neuron clusters.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:36b1a0a39c29186bb030
claim_id: claim:36b1a0a39c29186bb030
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
span_literal:
A majority of grafted TH+ cells were found to be positive for several markers distinctive to the PD-vulnerable A9-subtype (Fig 4g,h), such as SOX6 (84.67 ± 3.03%), ALDH1A1 (50.67 ± 2.37%) and AGTR1 (64.16 ± 4.97%).

summary:
In Homo sapiens, A9-subtype midbrain dopaminergic neurons are marked by expression of SOX6, ALDH1A1, and AGTR1.


claim_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf:claim:7cd9e4aad0625d690186
claim_id: claim:7cd9e4aad0625d690186
paper_key: biorxiv:fcdb6ae7-74e0-1014-aa4b-bcf60c40c2cf
summary: In Homo sapiens, A10-subtype midbrain dopaminergic neurons are marked by expression of Calbindin.
span_literal:
In contrast, a minority of the DANS stained positively for the A10-subtype marker Calbindin (29.92 ± 3.45%).


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:dc9dcd95db54c30767fa
claim_id: claim:dc9dcd95db54c30767fa
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
Ptx3-LECs in both humans and mice are distinguished from Marco-LECs by higher expression of the glycoprotein and scavenger receptor CD36, also known as Fatty Acid Translocase (FAT) (Figure 8A).

summary:
In Homo sapiens, Ptx3-lymphatic endothelial cells are distinguished from Marco-lymphatic endothelial cells by higher expression of CD36, also known as Fatty Acid Translocase.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:b81106cce90a7b6c9450
claim_id: claim:b81106cce90a7b6c9450
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
summary: In Homo sapiens, floor lymphatic endothelial cells are marked by BMP2, CCL20, CD74, and CSF1.
span_literal:
A number of mouse key subset specific marker DEGs are shared in the human including e.g. fLECs: Bmp2, Ccl20, Cd74 and Csf1; cLECs: Ackr4, Bmp4 and Cav1; Marco-LECs: Marco, Clec4g and C2; and Ptx3-LECs: Ptx3, Nrp2 and Flt4 (Vegfr3).


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:afbe0cefda6e1753171f
claim_id: claim:afbe0cefda6e1753171f
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
summary:
In Homo sapiens, Ptx3-lymphatic endothelial cells are marked by PTX3, NRP2, and FLT4 (vascular endothelial growth factor receptor 3).


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:14d4e6e506ad9589861b
claim_id: claim:14d4e6e506ad9589861b
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
ACKR1, also known as DARC (Duffy Antigen Receptor for Chemokines) marks human fLECs and Marco-LECs; but Ackr1 has very low expression in mouse LN LECs, without clear subset selectivity (Figure S8B).

summary:
In Homo sapiens, ACKR1, also known as Duffy Antigen Receptor for Chemokines, marks floor lymphatic endothelial cells and Marco-lymphatic endothelial cells.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:9ed1032439b47427972e
claim_id: claim:9ed1032439b47427972e
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
ACKR1, also known as DARC (Duffy Antigen Receptor for Chemokines) marks human fLECs and Marco-LECs; but Ackr1 has very low expression in mouse LN LECs, without clear subset selectivity (Figure S8B).

summary:
In Homo sapiens, ACKR1, also known as Duffy Antigen Receptor for Chemokines, marks Marco-lymphatic endothelial cells.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:b018c28ed564ace083df
claim_id: claim:b018c28ed564ace083df
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
summary: In Homo sapiens, floor lymphatic endothelial cells display high expression of IL-6.
span_literal:
Human but not mouse LN LECs also display high expression of IL-6 in fLECs (Figure S8B), likely reflecting a higher inflammatory basal state in human, especially compared to our SPF mice.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:66e5a956c58e782862bc
claim_id: claim:66e5a956c58e782862bc
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
Human Ptx3-LECs express MMP2 and LOX, genes missing in mouse LECs or expressed in different subsets (i.e. Lox expressed weakly in cLECs in mouse) (Figure S8B).

summary:
In Homo sapiens, Ptx3-lymphatic endothelial cells express matrix metalloproteinase 2 (MMP2) and lysyl oxidase (LOX).


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:03ad3a496db4aa4de1b3
claim_id: claim:03ad3a496db4aa4de1b3
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
summary: In Homo sapiens, CD209 and CLEC4M are specific markers for Marco-lymphatic endothelial cells.
span_literal:
In addition, CD209 and CLEC4M, which lack orthologues in mouse [26], are specific for human Marco-LECs.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:1d89d13667aeb8a1dfc3
claim_id: claim:1d89d13667aeb8a1dfc3
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
Importantly, human Ptx3-LECs (LEC IV) also share expression of PTX3 and lack PD-L1 (CD274) expression, similar to their mouse counterpart; and they express the inter-alpha-trypsin inhibitor gene family member ITIH3, functionally related to the mouse Ptx3-LEC marker Itih5 [63] (Figure 7).

summary:
In Homo sapiens, Ptx3-lymphatic endothelial cells express PTX3 and ITIH3 and lack Programmed Death-Ligand 1 (CD274) expression.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:8d33021b2dd56250c955
claim_id: claim:8d33021b2dd56250c955
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
cLEC s2, which we did not segregate previously, uniquely expresses high levels of Hairy/enhancer-of-split related with YRPW motif protein (HEY1), the chemokine CCL2 (Figure 6C) and E-Selectin (SELE) (data not shown).

summary:
In Homo sapiens, ceiling lymphatic endothelial cell s2 uniquely expresses high levels of Hairy/enhancer-of-split related with YRPW motif protein (HEY1), the chemokine CCL2, and E-Selectin (SELE).


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:398b3e0dba77de1a379d
claim_id: claim:398b3e0dba77de1a379d
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
Staining of CD36 in human head and neck LNs identified capillary-like, CD36high Lyve-1+ lymphatic cords, negative for MARCO and the Marco-LEC (LEC VI [26]) marker CLEC4M (Figures 8B and 8C).

summary:
In Homo sapiens, Ptx3-lymphatic endothelial cells in lymph node are CD36-high and LYVE-1-positive, and negative for MARCO and CLEC4M.


claim_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b:claim:6f863884ba4caefdea97
claim_id: claim:6f863884ba4caefdea97
paper_key: biorxiv:fd4da487-6bfd-1014-9109-ef3323dd2b7b
span_literal:
Co-expression of CCL21 and SPHK1 (enzyme required for S1P production) support a role of Ptx3-LECs in lymphocyte egress.

summary:
In Homo sapiens, Ptx3-lymphatic endothelial cells co-express CCL21 and sphingosine kinase 1 (SPHK1).


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:39863fc8f00542ab64e8
claim_id: claim:39863fc8f00542ab64e8
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal: Basal epithelia express cytokeratin 5 and the transcription factor p63.
summary:
In Homo sapiens prostate, basal epithelial cells express keratin 5 and the transcription factor p63.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:bb7d724df0f9aaa70d66
claim_id: claim:bb7d724df0f9aaa70d66
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
Familiar DEGs genes such as KRT5 , KRT14 , and TP63 , as well as lesser known genes such as NOTCH4 , LTBP2 , and DKK1 , characterize CD271 + basal epithelia.

summary:
In Homo sapiens prostate, CD271-positive basal epithelial cells are characterized by KRT5, KRT14, TP63, NOTCH4, LTBP2, and DKK1.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:116cd0bda8b8eea8c456
claim_id: claim:116cd0bda8b8eea8c456
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
The CD26 + luminal epithelia are marked by familiar DEGs such as KLK3 , ACPP , and MSMB , as well as lesser-known genes, including GP2 , NEFH , and NPY .

summary:
In Homo sapiens prostate, CD26-positive luminal epithelial cells are marked by KLK3, ACPP, MSMB, GP2, NEFH, and NPY.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:a4c3388836d4f3a53cbb
claim_id: claim:a4c3388836d4f3a53cbb
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
several of the top other epithelia DEGs include classic neuroendocrine line-age markers such as CHGA and CHGB and unknown markers such as LY6D , SCGB3A1 , and PSCA .

summary:
In Homo sapiens prostate, the other epithelial cell population includes neuroendocrine lineage markers CHGA and CHGB, as well as LY6D, SCGB3A1, and PSCA.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:ba1aa1cb6b2d6f448207
claim_id: claim:ba1aa1cb6b2d6f448207
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
The putative smooth muscle cluster expressed high levels of actin (ACTA2) and myosin (MYH11, MYL9, and TPM2) genes, while the putative fibroblast cell type expressed high levels of paracrine signaling factors such as growth factors (FGF2 and FGF7), prostaglandins (PTGDS and PTGS2), and WNT pathway regulators (RSPO3 and SFRP2).

summary:
In Homo sapiens prostate, smooth muscle cells express high levels of ACTA2, MYH11, MYL9, and TPM2, while fibroblast cells express high levels of FGF2, FGF7, PTGDS, PTGS2, RSPO3, and SFRP2.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:7469ba29774f317c0130
claim_id: claim:7469ba29774f317c0130
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
The putative smooth muscle cluster expressed high levels of actin (ACTA2) and myosin (MYH11, MYL9, and TPM2) genes, while the putative fibroblast cell type expressed high levels of paracrine signaling factors such as growth factors (FGF2 and FGF7), prostaglandins (PTGDS and PTGS2), and WNT pathway regulators (RSPO3 and SFRP2).

summary:
In Homo sapiens prostate, fibroblast cells express high levels of FGF2, FGF7, PTGDS, PTGS2, RSPO3, and SFRP2.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:20f9f62c8ed40bed9cfa
claim_id: claim:20f9f62c8ed40bed9cfa
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
MYH11) and Decorin (DCN) are enriched in smooth muscle and fibroblast cell types, respectively, in human prostate

summary:
In Homo sapiens prostate, Myosin 11 (MYH11) is enriched in smooth muscle cells and Decorin (DCN) is enriched in fibroblast cells.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:67db0fd6bbb0ec1b7c7a
claim_id: claim:67db0fd6bbb0ec1b7c7a
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
DEGs of each cluster confirm four epithelial cell types (luminal KLK3 + , basal KRT14 + , OE1 SCGB1A1 + , and OE2 KRT13 + )

summary:
In Homo sapiens prostate, luminal epithelial cells are KLK3-positive, basal epithelial cells are KRT14-positive, other epithelial cell type 1 cells are SCGB1A1-positive, and other epithelial cell type 2 cells are KRT13-positive.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:16fba734d383178c6d0f
claim_id: claim:16fba734d383178c6d0f
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
summary: In Homo sapiens prostate, neuroendocrine cells are marked by SCG2 and CHGA.
span_literal:
A marker gene for NE cells that was discovered in our dataset (SCG2) was tested in combination with a known NE cell marker (CHGA) and confirmed in situ


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:492d922f923b7fc033d1
claim_id: claim:492d922f923b7fc033d1
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal: SCGB1A1 positively marks a small population of KRT5 − luminal-like prostate epithelia.
summary:
In Homo sapiens prostate, SCGB1A1 positively marks a population of KRT5-negative luminal-like epithelial cells (club cells).


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:26966ae6f9543946be01
claim_id: claim:26966ae6f9543946be01
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
summary: In Homo sapiens prostate, KRT13-positive hillock epithelial cells co-express KRT5.
span_literal:
KRT13 + epithelia co-express KRT5, confirming GSEA showing a positive correlation with basal cells of the lung


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:dc279cf8bce459834975
claim_id: claim:dc279cf8bce459834975
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal: KRT14 + BE are low in KRT13 and represent a subpopulation of KRT5
summary:
In Homo sapiens prostate, KRT14-positive basal epithelial cells are low in KRT13 and represent a subpopulation of KRT5-positive basal epithelial cells.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:3923b2c102a17784b58e
claim_id: claim:3923b2c102a17784b58e
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
These data also led to the discovery of two previously unrecognized epithelial cell types marked by high expression of SCGB1A1 and KRT13 with an anatomical enrichment in the prostatic urethra and proximal prostatic ducts.

summary:
In Homo sapiens prostate, two previously unrecognized epithelial cell types (club cells and hillock cells) are marked by high expression of SCGB1A1 and KRT13, respectively, and are enriched in the prostatic urethra and proximal prostatic ducts.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:4037a794a978f43fe19f
claim_id: claim:4037a794a978f43fe19f
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
These data also led to the discovery of two previously unrecognized epithelial cell types marked by high expression of SCGB1A1 and KRT13 with an anatomical enrichment in the prostatic urethra and proximal prostatic ducts.

summary:
In Homo sapiens prostate, hillock epithelial cells are marked by high expression of KRT13 and are enriched in the prostatic urethra and proximal prostatic ducts.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:f2a7ed5496be1803a066
claim_id: claim:f2a7ed5496be1803a066
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
The top genes associated with the KRT13 + cell type are members of the androgen metabolism pathway (AKR1C1 and AKR1C2), which have been implicated in the development of castrate-resistant prostate cancer

summary:
In Homo sapiens prostate, the KRT13-positive hillock cell type is associated with AKR1C1 and AKR1C2, members of the androgen metabolism pathway.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:baffdc3528fd5a1e1f8d
claim_id: claim:baffdc3528fd5a1e1f8d
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
scRNA-seq also revealed PDPN as a positive marker of fibroblasts, which was used again on optimized FACS gates to confirm 91% purity of PDPN + fibroblasts and 93% purity of PDPN − smooth muscle

summary:
In Homo sapiens prostate, PDPN is a positive marker of fibroblast cells, while smooth muscle cells are PDPN-negative.


claim_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b:claim:5d58c8356ec7f40e1d6e
claim_id: claim:5d58c8356ec7f40e1d6e
paper_key: hca:0001_10.1016_j.celrep.2018.11.086_7aff07407b
span_literal:
PSCA was identified in the cluster-specific DEGs as a potential cell surface marker of both OE cell types (as well as a subpopulation of LE)

summary:
In Homo sapiens prostate, PSCA is a cell surface marker of both other epithelial cell types as well as a subpopulation of luminal epithelial cells.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:39e49f5285acaa45d275
claim_id: claim:39e49f5285acaa45d275
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens liver, EPCAM is a positive marker of bile duct cells (cholangiocytes).
span_literal:
our atlas comprises all the main liver cell types, including hepatocytes, EPCAM + bile duct cells (cholangiocytes), CLEC4G+ liver sinusoidal endothelial cells (LSECs), CD34 + PECAM high macro-vascular endothelial cells (MaVECs), hepatic stellate cells and myofibroblasts, Kupffer cells, and immune cells


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:05adf39cb0e4285b85ab
claim_id: claim:05adf39cb0e4285b85ab
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens liver, Kupffer cells are marked by positive expression of CD163 and VSIG4.
span_literal:
A detailed analysis of the CD163 + VSIG4 + Kupffer cell compartment revealed sub-populations with distinct gene expression signatures


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:ac807c626767787748df
claim_id: claim:ac807c626767787748df
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens liver, circulating B cells are marked by positive expression of MS4A1 and CD37.
span_literal:
We identified an MS4A1 + CD37 + B cell subset, which corresponds to circulating B cells upregulating MHC class II components, and a liver resident MZB1 + B cell subset expressing DERL3 , SSR4 , and IGHG4


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:8efc98dd2716be91fdf5
claim_id: claim:8efc98dd2716be91fdf5
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
We identified an MS4A1 + CD37 + B cell subset, which corresponds to circulating B cells upregulating MHC class II components, and a liver resident MZB1 + B cell subset expressing DERL3 , SSR4 , and IGHG4

summary:
In Homo sapiens liver, liver resident B cells are marked by positive expression of MZB1, DERL3, SSR4, and IGHG4.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:3d70048960d2c81e7132
claim_id: claim:3d70048960d2c81e7132
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens liver, NK cells (cluster 5) are marked by positive expression of CD56 (NCAM1).
span_literal:
we recovered a population of CD56 + NK cells (cluster 5) and CD56 - (cluster 3) as well as CD56 + (cluster 1) CD8A + NKT cells, expressing different combinations of chemokine ligands, granzymes, and killer cell lectin-like receptor genes


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:f83f5758def40c07bcfd
claim_id: claim:f83f5758def40c07bcfd
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
A focused analysis revealed that the EPCAM+ compartment is transcriptionally heterogeneous and consists of an ASGR1 + hepatocyte-biased population, KRT19 high CFTR high ALB low cholangiocyte populations, and a remaining population of putative naïve progenitor cells

summary:
In Homo sapiens liver, the EPCAM-positive hepatocyte-biased population is marked by positive expression of ASGR1.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:ceeb20f8712cc2ef7bad
claim_id: claim:ceeb20f8712cc2ef7bad
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
A focused analysis revealed that the EPCAM+ compartment is transcriptionally heterogeneous and consists of an ASGR1 + hepatocyte-biased population, KRT19 high CFTR high ALB low cholangiocyte populations, and a remaining population of putative naïve progenitor cells

summary:
In Homo sapiens liver, cholangiocyte populations within the EPCAM-positive compartment are marked by high KRT19, high CFTR, and low ALB expression.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:8ba01a7d89973b83474b
claim_id: claim:8ba01a7d89973b83474b
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens liver, the EPCAM-positive population is negative for the hepatoblast marker AFP.
span_literal:
The EPCAM + population exhibits only stochastic expression of proliferation markers MKI67 and PCNA and is negative for the hepatoblast marker AFP


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:9c5160ffad8a2143a8c9
claim_id: claim:9c5160ffad8a2143a8c9
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
LYVE1 and CD14 were previously identified as markers distinguishing midzonal and central LSECs periportal populations

summary:
In Homo sapiens liver, LYVE1 and CD14 are positive markers distinguishing midzonal and central liver sinusoidal endothelial cells from periportal populations.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:30246889379830f3b7a2
claim_id: claim:30246889379830f3b7a2
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
The central TROP2 int population is in itself heterogeneous and contains a MUC6 high population (cluster 7).

summary:
In Homo sapiens liver, the central TROP2-intermediate population cluster 7 is marked by high expression of MUC6.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:db195f15a202d1bfb11d
claim_id: claim:db195f15a202d1bfb11d
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
The TROP2 high cholangiocyte clusters comprise a CXCL8 + population (cluster 8) and an MMP7 + population (clusters 4 and 13)

summary:
In Homo sapiens liver, the TROP2-high cholangiocyte cluster 8 is marked by positive expression of CXCL8, and clusters 4 and 13 are marked by positive expression of MMP7.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:c297bed345488581e063
claim_id: claim:c297bed345488581e063
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
The TROP2 high cholangiocyte clusters comprise a CXCL8 + population (cluster 8) and an MMP7 + population (clusters 4 and 13)

summary:
In Homo sapiens liver, the TROP2-high cholangiocyte clusters 4 and 13 are marked by positive expression of MMP7.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:77be94cc23dd9957bf62
claim_id: claim:77be94cc23dd9957bf62
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
The central TROP2 int population stratified as bipotent based on the FateID-predicted bias expresses early developmental transcription factors such as HES1, which is essential for tubular bile duct formation( 21 ), and PROX1, an early specification marker for the developing liver in the mammalian foregut endoderm which is required for hepatocyte proliferation and migration during development( 22 )

summary:
In Homo sapiens liver, the central TROP2-intermediate bipotent progenitor population expresses early developmental transcription factors HES1 and PROX1.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:df254b7bedea51755a9c
claim_id: claim:df254b7bedea51755a9c
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
Differential gene expression analysis and immunohistochemistry revealed that cancer cells lose the expression of cytochrome P450 genes like CYP2E1 and CYP2C8 and the periportally zonated gene CPS1

summary:
In Homo sapiens, hepatocellular carcinoma cells lose expression of CYP2E1, CYP2C8, and CPS1 compared to normal hepatocytes.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:75e71c9e79b7dd54e1a5
claim_id: claim:75e71c9e79b7dd54e1a5
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
They up-regulate AKR1B10 , a known biomarker of HCC with potential involvement in hepatocellular carcinogenesis( 27 )

summary:
In Homo sapiens, hepatocellular carcinoma cells up-regulate AKR1B10, a known biomarker of hepatocellular carcinoma.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:5ea15d5e8eead808bd75
claim_id: claim:5ea15d5e8eead808bd75
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens, IL32 is highly upregulated in hepatocellular carcinoma cells.
span_literal:
immunohistochemistry confirmed that IL32, a pro-inflammatory TNF-alpha inducing cytokine, is highly upregulated in cancer cells


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:20b98b316741e3ef1a02
claim_id: claim:20b98b316741e3ef1a02
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
they do not express LSEC markers like CLEC4G but upregulate MaVEC markers like PECAM1 , AQP1 and CD34

summary:
In Homo sapiens, endothelial cells from hepatocellular carcinoma do not express the liver sinusoidal endothelial cell marker CLEC4G but upregulate macro-vascular endothelial cell markers PECAM1, AQP1, and CD34.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:7d9c29c75c9b2a1bfb6e
claim_id: claim:7d9c29c75c9b2a1bfb6e
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
summary: In Homo sapiens, hepatocellular carcinoma liver sinusoidal endothelial cells upregulate PLVAP.
span_literal:
Moreover, HCC LSECs upregulate PLVAP which makes them less permeable and could potentially restrict the access of lymphocytes and soluble antigens( 28 ) to the tumor


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:0956d1dda63b7da4c305
claim_id: claim:0956d1dda63b7da4c305
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
We discovered novel biliary and potential liver progenitor cell surface markers correlating with EPCAM or TROP1 expression; these include TACSTD2 ( TROP2) , FGFR2 , TM4SF4, and CLDN1 and immunohistochemistry confirmed predicted novel markers such as ANXA4 and the transcriptional co-activator WWTR1

summary:
In Homo sapiens liver, EPCAM-positive biliary and progenitor cells express novel markers TACSTD2 (TROP2), FGFR2, TM4SF4, CLDN1, ANXA4, and WWTR1.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:cde1d0c62f841c7ea61c
claim_id: claim:cde1d0c62f841c7ea61c
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal:
FateID infers similar probabilities of the central population to differentiate towards hepatocytes and cholangiocytes ( Fig. 3c ). The fate bias predictions are supported by a differential gene expression analysis revealing up-regulation of common genes comprising several signaling pathway components ( HES1 , SFRP5 , FGFR2 , FGFR3 ) in the central population

summary:
In Homo sapiens liver, the central EPCAM-positive progenitor population up-regulates signaling pathway components HES1, SFRP5, FGFR2, and FGFR3.


claim_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220:claim:8648ffd930b460fa7ddf
claim_id: claim:8648ffd930b460fa7ddf
paper_key: hca:0002_10.1038_s41586-019-1373-2_de5bb9e220
span_literal: Cluster 5 comprises mainly CD56 + CD8A - NK cells, some of which up-regulate CCL4 .
summary:
In Homo sapiens liver, NK cells (cluster 5) are CD56-positive, CD8A-negative, and some up-regulate CCL4.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:bbf1e57545fd97879247
claim_id: claim:bbf1e57545fd97879247
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal:
POU5F1 (known as OCT4 ), SOX2 , NANOG , and PRDM14 for epiblast cells, GATA6 , GATA4 , SOX17 , and PDGFRA for primitive endoderm cells, and GATA3 , GATA2 , TFAP2C , and KRT7 for trophoblast cells

summary:
In Homo sapiens post-implantation embryos, epiblast cells are marked by POU5F1, SOX2, NANOG, and PRDM14.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:a78613e23052cfb6b245
claim_id: claim:a78613e23052cfb6b245
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal:
POU5F1 (known as OCT4 ), SOX2 , NANOG , and PRDM14 for epiblast cells, GATA6 , GATA4 , SOX17 , and PDGFRA for primitive endoderm cells, and GATA3 , GATA2 , TFAP2C , and KRT7 for trophoblast cells

summary:
In Homo sapiens post-implantation embryos, primitive endoderm cells are marked by GATA6, GATA4, SOX17, and PDGFRA.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:a7b02bf747e20b76e894
claim_id: claim:a7b02bf747e20b76e894
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal:
POU5F1 (known as OCT4 ), SOX2 , NANOG , and PRDM14 for epiblast cells, GATA6 , GATA4 , SOX17 , and PDGFRA for primitive endoderm cells, and GATA3 , GATA2 , TFAP2C , and KRT7 for trophoblast cells

summary:
In Homo sapiens post-implantation embryos, trophoblast cells are marked by GATA3, GATA2, TFAP2C, and KRT7.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:d2965aeee77f43f5d603
claim_id: claim:d2965aeee77f43f5d603
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: CDH1 and TEAD4 , high expressions in cytotrophoblast cells, for pCTB (Cluster 2).
summary:
In Homo sapiens post-implantation embryos, primitive cytotrophoblast cells are marked by high expression of CDH1 and TEAD4.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:3a55e58795031d4d4019
claim_id: claim:3a55e58795031d4d4019
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
summary: In Homo sapiens post-implantation embryos, migrative trophoblast cells are marked by MMP2.
span_literal:
MMP2 , a member of the matrix metalloproteinase family, for migrative trophoblast cells (MTB) (Cluster 4).


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:15fb2f2319fd740c84a0
claim_id: claim:15fb2f2319fd740c84a0
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal:
We found that the cytoskeleton-associated genes GJA1 and TUBB4A were significantly downregulated during trophoblast differentiation, as shown in Figure 3B .

summary:
In Homo sapiens post-implantation embryos, the cytoskeleton-associated genes GJA1 and TUBB4A are significantly downregulated during trophoblast cell differentiation.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:eeca11c6568af30c3f47
claim_id: claim:eeca11c6568af30c3f47
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: Interestingly, we found the expression of ACTB also decreased during implantation
summary:
In Homo sapiens post-implantation embryos, ACTB expression decreases in trophoblast cells during implantation.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:9320afdf01ce830a8634
claim_id: claim:9320afdf01ce830a8634
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: The proliferating marker: PCNA and MKI67 were also downregulated during syncytialization
summary:
In Homo sapiens post-implantation embryos, the proliferation markers PCNA and MKI67 are downregulated in primitive syncytiotrophoblast during syncytialization.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:00303ee6cb04a70d6e29
claim_id: claim:00303ee6cb04a70d6e29
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: Among them, CGA , PGF , INSIG2 , LHB , and several PSG and CGB genes were highly expressed in pSTB2
summary:
In Homo sapiens post-implantation embryos, CGA, PGF, INSIG2, and LHB are highly expressed in primitive syncytiotrophoblast 2.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:38570aaa0560b47501a0
claim_id: claim:38570aaa0560b47501a0
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: we noticed that pSTB2 was also enriched for aging-associated genes, such as BCL2 , FOXO3 , and PTEN
summary:
In Homo sapiens post-implantation embryos, primitive syncytiotrophoblast 2 is enriched for aging-associated genes BCL2, FOXO3, and PTEN.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:a61a44cb7365732cf1ca
claim_id: claim:a61a44cb7365732cf1ca
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: It was revealed that the expression levels of LMNB1 were downregulated in pSTB of human embryos
summary:
In Homo sapiens post-implantation embryos, LMNB1 expression is downregulated in primitive syncytiotrophoblast.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:fb2673d37b67a67314ff
claim_id: claim:fb2673d37b67a67314ff
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal: we found that SNAI1 , BATF , KLF10 , and ZBTB7B were highly enriched in pFCC
summary:
In Homo sapiens post-implantation embryos, SNAI1, BATF, KLF10, and ZBTB7B are highly enriched in primitive fusion-competent cells.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:cbb542476021368983bb
claim_id: claim:cbb542476021368983bb
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal:
we identified that genes encoding the cytoskeleton, such as GJA1 , TUBB4A , and ACTB decreased during implantation

summary:
In Homo sapiens post-implantation embryos, cytoskeleton genes GJA1, TUBB4A, and ACTB decrease in trophoblast cells during implantation.


claim_key: hca:0006_10.3389_fcell.2022.835445_847c20f209:claim:90df641d89abae423ad2
claim_id: claim:90df641d89abae423ad2
paper_key: hca:0006_10.3389_fcell.2022.835445_847c20f209
span_literal:
we then checked the expression of cytoplasmic bridging markers, such as KIF4A , CENPE , PLK1 , and ANLN ( Hu et al., 2011 ; Kechad et al., 2012 ) in the scRNA-seq dataset. It was shown that these markers were decreased in pSTB

summary:
In Homo sapiens post-implantation embryos, cytoplasmic bridging markers KIF4A, CENPE, PLK1, and ANLN are decreased in primitive syncytiotrophoblast.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:d509d486f7a3970a6369
claim_id: claim:d509d486f7a3970a6369
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
AST1 and AST6, enriched for GFAP, are linked to injury responses, regeneration, autophagy, and amyloid fibril formation, likely representing reactive astrocytes

summary:
In Homo sapiens, astrocyte subpopulation 1 and astrocyte subpopulation 6 in the hippocampus are enriched for GFAP, likely representing reactive astrocytes.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:e9a99ded2fb24f43f77f
claim_id: claim:e9a99ded2fb24f43f77f
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
AST1 and AST6, enriched for GFAP, are linked to injury responses, regeneration, autophagy, and amyloid fibril formation, likely representing reactive astrocytes

summary:
In Homo sapiens, astrocyte subpopulation 6 in the hippocampus is enriched for GFAP, likely representing reactive astrocytes.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:b9d18a71deb832580aaf
claim_id: claim:b9d18a71deb832580aaf
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
SOX2- and EGFR-enriched AST2 is associated with gliogenesis, representing a putative progenitor cell population

summary:
In Homo sapiens, astrocyte subpopulation 2 in the hippocampus is enriched for SOX2 and EGFR, representing a putative progenitor cell population.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:835a00d4aae68ec5c19f
claim_id: claim:835a00d4aae68ec5c19f
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
OPC1, OPC2, and immatureOL share many progenitor genes (e.g., NG2/CSPG4, PCDH15, SOX6) related to cell growth and synapse organization

summary:
In Homo sapiens, oligodendrocyte precursor cell subpopulation 1, oligodendrocyte precursor cell subpopulation 2, and immature oligodendrocyte share progenitor genes NG2/CSPG4, PCDH15, and SOX6.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:d1641627229170fe7538
claim_id: claim:d1641627229170fe7538
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
OPC1, OPC2, and immatureOL share many progenitor genes (e.g., NG2/CSPG4, PCDH15, SOX6) related to cell growth and synapse organization

summary:
In Homo sapiens, oligodendrocyte precursor cell subpopulation 2 shares progenitor genes CSPG4, PCDH15, and SOX6.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:f038534cc031df6dd8e5
claim_id: claim:f038534cc031df6dd8e5
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
In addition, an immune response regulator, class II major histocompatibility complex (MHC-II)-associated gene, CD74, was highly enriched in OPC1, suggesting the non-progenitor roles of OPCs under physiological conditions

summary:
In Homo sapiens, oligodendrocyte precursor cell subpopulation 1 in the hippocampus is highly enriched for CD74, a class II major histocompatibility complex-associated gene.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:54aa0edfaac169030103
claim_id: claim:54aa0edfaac169030103
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
summary: In Homo sapiens, immature oligodendrocyte in the hippocampus is enriched for BCAS1.
span_literal:
Interestingly, BCAS1-enriched immatureOL shows enrichment of both myelination- and cell differentiation-related genes


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:2fcd25976700a5260c89
claim_id: claim:2fcd25976700a5260c89
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
In addition, the Oligo1 population that is related to oligodendrocyte differentiation ( Figures 4C and 4D ) shares gene signatures (e.g., OPALIN) with the “intermediate oligodendrocytes” in human white matter that are susceptible to MS

summary:
In Homo sapiens, oligodendrocyte subpopulation 1 in the hippocampus shares gene signatures including OPALIN with intermediate oligodendrocytes in white matter.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:a0b33a04035f7ae56066
claim_id: claim:a0b33a04035f7ae56066
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
For example, MG0 preferentially expresses CD83, EGR3, and CCL2, and is related to immune surveillance

summary:
In Homo sapiens, microglia subpopulation 0 in the hippocampus preferentially expresses CD83, EGR3, and CCL2.


claim_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c:claim:f37c1c5313e45ece4c25
claim_id: claim:f37c1c5313e45ece4c25
paper_key: hca:0007_10.1016_j.stem.2022.09.010_b0ba37bc2c
span_literal:
SPP1- and TREM2-enriched MG1 is related to autophagy and neuroinflammatory response, previously reported to be disease-associated and to play a role in de-/re-myelination in a mouse MS model

summary:
In Homo sapiens, microglia subpopulation 1 in the hippocampus is enriched for SPP1 and TREM2 and is related to autophagy and neuroinflammatory response.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:cd21f345758f14f1f5bc
claim_id: claim:cd21f345758f14f1f5bc
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
We found cluster-specific expression of GCG (alpha cells), INS (beta), SST (delta), PPY (PP), PRSS1 (acinar), KRT19 (duct), and COL1A1 (mesenchyme)

summary:
In Homo sapiens pancreas, GCG is a marker of alpha cells, INS of beta cells, SST of delta cells, PPY of pancreatic polypeptide cells, PRSS1 of acinar cells, KRT19 of ductal cells, and COL1A1 of mesenchymal cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:298a4c5c35c22686f7b3
claim_id: claim:298a4c5c35c22686f7b3
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
MAFA expression is restricted to beta cells, while MAFB expression is found in both alpha and beta cells, as previously reported in mice

summary:
In Homo sapiens pancreas, MAFA expression is restricted to beta cells, while MAFB expression is found in both alpha cells and beta cells. In Homo sapiens pancreas, MAFB is expressed in beta cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:da61d817f837a88bf964
claim_id: claim:da61d817f837a88bf964
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
Apart from the classically known alpha cell transcription factors IRX2 , ARX ( Dorrell et al., 2011b ), and PGR ( Doglioni et al., 1990 ), our analysis reveals transcription factors FEV , PTGER3 ( Kimple et al., 2013 ), SMARCA1 ( Rankin and Kushner, 2010 ), HMGB3 , and RFX6 ( Piccand et al., 2014 ) that, to our knowledge, have not been reported to be enriched in human alpha cells and have been previously implicated in beta cell function.

summary:
In Homo sapiens pancreas, the transcription factors IRX2, ARX, PGR, FEV, PTGER3, SMARCA1, HMGB3, and RFX6 are enriched in alpha cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:86ab6ff5dd3a2a8bd643
claim_id: claim:86ab6ff5dd3a2a8bd643
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
Classical beta cell markers like INS , MAFA , and PDX1 ( Kulkarni, 2004 ) top the beta cell list, and we detect PFKFB2 ( Arden et al., 2008 ), a gene thought to regulate insulin secretion, and the transcription factor SIX2 .

summary:
In Homo sapiens pancreas, classical beta cell markers INS, MAFA, and PDX1 are highly expressed in beta cells, along with PFKFB2 and the transcription factor SIX2.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:c659d5d784daf73e98af
claim_id: claim:c659d5d784daf73e98af
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
summary: In Homo sapiens pancreas, SST, HHEX, LEPR, and GHSR are expressed in delta cells.
span_literal:
Apart from the classical SST and HHEX expression in delta cells ( Zhang et al., 2014 ), genes like LEPR and GHSR imply a possible role of leptin and ghrelin on delta cell function.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:499fe72ea31b55d6c388
claim_id: claim:499fe72ea31b55d6c388
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
INS and IAPP were co-expressed in beta cells, LOXL4 was expressed with GCG (alpha cells), and PNLIP was expressed with PRSS1 .

summary:
In Homo sapiens pancreas, INS and IAPP are co-expressed in beta cells, LOXL4 and GCG are expressed in alpha cells, and PNLIP and PRSS1 are co-expressed in acinar cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:1690c8821158f9ae594c
claim_id: claim:1690c8821158f9ae594c
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
summary: In Homo sapiens pancreas, ALDH1A1 is enriched in alpha cells and co-expressed with GCG.
span_literal:
Further inspection of the top differentially expressed genes per cluster yielded new cell-type-specific genes, such as ALDH1A1 , which was enriched in alpha cells and co-expressed with GCG


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:db4c0050df5c06e102fb
claim_id: claim:db4c0050df5c06e102fb
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
We also identified several previously unreported cell-type-specific genes for both alpha cells ( CRYBA2 , TM4SF4 , and ALDH1A1 ) and beta cells ( ID1 , RBP4 , SQSTM1 , MT1X , FTL , and FTH1 )

summary:
In Homo sapiens pancreas, CRYBA2, TM4SF4, and ALDH1A1 are cell-type-specific genes for alpha cells, while ID1, RBP4, SQSTM1, MT1X, FTL, and FTH1 are cell-type-specific genes for beta cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:186ff7d1f550d7bc1902
claim_id: claim:186ff7d1f550d7bc1902
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
We also identified several previously unreported cell-type-specific genes for both alpha cells ( CRYBA2 , TM4SF4 , and ALDH1A1 ) and beta cells ( ID1 , RBP4 , SQSTM1 , MT1X , FTL , and FTH1 )

summary:
In Homo sapiens pancreas, ID1, RBP4, SQSTM1, MT1X, FTL, and FTH1 are cell-type-specific genes for beta cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:b132855a5d0db05f5c4d
claim_id: claim:b132855a5d0db05f5c4d
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
FTL expression was visible in insulin-producing cells and absent from GCG -positive alpha cells in the islets of Langerhans

summary:
In Homo sapiens pancreas, FTL is expressed in insulin-producing beta cells and absent from alpha cells in the islets of Langerhans.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:0feac0457e0c9eef24ef
claim_id: claim:0feac0457e0c9eef24ef
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
Within the islets of Langerhans, we detected ALDH1A1 expression only in glucagon-positive alpha cells, not in other cells in the islets.

summary:
In Homo sapiens pancreas, ALDH1A1 is expressed only in glucagon-positive alpha cells within the islets of Langerhans.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:797089562722fbfa38ef
claim_id: claim:797089562722fbfa38ef
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal: The serotonin transporter SLC6A4 is found predominantly in PP cells
summary:
In Homo sapiens pancreas, the serotonin transporter SLC6A4 is found predominantly in pancreatic polypeptide cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:1f8619ae4d384da2904d
claim_id: claim:1f8619ae4d384da2904d
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
summary: In Homo sapiens pancreas, the ghrelin receptor GHSR is only present in delta cells.
span_literal:
The ghrelin receptor GHSR is involved in several of these processes. This receptor is only present in delta cells


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:cd6d57b092d0e78a87ba
claim_id: claim:cd6d57b092d0e78a87ba
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
In beta cells, the most significant genes dictating this heterogeneity were SRXN1 , SQSTM1 , and three ferritin subunits: FTH1P3 , FTH1 , and FTL

summary:
In Homo sapiens pancreas, SRXN1, SQSTM1, FTH1P3, FTH1, and FTL are the most significant genes dictating heterogeneity within beta cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:7a318f70226760823a5f
claim_id: claim:7a318f70226760823a5f
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal: We found cell-surface markers CD24 and CD44 were restricted to acinar and ductal clusters
summary:
In Homo sapiens pancreas, cell-surface markers CD24 and CD44 are restricted to acinar cells and ductal cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:fd2f7bf3eb1c71294ee8
claim_id: claim:fd2f7bf3eb1c71294ee8
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
finding TM4SF4 , a tetraspanin family member that has been linked to pancreatic development ( Anderson et al., 2011 ) and to be specifically expressed in alpha cells, with sparse expression in PP cells

summary:
In Homo sapiens pancreas, TM4SF4 is specifically expressed in alpha cells, with sparse expression in pancreatic polypeptide cells.


claim_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a:claim:497c6d8d76a433b652c0
claim_id: claim:497c6d8d76a433b652c0
paper_key: hca:0008_10.1016_j.cels.2016.09.002_fd6b21337a
span_literal:
We also show that CD24 and TM4SF4 expression can be used to sort live alpha and beta cells with high purity.

summary:
In Homo sapiens pancreas, CD24 and TM4SF4 expression can be used to sort live alpha cells and beta cells with high purity.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:fe5d9a880881decb817f
claim_id: claim:fe5d9a880881decb817f
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
summary: In Homo sapiens, DLK1 is specifically expressed in beta cells of the pancreas.
span_literal:
Our study and others ( Li et al., 2016 ) show that DLK1 is specifically expressed in human beta cells


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:88564a68b624576c0f19
claim_id: claim:88564a68b624576c0f19
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
span_literal:
We confirmed the known specificities of transcription factors in endocrine cells: MAFA, NKX6-1 (beta), IRX1, IRX2 (alpha), HHEX (delta and duct), MAFB (alpha and beta), ARX (alpha, gamma, and epsilon), PDX1 (all types except alpha), PAX6 (all types but lower in delta and epsilon), and NEUROD1, INSM1, and NKX2-2 (all types)

summary:
In Homo sapiens, MAFA and NKX6-1 are specific to beta cells among endocrine cells of the pancreas. In Homo sapiens, MAFB is expressed in beta cells among endocrine cells of the pancreas.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:4c3ed007fd9ed077a162
claim_id: claim:4c3ed007fd9ed077a162
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
span_literal:
We confirmed the known specificities of transcription factors in endocrine cells: MAFA, NKX6-1 (beta), IRX1, IRX2 (alpha), HHEX (delta and duct), MAFB (alpha and beta), ARX (alpha, gamma, and epsilon), PDX1 (all types except alpha), PAX6 (all types but lower in delta and epsilon), and NEUROD1, INSM1, and NKX2-2 (all types)

summary:
In Homo sapiens, IRX1 and IRX2 are specific to alpha cells among endocrine cells of the pancreas. In Homo sapiens, MAFB is expressed in alpha cells and beta cells among endocrine cells of the pancreas. In Homo sapiens, ARX is expressed in alpha cells, gamma cells, and epsilon cells among endocrine cells of the pancreas. In Homo sapiens, PDX1 is expressed in all endocrine cell types except alpha cells of the pancreas. PDX1 is negative in alpha cells.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:48d78cc476a0870b0860
claim_id: claim:48d78cc476a0870b0860
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
span_literal:
For instance, POU3F1 is a previously unreported factor specific to delta cells, as are SIX3 and OLIG1 to beta cells.

summary:
In Homo sapiens, POU3F1 is a transcription factor specific to delta cells of the pancreas, while SIX3 and OLIG1 are specific to beta cells.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:2168ace772649a4a8c00
claim_id: claim:2168ace772649a4a8c00
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
span_literal: Two have profiles resembling PDX1: ETV1 and MEIS2 are restricted to non-alpha endocrine cells.
summary:
In Homo sapiens, ETV1 and MEIS2 are transcription factors restricted to non-alpha endocrine cells of the pancreas.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:462c403810913acfd79d
claim_id: claim:462c403810913acfd79d
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
summary: In Homo sapiens, POU6F2 is detected in alpha cells, gamma cells, and epsilon cells of the pancreas.
span_literal:
POU6F2 is detected in alpha, gamma, and epsilon cells, and although FEV is not detected in epsilon cells, this may be due to a relative under-sampling of the epsilon transcriptome.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:622aee20164abd2f44ab
claim_id: claim:622aee20164abd2f44ab
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
span_literal:
A similarly novel pattern involves transcription factors restricted to beta and delta cells, including SIX2, ESR1, and RXRG.

summary:
In Homo sapiens, SIX2, ESR1, and RXRG are transcription factors restricted to beta cells and delta cells of the pancreas.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:c928113e1f83bfd43764
claim_id: claim:c928113e1f83bfd43764
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
summary: In Homo sapiens, pancreatic stellate cells are identified by the marker gene PDGFRB.
span_literal:
we identified stellate cells in our dataset by their known marker gene PDGFRB along with specific gene expression of fibroblast growth factor (FGF), WNT, Activin A, transforming growth factor β (TGF-β), and numerous cytokines.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:f1352141c64d0a86a1cc
claim_id: claim:f1352141c64d0a86a1cc
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
span_literal:
These genes include SOX2, ID4, and FOXD3, which are transcription factors associated with Schwann cell dedifferentiation and repression of myelin sheath component expression, as well as GDNF, EDNRB, and NES

summary:
In Homo sapiens, Schwann cells undergoing dedifferentiation express SOX2, ID4, FOXD3, GDNF, EDNRB, and NES.


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:9cf2ca34b172082a2058
claim_id: claim:9cf2ca34b172082a2058
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
summary: In Homo sapiens, UCN3 is expressed in all endocrine cells except delta cells of the pancreas.
span_literal:
expand the list of human cell types that express UCN3 to include all human endocrine cells except delta cells


claim_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa:claim:0a65f6241be1b770170f
claim_id: claim:0a65f6241be1b770170f
paper_key: hca:0010_10.1016_j.cels.2016.08.011_1f66aabffa
summary: In Homo sapiens, IAPP is specifically restricted to beta cells of the pancreas.
span_literal:
IAPP is believed to be specifically restricted to beta cells ( Johnson et al., 1988 ), which our human expression data support


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:b16bc81e84f246fdeb82
claim_id: claim:b16bc81e84f246fdeb82
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
The chondrogenic marker gene SOX9 + and chondrocyte-specific ECM genes ( COL2A1 and ACAN ) were ubiquitously expressed in the three chondrocyte clusters (Fig. 1 c, d ).

summary:
In Homo sapiens intervertebral disc, chondrocytes are marked by positive expression of SOX9, COL2A1, and ACAN.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:c1fad8c9a3a51e6f95f6
claim_id: claim:c1fad8c9a3a51e6f95f6
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
The notochord origin marker gene, TBXT , 31 was dominantly expressed in the notochord cell cluster, along with notochord-derived cytokeratin genes, such as KRT8 32 (Fig. 1 c, d ).

summary:
In Homo sapiens intervertebral disc, notochord cells are marked by positive expression of TBXT and KRT8.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:ed637bcd52fb3f57e3cd
claim_id: claim:ed637bcd52fb3f57e3cd
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
FOXC2 , GJA1 , and HES4 , which are essential for stromal cell differentiation, 33 – 35 that were mainly expressed in the stromal cell cluster.

summary:
In Homo sapiens intervertebral disc, stromal cells are marked by positive expression of FOXC2, GJA1, and HES4.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:24fe0328aa19b383ccdc
claim_id: claim:24fe0328aa19b383ccdc
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Pericyte and EC clusters were identified by feature gene expression ( ACTA2 , TAGLN , and MCAM for pericytes 36 – 38 and PECAM1 , CD34 , CDH5 , ERG , and VWF for EC 39 – 42 ) (Fig. 1 c, d and Supplementary Table 2 ).

summary:
In Homo sapiens intervertebral disc, pericytes are marked by positive expression of ACTA2, TAGLN, and MCAM.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:0f3a07c9cf94ba4de196
claim_id: claim:0f3a07c9cf94ba4de196
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Pericyte and EC clusters were identified by feature gene expression ( ACTA2 , TAGLN , and MCAM for pericytes 36 – 38 and PECAM1 , CD34 , CDH5 , ERG , and VWF for EC 39 – 42 ) (Fig. 1 c, d and Supplementary Table 2 ).

summary:
In Homo sapiens intervertebral disc, endothelial cells are marked by positive expression of PECAM1, CD34, CDH5, ERG, and VWF.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:df7b17a1e7b9707207d0
claim_id: claim:df7b17a1e7b9707207d0
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
We found that PDGFRA (the mesenchymal progenitor marker), 43 PRRX1 (which is restricted to the mesodermal origin and regulator of mesenchymal precursors) 44 and IGF1 (a growth factor that effectively differentiates MSCs into NP-like cells) 45 were specifically expressed in the NPPC clusters (Fig. 1 c, d ).

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cells are marked by positive expression of PDGFRA, PRRX1, and IGF1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:2e07dae3fd9ccd7228d4
claim_id: claim:2e07dae3fd9ccd7228d4
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: We found that C1 preferentially expressed growth factor (GF) genes such as BMP2, TGFB1 , and FGF2 .
summary:
In Homo sapiens intervertebral disc, regulatory chondrocyte subcluster C1 preferentially expresses BMP2, TGFB1, and FGF2.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:73feaf2b689c2ed9e4db
claim_id: claim:73feaf2b689c2ed9e4db
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Subclusters C3 and C4 preferentially expressed the genes of the main ECM components of the IVD, such as ACAN and COL2A1 .

summary:
In Homo sapiens intervertebral disc, homeostatic chondrocyte subcluster C3 preferentially expresses ACAN and COL2A1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:c5d26fef463eb4edf188
claim_id: claim:c5d26fef463eb4edf188
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Subclusters C3 and C4 preferentially expressed the genes of the main ECM components of the IVD, such as ACAN and COL2A1 .

summary:
In Homo sapiens intervertebral disc, homeostatic chondrocyte subcluster C4 preferentially expresses ACAN and COL2A1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:9b55bd4cd5c168a5a82b
claim_id: claim:9b55bd4cd5c168a5a82b
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Subclusters C5 and C6 preferentially expressed PRG4 and CNMD , suggesting that they may play a protective role and stabilize the chondrocyte phenotype.

summary:
In Homo sapiens intervertebral disc, effector chondrocyte subcluster C5 preferentially expresses PRG4 and CNMD.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:b0e9e10a98dcb32f3fa7
claim_id: claim:b0e9e10a98dcb32f3fa7
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Subclusters C5 and C6 preferentially expressed PRG4 and CNMD , suggesting that they may play a protective role and stabilize the chondrocyte phenotype.

summary:
In Homo sapiens intervertebral disc, effector chondrocyte subcluster C6 preferentially expresses PRG4 and CNMD.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:f95d3b458e3afb07ff9a
claim_id: claim:f95d3b458e3afb07ff9a
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
The localization of the discogenic marker PAX1 confirmed the physical presence of the NPPC-1 subcluster.

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 1 is marked by positive expression of the discogenic marker PAX1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:601fa3195e60d1e522f0
claim_id: claim:601fa3195e60d1e522f0
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Subcluster NPPC-2 specifically expressed ANGPT1 , which is critical for the survival of nucleus pulposus cells.

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 2 specifically expresses ANGPT1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:be1f2fabee64a337f19b
claim_id: claim:be1f2fabee64a337f19b
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
PRG4 , the signature gene of NPPC-3, was also highly expressed in articular cartilage progenitor cells.

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 3 is marked by the signature gene PRG4.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:cb9b362f93cb32d860b5
claim_id: claim:cb9b362f93cb32d860b5
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: SOX9 expression indicated the chondrogenic priming of NPPC-4 (Fig. 3b ).
summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 4 expresses SOX9, indicating chondrogenic priming.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:1ff142bd9eb471b1a326
claim_id: claim:1ff142bd9eb471b1a326
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Interestingly, we found that NPPC-3 preferentially expressed PROCR (Fig. 3e ), a widely reported signature gene for progenitor cells in multiple organs, including the hematopoietic and vascular systems, 71 – 74 pancreas, 75 ovaries, 76 etc.

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 3 preferentially expresses PROCR, a widely reported signature gene for progenitor cells.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:1d99d444d31c93c3575e
claim_id: claim:1d99d444d31c93c3575e
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
We then combined the expression of the membranous marker genes PDGFRA and PROCR and the transcription factor PRRX1 as a signature for the identification of NPPC-3 (Fig. 3f and Supplementary Fig. 4e ) and performed immunofluorescence staining to examine their coexpression (Fig. 3 g).

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 3 is identified by the combined expression of PDGFRA, PROCR, and PRRX1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:135e8af321eb3b3648be
claim_id: claim:135e8af321eb3b3648be
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: we also confirmed the existence of progenitor cells in the IVD marked by PDGFRA and PROCR .
summary:
In Homo sapiens intervertebral disc, progenitor cells are marked by positive expression of PDGFRA and PROCR.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:7db273232fc87e59c4b5
claim_id: claim:7db273232fc87e59c4b5
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
three subclusters of fibroblasts (Fib1, Fib2, and Fib3) that expressed high levels of fibroblast signature genes, such as CEMIP , AKR1C1 , MGP , COMP , DNER , and MELTF , 80 , 81

summary:
In Homo sapiens nucleus pulposus, fibroblasts express high levels of fibroblast signature genes CEMIP, AKR1C1, MGP, COMP, DNER, and MELTF.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:9ff9a2c82cd2889327ac
claim_id: claim:9ff9a2c82cd2889327ac
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
two subclusters of neurogenic cells (Neu1 and Neu2) with high expression of the neurogenic markers SOX2 , NGFR , NCMAP , and CLDN19 , 82 – 85

summary:
In Homo sapiens nucleus pulposus, neurogenic cells are marked by high expression of SOX2, NGFR, NCMAP, and CLDN19.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:9b7c079438785030f191
claim_id: claim:9b7c079438785030f191
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
and osteogenic cells that expressed high levels of the osteogenic regulators RUNX2 and DLX5 (Supplementary Fig. 5b ). 86 – 88

summary:
In Homo sapiens nucleus pulposus, osteogenic cells express high levels of the osteogenic regulators RUNX2 and DLX5.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:15f8aba5c0c4049603b1
claim_id: claim:15f8aba5c0c4049603b1
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
we found a minor cluster that expressed high levels of the markers TBXT and KRT8 , which could be a rare but distinct notochord cell cluster.

summary:
In Homo sapiens intervertebral disc, notochord cells express high levels of the markers TBXT and KRT8.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:eaf8aef8e1d6652093c0
claim_id: claim:eaf8aef8e1d6652093c0
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Our scRNA-seq analysis and immunofluorescence staining revealed the existence of a rare cell cluster that differentially expressed the osteogenic genes RUNX2 , DLX5 , and SP7 , 86 – 88 which were defined as osteogenic cells (Supplementary Fig. 5a–c ).

summary:
In Homo sapiens intervertebral disc, osteogenic cells differentially express the osteogenic genes RUNX2, DLX5, and SP7.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:1fd521ac0008c735c8f6
claim_id: claim:1fd521ac0008c735c8f6
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: NPPC-3 preferentially expressed the SMAD2/3
summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 3 preferentially expresses the SMAD2/3 pathway, while nucleus pulposus progenitor cell subcluster 4 is enriched for NOTCH signaling.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:bfdd65b488beccf1f648
claim_id: claim:bfdd65b488beccf1f648
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: Among them, PDGFRA showed higher expression in NPPC-1, NPPC-2, and NPPC-3 than in NPPC-4.
summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subclusters 1, 2, and 3 show higher expression of PDGFRA than nucleus pulposus progenitor cell subcluster 4.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:e4da218abe7f7a0b4283
claim_id: claim:e4da218abe7f7a0b4283
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: Among them, PDGFRA showed higher expression in NPPC-1, NPPC-2, and NPPC-3 than in NPPC-4.
summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 2 shows higher expression of PDGFRA than nucleus pulposus progenitor cell subcluster 4.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:492bae868354e4e1072c
claim_id: claim:492bae868354e4e1072c
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal: Among them, PDGFRA showed higher expression in NPPC-1, NPPC-2, and NPPC-3 than in NPPC-4.
summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cell subcluster 3 shows higher expression of PDGFRA than nucleus pulposus progenitor cell subcluster 4.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:ec7999a13395836fb5f9
claim_id: claim:ec7999a13395836fb5f9
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
We also found that C5 and C6 highly expressed genes reflecting protective characteristics ( KLF2 and CHI3L1 ) (Fig. 2e ) 54 , 55 and existed in the dormant stage of proliferation (Fig. 2f ).

summary:
In Homo sapiens intervertebral disc, effector chondrocyte subclusters C5 and C6 highly express the protective genes KLF2 and CHI3L1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:2dd229bb8633bcb9ad85
claim_id: claim:2dd229bb8633bcb9ad85
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
We also found that C5 and C6 highly expressed genes reflecting protective characteristics ( KLF2 and CHI3L1 ) (Fig. 2e ) 54 , 55 and existed in the dormant stage of proliferation (Fig. 2f ).

summary:
In Homo sapiens intervertebral disc, effector chondrocyte subcluster C6 highly expresses the protective genes KLF2 and CHI3L1.


claim_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96:claim:00ca85751cbf6489d687
claim_id: claim:00ca85751cbf6489d687
paper_key: hca:0011_10.1038_s41413-021-00163-z_07f1a1af96
span_literal:
Surprisingly, we found a cluster of cells that exclusively expressed PDGFRA , a signature of MSCs, 77 , 137 , 138 and was mainly distributed in the NP (Supplementary Fig. 4 ).

summary:
In Homo sapiens intervertebral disc, nucleus pulposus progenitor cells exclusively express PDGFRA, a signature of mesenchymal stem cells, and are mainly distributed in the nucleus pulposus.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:fbcfaaf3bf29546ef82e
claim_id: claim:fbcfaaf3bf29546ef82e
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
span_literal: SCGB3A2 + SFTPB + terminal airway-enriched secretory cells
summary:
In Homo sapiens, terminal airway-enriched secretory cells (TASCs) are marked by expression of SCGB3A2 and SFTPB.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:6a19b9d46197a4fd63ee
claim_id: claim:6a19b9d46197a4fd63ee
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary: In Homo sapiens, intermediate cells are marked by high expression of SERPINB3.
span_literal:
The ASE family included BCs, intermediate cells (ICs; SERPINB3 high ), and previously described differentiated cell populations, such as secretory (S, including common [S1, SCGB1A1 high ] and mucus-producing [S-Muc]), ciliated (C, including common [C1] and serum amyloid A [ SAA ] gene-expressing [C-s] [ 19 ]), S-C-intermediate cells (deuterosomal pre-C cells [p-C] and hybrid cells sharing C- and S-markers [ 20 – 22 ]), ionocytes ( 23 , 24 ), and neuroendocrine cells.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:04b89d2975cc86ae85b8
claim_id: claim:04b89d2975cc86ae85b8
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary: In Homo sapiens, chondrocytes are marked by expression of SNORC.
span_literal:
Stromal cells included chondrocytes ( SNORC ), fibroblasts (including common [Fb1], CCL19 + [Fb2 including SFRP2 + Fbs ( 25 )], matrix (Fb3, ELN, COL1A1 , including ACTA2 + myoFbs), and Fb4 containing GPC3 + FGFR4 + alveolar Fbs ( 25 ), SM cells (SM1 and SM2 expressing vascular SM markers ADIRF , NOTCH3 , PDGFRB , and SM3 expressing airway SM markers DES and CNN1 ( 25 )].


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:f679dda52a5dc29d9581
claim_id: claim:f679dda52a5dc29d9581
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
span_literal:
Stromal cells included chondrocytes ( SNORC ), fibroblasts (including common [Fb1], CCL19 + [Fb2 including SFRP2 + Fbs ( 25 )], matrix (Fb3, ELN, COL1A1 , including ACTA2 + myoFbs), and Fb4 containing GPC3 + FGFR4 + alveolar Fbs ( 25 ), SM cells (SM1 and SM2 expressing vascular SM markers ADIRF , NOTCH3 , PDGFRB , and SM3 expressing airway SM markers DES and CNN1 ( 25 )].

summary:
In Homo sapiens, CCL19-positive fibroblasts (Fb2) are marked by expression of CCL19. In Homo sapiens, Fb2 fibroblasts include SFRP2-positive fibroblasts.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:ec30ab99c5dd87c59084
claim_id: claim:ec30ab99c5dd87c59084
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary:
In Homo sapiens, vascular smooth muscle cells (SM1 and SM2) express vascular smooth muscle markers ADIRF, NOTCH3, and PDGFRB.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:2a7641bdad7805d394bc
claim_id: claim:2a7641bdad7805d394bc
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary:
In Homo sapiens, airway smooth muscle cells (SM3) express airway smooth muscle markers DES and CNN1.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:ebceffda4efa47b7c05e
claim_id: claim:ebceffda4efa47b7c05e
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary: In Homo sapiens, glial/Schwann cells are marked by expression of CDH19, MPZ, and NRXN1.
span_literal:
Cells expressing markers of neuronal and glial/Schwann cells (Gli; CDH19 , MPZ , NRXN1 ) were also identified.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:e55265f5bfdf951cce54
claim_id: claim:e55265f5bfdf951cce54
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary: In Homo sapiens, venous endothelial cells express fenestrated endothelial markers ACKR1 and PLVAP.
span_literal:
En cells included arterial (En-a), common capillary (En-c1), cells expressing markers of alveolar capillary aerocytes ( 25 ) (En-ca), venous (En-v, including cells expressing fenestrated En-c markers ACKR1 and PLVAP [ 25 ]), En-sm coexpressing En and SM markers, and lymphatic (En-l).


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:f68b81253037bcf68f40
claim_id: claim:f68b81253037bcf68f40
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary: In Homo sapiens, inflammatory macrophages (M1) are marked by expression of SPP1 and CCL3.
span_literal:
Myeloid cells included neutrophils, mast cells, monocytes, macrophages (inflammatory [M1; SPP1 , CCL3 ], noninflammatory [M2; MSR1 , CCL18 ], and M1–2 mixed), and dendritic cells (conventional and plasmacytoid).


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:433235de0cc0ae02b94f
claim_id: claim:433235de0cc0ae02b94f
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
summary: In Homo sapiens, central and naive T cells (Tcn) are marked by expression of CCR7 and IL7R.
span_literal:
T cells included cells expressing markers of central and naive T cells (Tcn; CCR7 , IL7R ) ( 22 ), T-ifn expressing IFN response genes, CD8-enriched (including resident memory [Trm; CXCR6 , CCL5 ] ( 26 – 28 ) and remaining [CD8 + -T1]), and T cells expressing NK cell markers (T-NK).


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:dcbb620e245cc95c7ba7
claim_id: claim:dcbb620e245cc95c7ba7
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
span_literal:
Unlike other S cells, TASCs expressed SCGB3A2 , SFTPB , and genes also expressed in AT cells ( RNASE1 , SFTPA2 , HOPX , SFTPA1 ).

summary:
In Homo sapiens, terminal airway-enriched secretory cells express SCGB3A2, SFTPB, RNASE1, SFTPA2, HOPX, and SFTPA1, unlike other secretory cells.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:709a1bd271599c5a60ed
claim_id: claim:709a1bd271599c5a60ed
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
span_literal:
Compared with AT2 cells, TASCs expressed S cell genes SCGB1A1 and SCGB3A1 but showed significantly lower expression of AT2 markers SFTPC , SFTPA1 , and SFTPA2 .

summary:
In Homo sapiens, terminal airway-enriched secretory cells express SCGB1A1 and SCGB3A1 but show significantly lower expression of SFTPC, SFTPA1, and SFTPA2 compared with alveolar type 2 cells.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:60af8617d3f4efce1069
claim_id: claim:60af8617d3f4efce1069
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
span_literal:
Notably, SCGB3A2 and MGP were expressed in TASCs at higher levels than in both S and AT2 cells ( Figures 2C and 2D ; Table E6).

summary:
In Homo sapiens, terminal airway-enriched secretory cells express SCGB3A2 and MGP at higher levels than both secretory cells and alveolar type 2 cells.


claim_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40:claim:bbc0e6623f26ab388347
claim_id: claim:bbc0e6623f26ab388347
paper_key: hca:0012_10.1164_rccm.202207-1384oc_21f7132a40
span_literal: In contrast to AT2 cells, TASCs were typically SFTPC-negative ( Figure 2J ).
summary:
In Homo sapiens, terminal airway-enriched secretory cells are typically SFTPC-negative, in contrast to alveolar type 2 cells.


claim_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225:claim:5e87a087b957a3374481
claim_id: claim:5e87a087b957a3374481
paper_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225
span_literal:
We found evidence for the presence of immature neutrophils and neutrophil progenitors (pro-neutrophils) based on high expression of CD64 (Fc gamma receptor 1) and CD49d (integrin alpha 4), and decreased expression of CD10 (neutral endopeptidase)

summary:
In Homo sapiens, immature neutrophils and neutrophil progenitors (pro-neutrophils) are characterized by high expression of CD64 (Fc gamma receptor 1) and CD49d (integrin alpha 4), and decreased expression of CD10 (neutral endopeptidase).


claim_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225:claim:e3375d90b2dc31aaed91
claim_id: claim:e3375d90b2dc31aaed91
paper_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225
span_literal:
We found evidence for the presence of immature neutrophils and neutrophil progenitors (pro-neutrophils) based on high expression of CD64 (Fc gamma receptor 1) and CD49d (integrin alpha 4), and decreased expression of CD10 (neutral endopeptidase)

summary:
In Homo sapiens, neutrophil progenitors (pro-neutrophils) are characterized by high expression of CD64 (Fc gamma receptor 1) and CD49d (integrin alpha 4), and decreased expression of CD10 (neutral endopeptidase).


claim_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225:claim:d17b7b2cb0dfad671c2f
claim_id: claim:d17b7b2cb0dfad671c2f
paper_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225
span_literal:
We found that S100A8/9/12 hi HMGB2 -expressing cMono correlated with COVID-19 severity and were also increased in sepsis.

summary:
In Homo sapiens, a classical monocyte subset is marked by high expression of S100A8, S100A9, S100A12, and HMGB2.


claim_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225:claim:4d35d7410fa185894477
claim_id: claim:4d35d7410fa185894477
paper_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225
span_literal:
cMono expressing VCAN , which is implicated in cytokine release, were specifically increased in COVID-19 and reduced in influenza, while complement component C1Q -expressing ncMono were increased in influenza and sepsis, but not in COVID-19.

summary:
In Homo sapiens, a classical monocyte subset expresses VCAN, while a non-classical monocyte subset expresses C1Q.


claim_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225:claim:68a5c2ae2733c31dabc6
claim_id: claim:68a5c2ae2733c31dabc6
paper_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225
span_literal:
cMono expressing VCAN , which is implicated in cytokine release, were specifically increased in COVID-19 and reduced in influenza, while complement component C1Q -expressing ncMono were increased in influenza and sepsis, but not in COVID-19.

summary:
In Homo sapiens, a non-classical monocyte subset is marked by expression of complement component C1Q.


claim_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225:claim:4f82a7a247e37deca345
claim_id: claim:4f82a7a247e37deca345
paper_key: hca:0013_10.1016_j.cell.2022.01.012_62a71f9225
span_literal:
Analysis of gene expression in hospitalized COVID-19 patients showed the most significant clinical correlate involved activated NK cells (CD56 high CD16 low XCL1/2 expressing)

summary:
In Homo sapiens, activated natural killer cells are characterized by high CD56, low CD16, and expression of XCL1 and XCL2.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:1ac321a01ca923d299e0
claim_id: claim:1ac321a01ca923d299e0
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
summary: In Homo sapiens, endothelial cells are defined by positive staining of CDH5.
span_literal:
the cellular populations in the vessels are often defined by positive staining of one or two marker genes (i.e. CDH5 for endothelial cells)


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:7000cc1c0545f6f5fa72
claim_id: claim:7000cc1c0545f6f5fa72
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
summary: In Homo sapiens, endothelial cells are marked by CDH5 and VWF with high fidelity.
span_literal:
This preliminary analysis demonstrated high fidelity of canonical endothelial (CDH5, VWF) and immune cell markers (CD3D, CD68), but poor specificity of several frequently utilized “pericyte” (RGS5, CSPG4, PDGFRB) and “fibroblast” markers (COL1A1, FSP1/S100A4, PDGFRA), with robust expression seen in multiple populations (Figure S1A).


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:00b7a64bbedf08ea559e
claim_id: claim:00b7a64bbedf08ea559e
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
SMCs (as evidenced by RNAscope and spatial transcriptome), exist in a distinct gradient of hierarchical cell-states, MYOCD+>CNN1+>MYH11+>ACTA2+>TAGLN+ population.

summary:
In Homo sapiens, smooth muscle cells exist in a gradient of hierarchical cell states marked by MYOCD, CNN1, MYH11, ACTA2, and TAGLN.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:f5d44916cac414648bef
claim_id: claim:f5d44916cac414648bef
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
It is important to note that a subset of commonly applied smooth muscle markers (smooth muscle actin/ACTA2, and transgelin/TAGLN/SM22α) are expressed quite broadly, including very robust expression of ACTA2 and TAGLN in fibroblast and a subset of endothelial cells.

summary:
In Homo sapiens, ACTA2 and TAGLN, commonly applied as smooth muscle cell markers, are also robustly expressed in fibroblasts and a subset of endothelial cells.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:9ada862810f6042b7aa3
claim_id: claim:9ada862810f6042b7aa3
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal: pericytes were classically identified using expression of markers RGS5 and NG2/CSPG4
summary:
In Homo sapiens, microvascular mural cells / pericytes were classically identified using expression of RGS5 and CSPG4.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:bf70258fd920bde714d7
claim_id: claim:bf70258fd920bde714d7
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
Markers more specific to the smaller population of SMC (microvascular population) include COX4I2, IGFBP4 and OR51E1.

summary:
In Homo sapiens, the microvascular smooth muscle cell population is more specifically marked by COX4I2, IGFBP4, and OR51E1.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:d3dcb700d7f3342bb7e4
claim_id: claim:d3dcb700d7f3342bb7e4
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
these two populations of SMCs from the same segment have distinct patterns of adrenergic receptor expression with alpha adrenergic receptor 2A (ADRA2A) ([Figure 2F](612293v3_fig2.tif)) found only in the microvascular population, whereas ADRA2C is found more in the medial SMC (Figure S2D).

summary:
In Homo sapiens, alpha adrenergic receptor 2A (ADRA2A) is found only in the microvascular smooth muscle cell population, whereas ADRA2C is found more in medial smooth muscle cells.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:11b6c1fb66b76ae90104
claim_id: claim:11b6c1fb66b76ae90104
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
these two populations of SMCs from the same segment have distinct patterns of adrenergic receptor expression with alpha adrenergic receptor 2A (ADRA2A) ([Figure 2F](612293v3_fig2.tif)) found only in the microvascular population, whereas ADRA2C is found more in the medial SMC (Figure S2D).

summary:
In Homo sapiens, ADRA2C is found more in medial smooth muscle cells compared to microvascular smooth muscle cells.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:945cff88c02e54390522
claim_id: claim:945cff88c02e54390522
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal: one of the most specifically expressed genes in these SMC subclusters included TNFRSF11B and FN1.
summary:
In Homo sapiens, TNFRSF11B and FN1 are among the most specifically expressed genes in smooth muscle cell subclusters.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:b988d672dff492423c84
claim_id: claim:b988d672dff492423c84
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
Using the scRNAseq data, we additionally identified PI16, SFRP2, and MFAP5as the most specific marker genes for this adventitial fibroblast population ([Figures 3C](612293v3_fig3.tif) and [3D](612293v3_fig3.tif); Table S3).

summary:
In Homo sapiens, PI16, SFRP2, and MFAP5 are identified as the most specific marker genes for the adventitial fibroblast population.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:bbdd49d55293d57d81cd
claim_id: claim:bbdd49d55293d57d81cd
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal: adventitial fibroblast genes, including FBN1, TGFBR2, LOX, FBLN1, and MFAP5
summary:
In Homo sapiens, FBN1, TGFBR2, LOX, FBLN1, and MFAP5 are highly expressed specifically in the adventitial fibroblast population.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:0f858c9a2732fa5d0ffd
claim_id: claim:0f858c9a2732fa5d0ffd
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal: venous and capillary endothelium, (for example, ACKR1
summary:
In Homo sapiens, ACKR1 is a marker associated with venous and capillary endothelial cells, whereas HEY1 is associated with arterial endothelial cells.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:edd0b04e2e43a40a2918
claim_id: claim:edd0b04e2e43a40a2918
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
venous and capillary endothelium, (for example, ACKR1), whereas another subcluster expresses HEY1, a Notch signaling responsive gene previously associated with arterial endothelium

summary:
In Homo sapiens, HEY1 is a marker associated with arterial endothelial cells, distinguished from venous and capillary endothelial cells.


claim_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8:claim:dddb62d030d50f5dee73
claim_id: claim:dddb62d030d50f5dee73
paper_key: hca:0014_10.1101_2024.09.10.612293_d3a16eb9c8
span_literal:
endothelial cell population expresses a large number of distinct markers, many with known biological function and vascular disease relevance, including ITLN1, NRG1

summary:
In Homo sapiens, the endothelial cell 2 population expresses distinct markers including ITLN1 and NRG1.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:6abb596f55e9ed684131
claim_id: claim:6abb596f55e9ed684131
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
Thymic fibroblasts were further divided into two subtypes, neither of which has been previously described: fibroblast type 1 (Fb1) cells (COLEC11, C7, GDF10) and fibroblast type 2 (Fb2) cells (PI16, FN1, FBN1)

summary:
In Homo sapiens thymus, fibroblast type 1 cells are marked by COLEC11, C7, and GDF10, while fibroblast type 2 cells are marked by PI16, FN1, and FBN1.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:42993dc797613df230e7
claim_id: claim:42993dc797613df230e7
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
summary: In Homo sapiens thymus, fibroblast type 1 cells uniquely express COLEC11 and ALDH1A2.
span_literal:
Fb1 cells uniquely express COLEC11, which plays an important role in innate immunity ( 27 ), and ALDH1A2, an enzyme responsible for the production of retinoic acid, which regulates epithelial growth ( 28 ).


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:ef6f7362e4422cd6178a
claim_id: claim:ef6f7362e4422cd6178a
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
summary: In Homo sapiens thymus, cortical thymic epithelial cells are PSMB11-positive.
span_literal:
We were able to identify conserved TEC populations across species, including PSMB11-positive cTECs, KRT74-positive mTEC(I)s, AIRE-expressing mTEC(II)s, and KRT1-expressing mTEC(III)s


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:1dd4edb2a3ed5d57ceed
claim_id: claim:1dd4edb2a3ed5d57ceed
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
an intermediate population (mcTECs), marked by expression of DLK2, was evident in late fetal and pediatric human thymi

summary:
In Homo sapiens thymus, the intermediate medullary-cortical thymic epithelial cell population is marked by expression of DLK2.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:a16d7156120bbbcce06d
claim_id: claim:a16d7156120bbbcce06d
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
MYOD1- and MYOG-expressing myoid cells [TEC(myo)s] and (ii) NEUROD1-, NEUROG1-, and CHGA-expressing TEC(neuro)s, which resemble neuroendocrine cells

summary:
In Homo sapiens thymus, myoid thymic epithelial cells express MYOD1 and MYOG, while neuroendocrine-like thymic epithelial cells express NEUROD1, NEUROG1, and CHGA.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:7e497b92c7539f54f4c4
claim_id: claim:7e497b92c7539f54f4c4
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
MYOD1- and MYOG-expressing myoid cells [TEC(myo)s] and (ii) NEUROD1-, NEUROG1-, and CHGA-expressing TEC(neuro)s, which resemble neuroendocrine cells

summary:
In Homo sapiens thymus, neuroendocrine-like thymic epithelial cells express NEUROD1, NEUROG1, and CHGA.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:32725468d2d4f5dd6462
claim_id: claim:32725468d2d4f5dd6462
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
summary: In Homo sapiens thymus, dendritic cell type 1 is XCR1-positive and CLEC9A-positive.
span_literal:
We identified three previously well-characterized thymic DC subtypes: DC1 (XCR1 + CLEC9A + ), DC2 (SIRPA + CLEC10A + ), and pDC (IL3RA + CLEC4C + )


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:6c215f80e947eae03650
claim_id: claim:6c215f80e947eae03650
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
summary: In Homo sapiens thymus, activated dendritic cells are characterized by LAMP3 and CCR7 expression.
span_literal:
We also identified a population that was previously incompletely described, which we call “activated DCs” (aDCs), characterized by LAMP3 and CCR7 expression


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:1b468fe8f792cc825cad
claim_id: claim:1b468fe8f792cc825cad
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
Relative to canonical T regs , T reg(diff ) cells displayed lower expression of FOXP3 and CTLA4 and higher expression of IKZF4, GNG8 , and PTGIR

summary:
In Homo sapiens thymus, differentiating regulatory T cells display lower expression of FOXP3 and CTLA4 and higher expression of IKZF4, GNG8, and PTGIR relative to canonical regulatory T cells.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:9d40b65d4bbce3eb3f0a
claim_id: claim:9d40b65d4bbce3eb3f0a
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
There were three distinct populations of CD8αα + Tcells: GNG4 + CD8αα + T(I) cells, ZNF683 + CD8αα + T(II) cells, and a CD8αα + NKT-like population marked by EOMES

summary:
In Homo sapiens thymus, CD8αα+ T(I) cells are marked by GNG4, CD8αα+ T(II) cells are marked by ZNF683, and CD8αα+ natural killer T-like cells are marked by EOMES.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:1f107f5d1560e55eaf93
claim_id: claim:1f107f5d1560e55eaf93
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
summary: In Homo sapiens thymus, EOMES-positive natural killer T-like cells express NKG7, IFNG, and TBX21.
span_literal:
EOMES + NKT-like cells have a shared gene expression profile with NK cells ( NKG7, IFNG, TBX21 ) and are enriched in γδ T cells


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:33e0b7364bc7af1752b5
claim_id: claim:33e0b7364bc7af1752b5
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
we found another fetal-specific cell cluster that we named “T H 17-like cells” based on CD4, CD40LG, RORC , and CCR6 expression

summary:
In Homo sapiens thymus, T helper 17-like cells are defined by CD4, CD40LG, RORC, and CCR6 expression.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:5874142b52cf3ca49818
claim_id: claim:5874142b52cf3ca49818
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
T H 17-like cells and NKT-like cells expressed KLRB1 and ZBTB16 , which are hallmarks of innate lymphocytes

summary:
In Homo sapiens thymus, T helper 17-like cells express KLRB1 and ZBTB16, which are hallmarks of innate lymphocytes.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:06e9521683ddbd7cb025
claim_id: claim:06e9521683ddbd7cb025
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
T H 17-like cells and NKT-like cells expressed KLRB1 and ZBTB16 , which are hallmarks of innate lymphocytes

summary:
In Homo sapiens thymus, natural killer T-like cells express KLRB1 and ZBTB16, which are hallmarks of innate lymphocytes.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:a890fc614f69adb7c211
claim_id: claim:a890fc614f69adb7c211
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
we focused on our newly identified GNG4 + CD8αα + T(I) cells, as they have a unique gene expression profile ( GNG4, CREB3L3 , and CD72 ).

summary:
In Homo sapiens thymus, GNG4-positive CD8αα+ T(I) cells have a unique gene expression profile including GNG4, CREB3L3, and CD72.


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:ef435bc5ebdab67ada19
claim_id: claim:ef435bc5ebdab67ada19
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
summary: In Homo sapiens thymus, CD8αα+ T(II) cells express known markers ZNF683 and MME.
span_literal:
This is in contrast to CD8αα + T(II) cells, which express known markers of CD8αα + T cells such as ZNF683 and MME


claim_key: hca:0015_10.1126_science.aay3224_2393e60089:claim:cac41b154140da1a60f6
claim_id: claim:cac41b154140da1a60f6
paper_key: hca:0015_10.1126_science.aay3224_2393e60089
span_literal:
Moreover, the expression level of KLF2 , a regulator of thymic emigration, was extremely low in CD8αα + T(I) cells, which suggests that they may be thymic-resident

summary:
In Homo sapiens thymus, CD8αα+ T(I) cells have extremely low expression of KLF2, suggesting they may be thymic-resident.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:da082a1c54da5dae4c72
claim_id: claim:da082a1c54da5dae4c72
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Supervised analysis using neuroendocrine ( CHGA , ASCL1 , INSM1 , HOXB5 ) and tuft ( DCLK1 , ASCL2 ) 3 cell marker genes identified a small number of cells with neuroendocrine-like features present only in lower airways

summary:
In Homo sapiens, neuroendocrine cells are marked by CHGA, ASCL1, INSM1, and HOXB5 in the lower airways of the lung.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:16afe6425978af2949fb
claim_id: claim:16afe6425978af2949fb
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
The two basal cell states corresponded to differentiation stages, with the less-mature basal 1 cell state expressing higher levels of TP63 and NPPC compared with more-mature basal 2 cells

summary:
In Homo sapiens, basal 1 cells express higher levels of TP63 and NPPC compared with basal 2 cells in the airway.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:54142cd72deee0265339
claim_id: claim:54142cd72deee0265339
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Goblet 1 and 2 cells were both characterized by high expression of CEACAM5 , S100A4 and MUC5AC , and lack of MUC5B

summary:
In Homo sapiens, goblet 1 cells are characterized by high expression of CEACAM5, S100A4, and MUC5AC, and lack of MUC5B.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:b4a6b3ca561437622af5
claim_id: claim:b4a6b3ca561437622af5
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Goblet 1 and 2 cells were both characterized by high expression of CEACAM5 , S100A4 and MUC5AC , and lack of MUC5B

summary:
In Homo sapiens, goblet 2 cells are characterized by high expression of CEACAM5, S100A4, and MUC5AC, and lack of MUC5B.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:36e30d88b61c7a2f9afa
claim_id: claim:36e30d88b61c7a2f9afa
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Genes involved in recruitment of neutrophils, monocytes, dendritic cells, and T cells 5 , such as IDO1 , NOS2 , IL19 , CSF3 (granulocyte-colony stimulating factor), and CXCL10 are expressed at high levels in goblet 2 cells

summary:
In Homo sapiens, goblet 2 cells express high levels of IDO1, NOS2, IL19, CSF3 (granulocyte-colony stimulating factor), and CXCL10.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:0c66449aad797fb51897
claim_id: claim:0c66449aad797fb51897
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Nasal epithelial ciliated 2 cells express proinflammatory genes, such as CCL20 , and higher levels of metabolic ( ATP12A and COX7A1 ) and vesicle transport ( AP2B1 and SYT5 6 ) genes compared with the ciliated 1 cells

summary:
In Homo sapiens, ciliated 2 cells express CCL20, ATP12A, COX7A1, AP2B1, and SYT5 at higher levels compared with ciliated 1 cells in the nasal epithelium.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:4004576cbebb5e641116
claim_id: claim:4004576cbebb5e641116
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, ciliated 1 cells from the lower airways specifically express PROS1 and FXYD1.
span_literal:
the ciliated 1 cells from lower airways specifically expressed genes involved in cytoprotection ( PROS1 7 ) and fluid reabsorption ( FXYD1 8 )


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:47cda448825446965af2
claim_id: claim:47cda448825446965af2
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, ionocytes are particularly high expressors of the CFTR gene.
span_literal:
Cell type-specific expression patterns of genes associated with Mendelian disorders (based on the Online Mendelian Inheritance in Man (OMIM) database) confirmed ionocytes as particularly high expressors of the CFTR gene, mutated in cystic fibrosis


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:e895bd6f0e7f259e935e
claim_id: claim:e895bd6f0e7f259e935e
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, ionocytes express SCNN1B.
span_literal:
These cells also express SCNN1B , mutations of which can cause bronchiectasis, another feature of cystic fibrosis, suggesting a pathological role for ionocytes in both bronchiectasis and cystic fibrosis.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:d443a2e3d136d5b17138
claim_id: claim:d443a2e3d136d5b17138
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, type 2 alveolar epithelial cells are enriched for expression of SERPINA1.
span_literal:
expression of SERPINA1 (Fig. 1i ) was found to be enriched in type 2 alveolar epithelial cells, underscoring their role in alpha-1-antitrypsin deficiency


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:5c88c530fd8bbff9ab10
claim_id: claim:5c88c530fd8bbff9ab10
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, macrophages share high expression of MARCO, CCL18, APOC1, and APOE in the lung.
span_literal:
they all shared high expression of MARCO , CCL18 , and genes involved in apolipoprotein metabolism ( APOC1 and APOE )


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:48f442fdd4d2d830ad13
claim_id: claim:48f442fdd4d2d830ad13
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, lung neutrophils express high levels of S100A8, S100A12, and LILRA5.
span_literal:
Lung neutrophils express high levels of the granulocyte markers S100A8 , S100A12 10 , and LILRA5 , a receptor poorly characterized in the lungs that has been shown to have a proinflammatory function in synovial fluid macrophages


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:7a5420eae2539e03b9e1
claim_id: claim:7a5420eae2539e03b9e1
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, cycling basal cells are characterized by expression of MKI67 and TOP2A.
span_literal:
Cycling basal cells are characterized by expression of canonical marker genes of proliferating cells ( MKI67 and TOP2A )


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:7e5ae16e7d1c46b12aa5
claim_id: claim:7e5ae16e7d1c46b12aa5
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal: this is the only cluster of airway epithelial cells expressing the squamous cell marker KRT13
summary:
In Homo sapiens, cycling basal cells are the only airway epithelial cell cluster expressing the squamous cell marker KRT13.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:afa4da392fc177bbeb17
claim_id: claim:afa4da392fc177bbeb17
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, mucous ciliated cells co-express MUC5AC, CEACAM5, FOXJ1, and PIFO.
span_literal:
we identified a strong increase in mucous ciliated cells, a novel cell state highly similar to ciliated cells, but co-expressing a number of mucous genes also observed in goblet cells, including MUC5AC and CEACAM5 and the ciliated genes FOXJ1 and PIFO


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:552a941ef010ca562957
claim_id: claim:552a941ef010ca562957
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Mast cells in asthmatic airways lack chymase 1 expression ( CMA1 ) and express high levels of tryptase genes ( TPSB2 , TPSAB1 ) and prostaglandin synthetase genes PTGS2 and HPGDS

summary:
In Homo sapiens, mast cells in asthmatic airways lack CMA1 expression and express high levels of TPSB2, TPSAB1, PTGS2, and HPGDS.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:4a72c41c4ebb5fb0cf0a
claim_id: claim:4a72c41c4ebb5fb0cf0a
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
TRM cells in airway wall also expressed high levels of CXCR6 and ITGA1 , chemokines ( CCL4 , CCL4L2, CCL5 ) and effector molecules ( PRF1 , GZMB , GZMA , GZMH )

summary:
In Homo sapiens, tissue-resident memory T cells in the airway wall express high levels of CXCR6, ITGA1, CCL4, CCL4L2, CCL5, PRF1, GZMB, GZMA, and GZMH.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:96196aabb447c4dd3c66
claim_id: claim:96196aabb447c4dd3c66
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, tissue migratory CD4+ T cells express S1PR1, CCR7, SELL, LEF1, SATB1, and KLF3.
span_literal:
TMC cells expressed the tissue egression markers S1PR1 , CCR7 , and SELL (CD62L) (Fig. 5f ) as well as several transcription factors highly expressed in circulating cells such as LEF1 , SATB1 , and KLF3


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:6a5c45ac89f1d13002bc
claim_id: claim:6a5c45ac89f1d13002bc
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
In addition to the signature cytokines IL4 , IL5 , and IL13 and the transcription factor GATA3 (Extended Data Fig. 10 ), airway wall T H 2 cells express HGPDS , identifying them as pathogenic effector T H 2 (peT H 2) cells, previously associated with eosinophilic inflammation of the gastrointestinal tract and skin

summary:
In Homo sapiens, pathogenic effector type 2 helper T cells in the airway wall express IL4, IL5, IL13, GATA3, and HPGDS.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:077e4ca69df848208c68
claim_id: claim:077e4ca69df848208c68
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
span_literal:
Airway T H 2 cells also express the transcription factor PPARG and the cytokine receptors IL17RB and IL9R

summary:
In Homo sapiens, airway type 2 helper T cells express the transcription factor PPARG and the cytokine receptors IL17RB and IL9R.


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:e708a2c46296117b1209
claim_id: claim:e708a2c46296117b1209
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, activated basal cells express the proinflammatory gene POSTN.
span_literal:
Activated basal cells closely resemble basal 1 cells, but also express proinflammatory genes such as POSTN


claim_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70:claim:bc98b43e4bd69d16710c
claim_id: claim:bc98b43e4bd69d16710c
paper_key: hca:0016_10.1038_s41591-019-0468-5_ffb52d8b70
summary: In Homo sapiens, dendritic cells express FCER1A (immunoglobulin E receptor) and CCL17 in the lung.
span_literal:
and of FCER1A (IgE receptor) and CCL17 , which have a key role in inflammatory conditions such as asthma


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:53b54e3f8f76a98ce29a
claim_id: claim:53b54e3f8f76a98ce29a
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
Representative gene expression maps of lineage defining genes (PLEK, Meg; HBB, E; MPO, G; SPIB, DC; CD79A, and DNTT, Ly1/2).

summary:
In Homo sapiens, megakaryocytes are marked by PLEK expression in hematopoietic progenitors from bone marrow.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:63ce18da17846911c7ff
claim_id: claim:63ce18da17846911c7ff
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
Representative gene expression maps of lineage defining genes (PLEK, Meg; HBB, E; MPO, G; SPIB, DC; CD79A, and DNTT, Ly1/2).

summary:
In Homo sapiens, erythroid cells are marked by HBB expression in hematopoietic progenitors from bone marrow.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:9ad5d558900d804ccd6f
claim_id: claim:9ad5d558900d804ccd6f
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
Representative gene expression maps of lineage defining genes (PLEK, Meg; HBB, E; MPO, G; SPIB, DC; CD79A, and DNTT, Ly1/2).

summary:
In Homo sapiens, granulocytes are marked by MPO expression in hematopoietic progenitors from bone marrow.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:67b608da5645a74f7a81
claim_id: claim:67b608da5645a74f7a81
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
summary:
In Homo sapiens, dendritic cells are marked by SPIB expression in hematopoietic progenitors from bone marrow.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:ef390f0a78ae2b8f7c53
claim_id: claim:ef390f0a78ae2b8f7c53
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
summary:
In Homo sapiens, lymphoid cells are marked by CD79A and DNTT expression in hematopoietic progenitors from bone marrow.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:5421e8711a3ae3d7d056
claim_id: claim:5421e8711a3ae3d7d056
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
Finally, we identify the sialomucin CD164, as a reliable marker for the earliest branches of HSPCs specification and we showed how its use can foster the design of alternative transplantation cell products.

summary:
In Homo sapiens, CD164 is identified as a reliable marker for the earliest branches of hematopoietic stem and progenitor cell specification.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:4568c0bbbfb1b6f48967
claim_id: claim:4568c0bbbfb1b6f48967
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal: Human HSPCs are commonly identified by expression of the antigen CD34 18 .
summary:
In Homo sapiens, hematopoietic stem and progenitor cells are commonly identified by expression of CD34.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:f38cc0935bbca44f9045
claim_id: claim:f38cc0935bbca44f9045
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
Interrogating scRNA-Seq data for enrichment of transcripts encoding for surface antigens in early progenitors (Fig. 1g ), CD164 emerged as the gene whose expression displayed the most-pronounced difference in early vs late progenitors.

summary:
In Homo sapiens, CD164 emerged as the gene with the most pronounced expression difference in early progenitors versus late progenitors.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:ee66c29c746c44a31402
claim_id: claim:ee66c29c746c44a31402
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
The CD164 RNA is selectively expressed at high level not only in CD38− multipotent progenitors (as previous studies suggested) but also in CD90+ precursors (which in humans comprise both HSC and early CMP), in the most primitive fraction of MEP and to a lesser extent, in MLP (Fig. 1g ).

summary:
In Homo sapiens, CD164 RNA is selectively expressed at high level in CD38-negative multipotent progenitors, CD90-positive precursors, the most primitive fraction of megakaryocyte-erythroid progenitors, and to a lesser extent in multi-lymphoid progenitors.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:93c81e85b5ba83e303fb
claim_id: claim:93c81e85b5ba83e303fb
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
The CD164 RNA is selectively expressed at high level not only in CD38− multipotent progenitors (as previous studies suggested) but also in CD90+ precursors (which in humans comprise both HSC and early CMP), in the most primitive fraction of MEP and to a lesser extent, in MLP (Fig. 1g ).

summary:
In Homo sapiens, CD164 RNA is selectively expressed at high level in CD90-positive precursors, which comprise both hematopoietic stem cells and early common myeloid progenitors.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:4a11c605fc0ed40f8e3d
claim_id: claim:4a11c605fc0ed40f8e3d
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
The CD164 RNA is selectively expressed at high level not only in CD38− multipotent progenitors (as previous studies suggested) but also in CD90+ precursors (which in humans comprise both HSC and early CMP), in the most primitive fraction of MEP and to a lesser extent, in MLP (Fig. 1g ).

summary:
In Homo sapiens, CD164 RNA is selectively expressed at high level in the most primitive fraction of megakaryocyte-erythroid progenitors.


claim_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8:claim:acd0c4eb3d5f423a7248
claim_id: claim:acd0c4eb3d5f423a7248
paper_key: hca:0017_10.1038_s41467-019-10291-0_971d922fd8
span_literal:
Notably, we see the same progression from TRIB2 -expressing to CA2 -expressing erythroid progenitors (Fig. 4c ), suggesting the existence of the same two precursors subclasses in humans.

summary:
In Homo sapiens, early erythroid progenitors express TRIB2 and committed erythroid progenitors express CA2, suggesting the existence of two erythroid precursor subclasses.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:ed82c75fe533fb2a11ee
claim_id: claim:ed82c75fe533fb2a11ee
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal: MECs and stromal cells were distinguished by EPCAM expression
summary:
In Homo sapiens breast tissue, mammary epithelial cells are distinguished from stromal cells by EPCAM expression.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:1dcd2d494c94a19f3b36
claim_id: claim:1dcd2d494c94a19f3b36
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
BA cells were clearly distinct from stromal cells based on co-expression of BA lineage markers (K14, K17, CD10)

summary:
In Homo sapiens breast tissue, basal/myoepithelial cells are distinguished from stromal cells by co-expression of K14, K17, and CD10.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:e76b23355f44a18bbee5
claim_id: claim:e76b23355f44a18bbee5
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
summary: In Homo sapiens breast tissue, alveolar cells are marked by CD133 and ANXA8 expression.
span_literal:
Luminal cells were further subdivided into the AV and HS types based on expression of key markers CD133 and ANXA8 (AV) or GATA3 and MUC1 (HS)


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:29b4e3ae25890519f387
claim_id: claim:29b4e3ae25890519f387
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
summary: In Homo sapiens breast tissue, fibroblasts are identified by CD140B and EGFR expression.
span_literal:
Stromal cells were identified by canonical markers for fibroblasts (CD140B and EGFR), vascular/lymphatic cells (CD31 for endothelial cells and SMA for pericytes), and immune cells (CD45)


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:0007e54cb7af213fae94
claim_id: claim:0007e54cb7af213fae94
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
The fibroblast subtypes (F1–3) were distinguished by high expression of 1) hormone receptors (HRs; ESR1 , AR , PRLR , LEPR ) and cathepsin proteases ( CTSB/D/F ), 2) tubulins ( TUBB2A/B , TUBB6 ), and 3) fibulins ( FBLN2/5 ) and ductal branching regulator SPRY1

summary:
In Homo sapiens breast tissue, fibroblast subtype 1 is distinguished by high expression of ESR1, AR, PRLR, LEPR, CTSB, CTSD, and CTSF.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:a848d551f628a34917ea
claim_id: claim:a848d551f628a34917ea
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
Vascular/lymphatic cells included lymphatic endothelial cells ( LYVE1 , PDPN , PROX1 ), vascular endothelial cells ( SOX17 , PLVAP , SELE ), and pericytes/smooth muscle cells ( NOTCH3 , ACTA2 , RGS5 )

summary:
In Homo sapiens breast tissue, lymphatic endothelial cells are marked by LYVE1, PDPN, and PROX1 expression.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:a688ebded9c7c5ef9dbb
claim_id: claim:a688ebded9c7c5ef9dbb
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
Vascular/lymphatic cells included lymphatic endothelial cells ( LYVE1 , PDPN , PROX1 ), vascular endothelial cells ( SOX17 , PLVAP , SELE ), and pericytes/smooth muscle cells ( NOTCH3 , ACTA2 , RGS5 )

summary:
In Homo sapiens breast tissue, vascular endothelial cells are marked by SOX17, PLVAP, and SELE expression.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:f72c9a9e862b69589064
claim_id: claim:f72c9a9e862b69589064
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
Vascular/lymphatic cells included lymphatic endothelial cells ( LYVE1 , PDPN , PROX1 ), vascular endothelial cells ( SOX17 , PLVAP , SELE ), and pericytes/smooth muscle cells ( NOTCH3 , ACTA2 , RGS5 )

summary:
In Homo sapiens breast tissue, pericytes/smooth muscle cells are marked by NOTCH3, ACTA2, and RGS5 expression.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:e545b17a51e1e1dd4160
claim_id: claim:e545b17a51e1e1dd4160
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
BL cells, unlike AP cells, co-expressed intermediate levels of several BA ( KRT5/14/17 , CAV1 ) and HS markers ( MUC1 , SERPINA1 , AGR2 /3)

summary:
In Homo sapiens breast tissue, basal-luminal cells co-express KRT5, KRT14, KRT17, CAV1, MUC1, SERPINA1, AGR2, and AGR3, unlike alveolar progenitor cells.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:2a11a5a5b8a38068f034
claim_id: claim:2a11a5a5b8a38068f034
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal: Relative to AP cells, BL cells expressed high levels of the progenitor gene ALDH1A3
summary:
In Homo sapiens breast tissue, basal-luminal cells express high levels of the progenitor gene ALDH1A3 relative to alveolar progenitor cells.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:c5e01db07c27d277c8f3
claim_id: claim:c5e01db07c27d277c8f3
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal: Relative to AP cells, BL cells expressed high levels of the progenitor gene ALDH1A3
summary:
In Homo sapiens breast tissue, alveolar progenitor cells express low levels of ALDH1A3 relative to basal-luminal cells.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:afa5867ca94b898ab451
claim_id: claim:afa5867ca94b898ab451
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
BL cells were clearly distinct from these lineages by low/no expression of many canonical BA ( ACTA2 , MYLK ) and HS genes ( FOXA1 , AREG ) and by expression of AV markers ( CD14, FOLR1 )

summary:
In Homo sapiens breast tissue, basal-luminal cells show low/no expression of ACTA2, MYLK, FOXA1, and AREG, and express the alveolar markers CD14 and FOLR1.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:834bc0d5e33b1329ec93
claim_id: claim:834bc0d5e33b1329ec93
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
The HSα subtype expressed higher levels of estrogen receptor (ER, encoded by ESR1 ), ER target genes ( PDZK1 , SERPINA1 , SPDEF ), and selective ER coactivator CITED1

summary:
In Homo sapiens breast tissue, the hormone-sensing alpha subtype expresses higher levels of ESR1, PDZK1, SERPINA1, SPDEF, and CITED1.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:348342582c06a30336ec
claim_id: claim:348342582c06a30336ec
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
HSβ cells highly expressed canonical progesterone receptor (PR) target genes ( KCNK1 , AKAP13 , WNT4 )

summary:
In Homo sapiens breast tissue, hormone-sensing beta cells highly express the progesterone receptor target genes KCNK1, AKAP13, and WNT4.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:1652683911c69dec965c
claim_id: claim:1652683911c69dec965c
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
the BAα cells also exhibited higher expression of contractility genes ( OXTR, MYL9 , MYH11 , FSCN1 )

summary:
In Homo sapiens breast tissue, basal/myoepithelial alpha cells exhibit higher expression of the contractility genes OXTR, MYL9, MYH11, and FSCN1.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:e410f606fc62b5b04902
claim_id: claim:e410f606fc62b5b04902
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
two BA clusters (BA P3 and BA P2 ) displayed higher contractility gene levels ( ACTG2 , MYL9 , OXTR )

summary:
In Homo sapiens breast tissue, basal/myoepithelial P3 and basal/myoepithelial P2 subtypes display higher levels of the contractility genes ACTG2, MYL9, and OXTR.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:4031bd69c41f5ba0b115
claim_id: claim:4031bd69c41f5ba0b115
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
two BA clusters (BA P3 and BA P2 ) displayed higher contractility gene levels ( ACTG2 , MYL9 , OXTR )

summary:
In Homo sapiens breast tissue, basal/myoepithelial P2 subtype displays higher levels of the contractility genes ACTG2, MYL9, and OXTR.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:dd03e49d88c14d3f1268
claim_id: claim:dd03e49d88c14d3f1268
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal: AP2 cells highly expressed several immune-related genes ( CD47 , TAPBP , CTSS ).
summary:
In Homo sapiens breast tissue, alveolar progenitor 2 cells highly express the immune-related genes CD47, TAPBP, and CTSS.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:cb14b77fbac03846b302
claim_id: claim:cb14b77fbac03846b302
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
Compared to BL2 cells, BL1 cells expressed higher levels of BA genes ( KRT14/5 , VIM ), lower levels of AV genes ( ELF5 , STAT5A , MFGE8 ), and higher levels of BL-unique genes ( RARRES2 , PTN , kallikreins), suggesting BL1 cells exhibit particularly high lineage infidelity.

summary:
In Homo sapiens breast tissue, basal-luminal 1 cells express higher levels of KRT14, KRT5, VIM, RARRES2, and PTN, and lower levels of ELF5, STAT5A, and MFGE8 compared to basal-luminal 2 cells.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:94fe0d30445b002116bc
claim_id: claim:94fe0d30445b002116bc
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
summary: In Homo sapiens breast tissue, SOX9 was identified as a marker gene of basal-luminal 1 cells.
span_literal:
SOX9 , required to induce mixed basal-luminal gene expression in normal and precancerous AV cells ( Christin et al., 2020 ; Guo et al., 2012 ), was also identified as a BL1 marker gene.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:b7b7edb1a20ac2bc0676
claim_id: claim:b7b7edb1a20ac2bc0676
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
AP2 cells highly expressed immunosurveillance-related markers such as HLA-A/B/C (MHC I proteins), CD95 (FAS), and CD47

summary:
In Homo sapiens breast tissue, alveolar progenitor 2 cells highly express the immunosurveillance-related markers HLA-A/B/C, CD95, and CD47.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:22049d37af7509cf393d
claim_id: claim:22049d37af7509cf393d
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
HS1 cells were differentiated from HS2 cells by higher levels of four HRs, chiefly PR-B but also ER, glucocorticoid receptor (GR), and androgen receptor (AR)

summary:
In Homo sapiens breast tissue, hormone-sensing 1 cells are differentiated from hormone-sensing 2 cells by higher levels of PR-B, estrogen receptor, glucocorticoid receptor, and androgen receptor.


claim_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d:claim:aa09fa8b39f8f006f88e
claim_id: claim:aa09fa8b39f8f006f88e
paper_key: hca:0018_10.1016_j.devcel.2022.05.003_fb5132407d
span_literal:
among the top genes specific to AP1 cells ( Figure S3F ; Table S3 ) were several milk-related and casein-cluster genes ( CSN1S1 , FDCSP , PLIN2 ), whose expression further highlights this cell subtype’s parity association.

summary:
In Homo sapiens breast tissue, alveolar progenitor 1 cells specifically express the milk-related and casein-cluster genes CSN1S1, FDCSP, and PLIN2.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:77daa91e6e220a9d6354
claim_id: claim:77daa91e6e220a9d6354
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, microglia are marked by OLR1, SIGLEC10, RP11-480C22.1, CLEC7A, TLR7, and CCL3.
span_literal:
OLR1 , SIGLEC10 and noncoding RNA RP11–480C22.1 are amongst the strongest markers of microglia, together with more established microglial markers such as CLEC7A ( 89 ), TLR7 ( 90 ), and CCL3 ( 91 ).


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:1811c6d34e1ca1c6d56f
claim_id: claim:1811c6d34e1ca1c6d56f
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
cerebral excitatory neurons exhibited a continuous trajectory from PAX6 + neuronal progenitors to NEUROD6 + differentiating neurons ( 92 ) to SLC17A7 + mature neurons ( 93 )

summary:
In Homo sapiens, cerebral excitatory neuronal progenitors are marked by PAX6, differentiating neurons by NEUROD6, and mature neurons by SLC17A7.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:acd5650a616d88a6d890
claim_id: claim:acd5650a616d88a6d890
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, hepatic progenitors are marked by DLK1, KRT8, and KRT18.
span_literal:
In the liver, hepatic progenitors ( DLK1 +, KRT8 +, KRT18 +) ( 94 , 95 ) exhibited a continuous trajectory to functional hepatoblasts ( SLC22A25 +, ACSS2 +, ASS1 +)


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:bc78a6e1f93f3a8ebd8c
claim_id: claim:bc78a6e1f93f3a8ebd8c
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, dendritic cell subtypes are marked by CD1C, S100A9, and CLEC9A.
span_literal:
myeloid cells separate into microglia, macrophages and diverse dendritic cell subtypes ( CD1C +, S100A9 +, CLEC9A + and pDCs) ( 106 )


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:870b596e7887a1e8d3ba
claim_id: claim:870b596e7887a1e8d3ba
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, innate lymphoid cell type 3 cells are marked by RORC, KIT, SORCS1, and JMY.
span_literal:
ILC 3 cells, whose annotation was determined on the basis of their expression of RORC ( 115 ) and KIT ( 116 ), were more specifically marked by SORCS1 and JMY


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:d7527c194a75647e421f
claim_id: claim:d7527c194a75647e421f
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
HSPCs outside of the liver, as well as a subset of liver HSPCs, expressed differentiation markers such as LYZ ( 118 ), ACTG1 ( 119 ) and ANK1 ( 120 ), while most liver HSPCs expressed MECOM and NRIP1 , both required for the maintenance and function of normal quiescent HSPCs ( 121 , 122 )

summary:
In Homo sapiens, hematopoietic stem/progenitor cells outside the liver express differentiation markers LYZ, ACTG1, and ANK1, while most liver hematopoietic stem/progenitor cells express MECOM and NRIP1.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:6040d0da8b8bc4733eee
claim_id: claim:6040d0da8b8bc4733eee
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
we further partitioned the continuum of erythroid states into three stages: early erythroid progenitors (EEPs; marked by SLC16A9 and FAM178B ), committed erythroid progenitors (CEPs; marked by KIF18B and KIF15 ), and cells in the erythroid terminal differentiation state (ETDs; marked by TMCC2 and HBB )

summary:
In Homo sapiens, early erythroid progenitors are marked by SLC16A9 and FAM178B, committed erythroid progenitors by KIF18B and KIF15, and erythroid terminal differentiation state cells by TMCC2 and HBB.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:6a97e3b59b2edd35dcec
claim_id: claim:6a97e3b59b2edd35dcec
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, activated microglia are marked by IL1B and TNFRSF10D.
span_literal:
microglia were divided into three sub-clusters, one of which, marked by IL1B and TNFRSF10D , likely represents activated microglia expressing pro-inflammatory cytokines involved in the normal development of the nervous system ( 129 , 130 ).


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:ccc5da4c35939eafc6ab
claim_id: claim:ccc5da4c35939eafc6ab
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
The other microglial clusters were marked by expression of TMEM119 and CX3CR1 ( 131 ) (more common in cerebrum) or PTPRG and CDC14B ( 132 ) (more common in cerebellum).

summary:
In Homo sapiens, a microglial subcluster more common in the cerebrum is marked by TMEM119 and CX3CR1, while a microglial subcluster more common in the cerebellum is marked by PTPRG and CDC14B. In Homo sapiens, a microglial subcluster more common in the cerebellum is marked by PTPRG and CDC14B.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:0bf037c01daf37b63a1e
claim_id: claim:0bf037c01daf37b63a1e
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
antigen-presenting macrophages, found mostly in GI tract organs (intestine and stomach) and marked by high expression of antigen-presenting ( e.g. HLA-DPB1 , HLA-DQA1 ) and inflammatory activation ( e.g. AHR ( 133 )) genes

summary:
In Homo sapiens, antigen-presenting macrophages are marked by high expression of HLA-DPB1, HLA-DQA1, and AHR.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:cec707aea7adfd68a88c
claim_id: claim:cec707aea7adfd68a88c
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, perivascular macrophages are marked by F13A1, COLEC12, RNASE1, and LYVE1.
span_literal:
perivascular macrophages, found in most organs, with specific expression of markers such as F13A1 ( 134 ) and COLEC12 ( 135 ), as well as novel markers such as RNASE1 and LYVE1 .


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:87f6a9cc8447584eb71b
claim_id: claim:87f6a9cc8447584eb71b
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, phagocytic macrophages are marked by CD5L, TIMD4, and VCAM1.
span_literal:
phagocytic macrophages, enriched in the liver, spleen and adrenal gland ( Fig. 5I ), with specific expression of markers such as CD5L ( 136 ), TIMD4 ( 137 ) and VCAM1 ( 138 ).


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:736e33c5b304b9f20314
claim_id: claim:736e33c5b304b9f20314
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, lymphatic endothelial cells specifically express TBX1.
span_literal:
LECs specifically expressed TBX1, brain VECs specifically expressed FOXQ1 and FOXF2, and liver VECs specifically expressed DAB2 , all consistent with observations in mice ( 139 , 144 , 145 ).


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:433b1707548f2e76c40c
claim_id: claim:433b1707548f2e76c40c
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, adrenal chromaffin cells are marked by specific expression of HMX1.
span_literal:
The simpler of these corresponded to adrenal chromaffin cells and was marked by the specific expression of HMX1 ( NKX-5–3 ), a TF involved in sympathetic neuron diversification ( 146 ).


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:d60514ec1cbd7841ef2d
claim_id: claim:d60514ec1cbd7841ef2d
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
The other cluster comprised neuroendocrine cells from multiple organs (stomach, intestine, pancreas, lung) and was marked by specific expression of NKX2–2 , a TF with a key role in pancreatic islet and enteroendocrine differentiation ( 147 ).

summary:
In Homo sapiens, neuroendocrine cells from multiple organs are marked by specific expression of NKX2-2.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:35e13df46084b97cd425
claim_id: claim:35e13df46084b97cd425
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal: pancreatic islet alpha/gamma cells, marked by pancreatic polypeptide and glucagon expression
summary:
In Homo sapiens, pancreatic islet alpha/gamma cells are marked by pancreatic polypeptide and glucagon expression.


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:abf4720f026ad6ce9951
claim_id: claim:abf4720f026ad6ce9951
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, pulmonary neuroendocrine cells are marked by expression of ASCL1 and NKX2-1.
span_literal:
pulmonary neuroendocrine cells (PNECs), marked by expression of ASCL1 and NKX2–1 , both TFs with key roles in specifying this lineage in the lung ( 148 , 149 )


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:4f06f3aa2f05a0274dee
claim_id: claim:4f06f3aa2f05a0274dee
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, nephron progenitors specifically express high levels of MEOX1, MEIS1, and MEIS2.
span_literal:
nephron progenitors in the metanephric trajectory specifically expressed high levels of mesenchyme and meis homeobox genes ( MEOX1, MEIS1, MEIS2 ) ( 159 )


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:d2f5ba0f3480ab9953bf
claim_id: claim:d2f5ba0f3480ab9953bf
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
summary: In Homo sapiens, HNF4A is specifically expressed in proximal tubule cells.
span_literal:
HNF4A was specifically expressed in proximal tubule cells; a mutation of this gene causes Fanconi renotubular syndrome, a disease that specifically affects the proximal tubule, and HNF4A was recently shown to be required for formation of the proximal tubule in mice ( 162 ).


claim_key: hca:0019_10.1126_science.aba7721_1646acb14b:claim:30deacdd80ff4e3c2f1e
claim_id: claim:30deacdd80ff4e3c2f1e
paper_key: hca:0019_10.1126_science.aba7721_1646acb14b
span_literal:
PNECs showed specific expression of trefoil factor 3, involved in mucosal protection and lung ciliated cell differentiation ( 155 ), gastrin-releasing peptide, which stimulates gastrin release from G cells in the stomach ( 156 ), and SCGB3A2 , a surfactant associated with lung development ( 157 ).

summary:
In Homo sapiens, pulmonary neuroendocrine cells show specific expression of trefoil factor 3, gastrin-releasing peptide, and SCGB3A2.


claim_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129:claim:810737ada631dc8aa10e
claim_id: claim:810737ada631dc8aa10e
paper_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129
span_literal:
For example, cardiomyocytes expressed genes encoding troponin ( TNNT2) , myosin heavy chain (MYH) 7 ( MYH7 ; Extended Data Fig. 2d )

summary:
In Homo sapiens, cardiomyocytes expressed troponin T2 (TNNT2) and myosin heavy chain 7 (MYH7) as marker genes in the human heart.


claim_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129:claim:64b5b79c0ef5b92058d1
claim_id: claim:64b5b79c0ef5b92058d1
paper_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129
span_literal:
endothelial cells expressed genes encoding vascular endothelial (VE)-cadherin ( CDH5 ) and CD31 ( PECAM1 ; Extended Data Fig. 2d )

summary:
In Homo sapiens, endothelial cells expressed vascular endothelial cadherin (CDH5) and CD31 (PECAM1) as marker genes in the human heart.


claim_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129:claim:13d671d0c9181daa149a
claim_id: claim:13d671d0c9181daa149a
paper_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129
span_literal:
and fibroblasts were characterized by PDGFRA (platelet-derived growth factor receptor α) and LAMB1 (laminin subunit β1; Extended Data Fig. 2d ) expression

summary:
In Homo sapiens, fibroblasts were characterized by expression of platelet-derived growth factor receptor alpha (PDGFRA) and laminin subunit beta 1 (LAMB1) in the human heart.


claim_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129:claim:d3acaadf2734268cde4a
claim_id: claim:d3acaadf2734268cde4a
paper_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129
span_literal:
One cluster contained neuronal markers (such as neurexins, NRXN ) but did not express typical Purkinje cell-specific or other established neuronal cell-specific genes and was therefore annotated as containing ‘neuronal-like’ cells (NLC).

summary:
In Homo sapiens, neuronal-like cells expressed neurexins (NRXN) as a marker gene in the human heart.


claim_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129:claim:efafc622a0d8bb054ca6
claim_id: claim:efafc622a0d8bb054ca6
paper_key: hca:0020_10.1038_s44161-022-00019-7_10ae5c8129
span_literal:
EFNB2 is highly expressed and enriched in endothelial cells compared to other cells of the heart (Fig. 4a,b and Extended Data Fig. 8e ).

summary:
In Homo sapiens, ephrin B2 (EFNB2) is highly expressed and enriched in endothelial cells compared to other cells of the heart.


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:e3d149a737861b92b94b
claim_id: claim:e3d149a737861b92b94b
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, distal mesenchyme is marked by LHX2, MSX1, and SP9.
span_literal:
separating three distal progenitor populations that we named ‘distal’ ( LHX2 + MSX1 + SP9 + ), ‘ RDH10 + distal’ ( RDH10 + LHX2 + MSX1 + ) and ‘transitional’ ( IRX1 + MSX1 + ) mesenchyme


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:2b3403b7a3100e2b8921
claim_id: claim:2b3403b7a3100e2b8921
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, prehypertrophic chondrocytes are marked by IHH.
span_literal:
IHH + prehypertrophic chondrocytes (PHCs) localized to the mid-diaphysis of the forming tibia and the metatarsals


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:a835f878e8ff2f01e3de
claim_id: claim:a835f878e8ff2f01e3de
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, neural fibroblasts are marked by FOXS1.
span_literal:
Glial cells expressing myelin genes (Extended Data Fig. 1b ) were co-located with a FOXS1 + fibroblast subtype (‘neural fibroblast’) in the periphery of the sciatic and tibial nerves


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:8779e7b63856a8f8960e
claim_id: claim:8779e7b63856a8f8960e
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
span_literal:
two clusters expressed the tendon markers scleraxis ( SCX ) and tenomodulin ( TNMD ), with one expressing the extracellular matrix genes biglycan ( BGN ) and keratocan ( KERA ), whereas the other expressed pro-glucagon ( GCG )

summary:
In Homo sapiens, tenocytes express the tendon markers scleraxis (SCX) and tenomodulin (TNMD), as well as biglycan (BGN) and keratocan (KERA).


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:0c2fb04d36ca64fe0ce3
claim_id: claim:0c2fb04d36ca64fe0ce3
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
span_literal:
two clusters expressed the tendon markers scleraxis ( SCX ) and tenomodulin ( TNMD ), with one expressing the extracellular matrix genes biglycan ( BGN ) and keratocan ( KERA ), whereas the other expressed pro-glucagon ( GCG )

summary:
In Homo sapiens, perimysium cells express scleraxis (SCX), tenomodulin (TNMD), and pro-glucagon (GCG).


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:8fe41b76d8fb157cc7b6
claim_id: claim:8fe41b76d8fb157cc7b6
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, proximal mesenchymal cells express MEIS2 and WT1.
span_literal:
A first mesenchymal population, proximal mesenchymal cells, expressed the regulator of stylopod identity, MEIS2 , together with WT1 , which marks the point of limb–torso junction


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:b05d5fc38444f3a93329
claim_id: claim:b05d5fc38444f3a93329
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, Mes1 cells lack WT1 expression.
span_literal:
Mes1 cells exhibited a similar expression profile but lacked WT1 , probably representing the mesenchyme just distal to the limb–torso junction


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:875dae2b3e15b51c0bd5
claim_id: claim:875dae2b3e15b51c0bd5
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, ISL1-positive mesenchyme expresses ISL1 and MEIS2 but not WT1.
span_literal:
We also identified a mesenchymal population within the posterior aspect of the developing hindlimb that expressed ISL1 ( ISL1 + Mes) in addition to MEIS2 , but not WT1


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:56b451eed8608e8a1fdf
claim_id: claim:56b451eed8608e8a1fdf
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, Mes2 and Mes3 clusters express CITED1.
span_literal:
Two further clusters (Mes2 and Mes3) expressed CITED1 , a gene encoding a molecule that localizes to the proximal domain of the limb and has an unclear role in limb development


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:c6816a8444b3fb4a20b4
claim_id: claim:c6816a8444b3fb4a20b4
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, the Mes4 cluster lacks LHX2 and IRX1 expression.
span_literal:
The Mes4 cluster exhibited similar expression patterns to distal and transitional mesenchymal cells but lacked LHX2 and IRX1


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:5bcda226ca64abb73fb9
claim_id: claim:5bcda226ca64abb73fb9
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, osteochondral progenitors are PRRX1-high, SOX-low, and COL2A1-low.
span_literal:
Mesenchymal condensate cells, SOX low COL2A1 low PRRX1 hi osteochondral progenitors and SOX9 hi COL2A1 low chondrocyte progenitors gave way to three populations of SOX9 hi COL2A1 hi chondrocytes: UCMA + resting, UCMA − IHH − proliferating (with a greater proportion of cells in G2, M and S phases) and IHH + PHCs


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:785a67470bbbfb1dc608
claim_id: claim:785a67470bbbfb1dc608
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary:
In Homo sapiens, proliferating chondrocytes are SOX9-high, COL2A1-high, UCMA-negative, and IHH-negative.


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:9ea52888970bfc1fb421
claim_id: claim:9ea52888970bfc1fb421
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, interzone cells express the marker GDF5.
span_literal:
These data contained a cluster expressing the interzone marker GDF5 and articular chondrocytes expressing lubricin ( PRG4 ; log fold change = 5.15, P = 4.1 × 10 −26 )


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:3afcbb0d85db60760c9f
claim_id: claim:3afcbb0d85db60760c9f
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, tendon progenitors are SCX-high and TNMD-low.
span_literal:
SCX hi TNMD low tendon progenitors emerged during PCW5 before being replaced by TNMD hi tenocytes and perimysium from PCW7 onwards


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:4d10e7782599dcaa8fd7
claim_id: claim:4d10e7782599dcaa8fd7
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
span_literal:
Comparing these pathways, PAX3 is almost absent in fetal myogenesis, whereas it persists to late states along the embryonic pathway, consistent with a previous study that captured Pax3 + Myog + cells in the mouse limb

summary:
In Homo sapiens, PAX3 persists in embryonic myogenesis cells but is almost absent in fetal myogenesis cells.


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:fb7d44c7f25adcac235c
claim_id: claim:fb7d44c7f25adcac235c
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
span_literal:
Additional genes such as FST , RGS4 , NEFM and SAMD11 were also identified to be marking the first myogenic pathway, whereas TNFSF13B , KRT31 and RGR mark the second myogenic pathway

summary:
In Homo sapiens, the first myogenic pathway (embryonic myogenesis) is marked by FST, RGS4, NEFM, and SAMD11.


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:bdf9fa63ed8048872317
claim_id: claim:bdf9fa63ed8048872317
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
span_literal:
Additional genes such as FST , RGS4 , NEFM and SAMD11 were also identified to be marking the first myogenic pathway, whereas TNFSF13B , KRT31 and RGR mark the second myogenic pathway

summary:
In Homo sapiens, the second myogenic pathway (fetal myogenesis) is marked by TNFSF13B, KRT31, and RGR.


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:2ed3e53cd9aa69fafdda
claim_id: claim:2ed3e53cd9aa69fafdda
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
span_literal: ID1 , ID2 , ID3 , HEY1 , MSC and HES1 in PAX7 + skeletal progenitors
summary:
In Homo sapiens, PAX7-positive skeletal muscle progenitors specifically express ID1, ID2, ID3, HEY1, MSC, and HES1.


claim_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3:claim:9f0d685aa931dbab744f
claim_id: claim:9f0d685aa931dbab744f
paper_key: hca:0021_10.1038_s41586-023-06806-x_7900919dd3
summary: In Homo sapiens, the apical ectodermal ridge-like cluster broadly expresses SP8 and WNT6.
span_literal:
one apical ectodermal ridge-like cluster, which broadly expressed SP8 and WNT6 and contained nine FGF8 + cells originating from PCW5 and PCW6


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:3ae034c98ea18c8c97d6
claim_id: claim:3ae034c98ea18c8c97d6
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
summary: In Homo sapiens, adipose stem cells are marked by positive expression of DPP4, CD55, and PI16.
span_literal:
ASCs from all depots shared a gene signature enriched for DPP4, CD55, and PI16, and showed enrichment in genes involved in proliferation, collagen synthesis and stemness


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:12e090f0bb207b77553a
claim_id: claim:12e090f0bb207b77553a
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
PreAs differentially expressed known markers of committed adipogenic cells such as PPARG, FABP4, PDGFRA, APOC, and APOE, and showed enrichment of terms linked to differentiation, commitment, and lipid transport

summary:
In Homo sapiens, pre-adipocytes are marked by positive expression of PPARG, FABP4, PDGFRA, APOC, and APOE.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:750929991b25c8ea3468
claim_id: claim:750929991b25c8ea3468
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal: characterized by high expression of THY1 and PDGFRA
summary:
In Homo sapiens, human adipose stem and progenitor cells are characterized by high expression of THY1 and PDGFRA.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:253a9c7b4b4fec9f259e
claim_id: claim:253a9c7b4b4fec9f259e
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
We classified the first and major population retrieved in all depots as VSMPs, since it expressed muscle-related markers such as MYH11 but also ACTA2 and TAGLN

summary:
In Homo sapiens, vascular smooth muscle progenitor cells are marked by positive expression of MYH11, ACTA2, and TAGLN.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:bad5414eeae955f00554
claim_id: claim:bad5414eeae955f00554
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
Among the top differentially expressed genes of the ubiquitous HHIP+ cluster, we recognized several ortholog markers of a mouse stromal subpopulation that we have previously characterized as having non- and anti-adipogenic properties, and accordingly named Adipogenesis Regulators (Aregs)[12](https://doi.org/10.1038/s41586-018-0226-8), [17](https://doi.org/10.15252/embj.2021108206). These are F3, CLEC11A, GDF10, MGP, and INMT

summary:
In Homo sapiens, the HHIP+ adipose stem and progenitor cell cluster is marked by positive expression of F3, CLEC11A, GDF10, MGP, and INMT.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:f096e25a6400b227d853
claim_id: claim:f096e25a6400b227d853
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
Another small stromal population, the IFIT+ cluster, which we observed to be present in every depot and donor, is defined by an extremely specific expression of interferon-related genes such as IFIT3, IFI6, and IFI27

summary:
In Homo sapiens, the IFIT+ adipose stem and progenitor cell cluster is defined by positive expression of IFIT3, IFI6, and IFI27.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:6b1f1ca4d77b02138b65
claim_id: claim:6b1f1ca4d77b02138b65
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
The SFRP4+ cluster was characterized by high expression of Secreted frizzled-related proteins 2 and 4 (SFRP2 and SFRP4)

summary:
In Homo sapiens, the SFRP4+ adipose stem and progenitor cell cluster is characterized by high expression of SFRP2 and SFRP4.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:a0c9255bdcb140b10778
claim_id: claim:a0c9255bdcb140b10778
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal: The mesothelial cells, defined by the expression of MSLN, UP3KB, LRRN4, and Keratin-related genes
summary:
In Homo sapiens, mesothelial cells are defined by positive expression of MSLN, UPK3B, LRRN4, and keratin-related genes.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:e7b8f2aaad593bfe2acd
claim_id: claim:e7b8f2aaad593bfe2acd
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
summary: In Homo sapiens, IGFBP2+ stromal cells express specific markers IGFBP2, RBP1, WNT4, and WNT6.
span_literal:
we found that these cells express, on the one hand, specific markers such as IGFBP2, RBP1, WNT4, or WNT6


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:ee069aa7a9dfc12acbb0
claim_id: claim:ee069aa7a9dfc12acbb0
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
The second layer involves Vascular-adhesion protein 1 (VAP1), encoded by the gene AOC3, which is highly expressed in VSMPs

summary:
In Homo sapiens, AOC3 (encoding vascular adhesion protein 1) is highly expressed in vascular smooth muscle progenitor cells.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:64feb867f263ff083872
claim_id: claim:64feb867f263ff083872
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
we selected the transmembrane 4 L6 family member 1 (TM4SF1) as a marker to first exclude OM-specific populations from downstream functional assays

summary:
In Homo sapiens, TM4SF1 (transmembrane 4 L6 family member 1) is a marker of omentum-specific stromal populations including mesothelial cells and IGFBP2+ stromal cells.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:a0ba7c27d6a65d9acaf2
claim_id: claim:a0ba7c27d6a65d9acaf2
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
several genes that were previously linked to the non-adipogenic phenotype of OM SVF-adherent cells were specific to mesothelial and/or IGFBP2+ cells (e.g., CD200[47](https://doi.org/10.1016/j.stemcr.2014.01.002), WT1, and ALDH1A2

summary:
In Homo sapiens, CD200, WT1, and ALDH1A2 are specifically expressed by mesothelial cells and/or IGFBP2+ stromal cells in the omentum.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:0ebfd518196f85cddd93
claim_id: claim:0ebfd518196f85cddd93
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
several genes that were previously linked to the non-adipogenic phenotype of OM SVF-adherent cells were specific to mesothelial and/or IGFBP2+ cells (e.g., CD200[47](https://doi.org/10.1016/j.stemcr.2014.01.002), WT1, and ALDH1A2

summary:
In Homo sapiens, CD200, WT1, and ALDH1A2 are specifically expressed by IGFBP2+ stromal cells and/or mesothelial cells in the omentum.


claim_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021:claim:866649caa3bd8d1f04bd
claim_id: claim:866649caa3bd8d1f04bd
paper_key: hca:0024_10.1101_2023.05.01.538871_7e4c731021
span_literal:
while F3 is a specific marker for this anti-adipogenic stromal populations in mice, it is much less specific in humans, where HHIP appears to be a more specific marker for this cell population

summary:
In Homo sapiens, HHIP is a more specific marker than F3 for the anti-adipogenic HHIP+ adipose stem and progenitor cell population.


claim_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb:claim:9e563445f1b8b4cd92d7
claim_id: claim:9e563445f1b8b4cd92d7
paper_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb
span_literal:
(i) astrocytes ( GFAP ) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes ( OLR1 ) and an astrocyte-2 ( GINS3 ) population expressing genes associated with growth and reparative functions

summary:
In Homo sapiens substantia nigra, astrocytes are marked by GFAP, with astrocyte-1 subtype expressing OLR1 and astrocyte-2 subtype expressing GINS3.


claim_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb:claim:7429914fb966e2fbfd1d
claim_id: claim:7429914fb966e2fbfd1d
paper_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb
span_literal:
(i) astrocytes ( GFAP ) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes ( OLR1 ) and an astrocyte-2 ( GINS3 ) population expressing genes associated with growth and reparative functions

summary:
In Homo sapiens substantia nigra, astrocyte-2 expresses GINS3, associated with growth and reparative functions.


claim_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb:claim:f606d3d54441c4b9ab63
claim_id: claim:f606d3d54441c4b9ab63
paper_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb
span_literal:
(ii) oligodendrocytes (ODCs) ( MOG , MOBP ) with three subtypes discriminated by oligodendrocyte marker genes PALM2 , LGALS1 & PPM1G

summary:
In Homo sapiens substantia nigra, oligodendrocytes are marked by MOG and MOBP, with subtypes discriminated by PALM2, LGALS1, and PPM1G.


claim_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb:claim:e17ad8db690bc20589e3
claim_id: claim:e17ad8db690bc20589e3
paper_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb
span_literal:
(vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing gamma-aminobutyric acid (GABA) receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis

summary:
In Homo sapiens substantia nigra pars reticulata, GABAergic neurons express gamma-aminobutyric acid receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2.


claim_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb:claim:19df0cf5ee0149c0875a
claim_id: claim:19df0cf5ee0149c0875a
paper_key: hca:0025_10.1038_s41467-020-17876-0_159e232bbb
span_literal:
Notably, we observe expression of the known PD gene LRRK2 to be significantly higher in OPCs than other SN cell types

summary:
In Homo sapiens substantia nigra, LRRK2 expression is significantly higher in oligodendrocyte precursor cells than other substantia nigra cell types.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:a8ee1bd9893f9dcd52a7
claim_id: claim:a8ee1bd9893f9dcd52a7
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
WIF1 + HHIP + CA2 + ) expressed higher levels of some canonical AT2 markers ( SFTPA1 , SFTPC , ETV5 ) and selectively expressed inhibitors of Wnt ( WIF1 ) and Hedgehog ( HHIP ) signaling and the cell cycle ( CDKN1A

summary:
In Homo sapiens, alveolar type 2 cells selectively express WIF1, HHIP, CA2, and higher levels of SFTPA1, SFTPC, ETV5, and CDKN1A compared to alveolar type 2 signaling cells.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:a485eb5719c5a266229f
claim_id: claim:a485eb5719c5a266229f
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
The other, 10-fold less abundant cluster (AT2-signaling, AT2-s) selectively expressed Wnt signaling ( WNT5A , LRP5 , CTNNBIP,TCF4/TCF7L2 ) and detoxification ( CP , GSTA1 , CYP4B1 ) genes

summary:
In Homo sapiens, alveolar type 2 signaling cells selectively express Wnt signaling genes WNT5A, LRP5, CTNNBIP, TCF4/TCF7L2 and detoxification genes CP, GSTA1, CYP4B1.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:79d9ae9176bb3c02027e
claim_id: claim:79d9ae9176bb3c02027e
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
Another cluster (Bas-d) had reduced KRT5 and increased HES1 , KRT7 , and SCGB3A2 expression, indicating active differentiation to other epithelial fates

summary:
In Homo sapiens, differentiating basal cells show reduced KRT5 and increased HES1, KRT7, and SCGB3A2 expression.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:bcf4166046f51dcd7396
claim_id: claim:bcf4166046f51dcd7396
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
Bas-px and Bas are distinguished by hundreds of genes, suggesting they are molecularly distinct cell types differing in hormone production ( ALOX15 , ADH7 , SNCA ) and adhesion ( POSTN , ISLR , PCDH7 )

summary:
In Homo sapiens, proximal basal cells and basal cells are distinguished by genes involved in hormone production (ALOX15, ADH7, SNCA) and adhesion (POSTN, ISLR, PCDH7).


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:12fe89ca0ccf38e344a2
claim_id: claim:12fe89ca0ccf38e344a2
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
Two populations were identified as bronchial (Bro1, Bro2) by their localization around bronchi ( Fig. ED3k ). Thus bronchial endothelial cells are distinct from their counterparts in the pulmonary circulation, distinguished by matrix ( VWA1 , HSPG2 ), fenestrated morphology 27 ( PLVAP ) and cell cycle associated ( MYC , HBEGF ) genes.

summary:
In Homo sapiens, bronchial endothelial cells are distinguished from pulmonary circulation endothelial cells by expression of VWA1, HSPG2, PLVAP, MYC, and HBEGF.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:3b63f5993ff26d6ed56e
claim_id: claim:3b63f5993ff26d6ed56e
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
expression of voltage-gated sodium channel SCN7A and glutamate receptor GRIA1 suggest alveolar fibroblasts are excitable cells with glutamatergic input

summary:
In Homo sapiens, alveolar fibroblasts express voltage-gated sodium channel SCN7A and glutamate receptor GRIA1.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:dfed98d4f9d8f6072e20
claim_id: claim:dfed98d4f9d8f6072e20
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
summary: In Homo sapiens, fibromyocytes show higher expression of contractile genes MYH11, CNN1, and TAGLN.
span_literal:
The other (named “fibromyocytes”) showed higher expression of contractile genes ( MYH11 , CNN1 , TAGLN )


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:931d102d6b673ca61e82
claim_id: claim:931d102d6b673ca61e82
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
IGSF21+ and rare EREG+ dendritic cells express asthma genes ( CCL2 , CCL13,IGSF21 ) and developmental signals ( EREG , VEGFA , AREG ), respectively

summary:
In Homo sapiens, IGSF21-positive dendritic cells express asthma genes CCL2, CCL13, and IGSF21, while EREG-positive dendritic cells express developmental signals EREG, VEGFA, and AREG.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:b4eeb454e1af1a2dad58
claim_id: claim:b4eeb454e1af1a2dad58
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
TREM2+ dendritic cells localize to vessels and alveoli and express lipid machinery ( APOC1 , APOE , CYP27A1 )

summary:
In Homo sapiens, TREM2-positive dendritic cells express lipid machinery genes APOC1, APOE, and CYP27A1.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:be855d8cf1bffe1c6a04
claim_id: claim:be855d8cf1bffe1c6a04
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
NECTIN4 (measles virus receptor) was enriched in club, ciliated, differentiating basal, and goblet cells

summary:
In Homo sapiens, NECTIN4 (measles virus receptor) is enriched in club cells, ciliated cells, differentiating basal cells, and goblet cells.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:47c67f369660f9d6ce9b
claim_id: claim:47c67f369660f9d6ce9b
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal: CDHR3 (“common cold” Rhinovirus C) was enriched in ciliated
summary:
In Homo sapiens, CDHR3 (Rhinovirus C receptor) is enriched in ciliated cells and neuroendocrine cells.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:522e409b37c44f6177f6
claim_id: claim:522e409b37c44f6177f6
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
These include what may be long-sought master regulators of AT1 cells (e.g. MYRF ), which comprise the gas exchange surface, and of pericytes ( TBX5 )

summary:
In Homo sapiens, MYRF is a putative master regulator transcription factor of alveolar type 1 cells, and TBX5 is a putative master regulator of pericytes.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:04e7157ae3f6e7f7be61
claim_id: claim:04e7157ae3f6e7f7be61
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
Other hormones have specific and unexpected targets, such as somatostatin ( SSTR1 , arteries), melanocortin ( MC1R , ionocytes), and oxytocin ( OXTR , ciliated cells).

summary:
In Homo sapiens, SSTR1 (somatostatin receptor) is selectively expressed in arterial cells, MC1R (melanocortin receptor) in ionocytes, and OXTR (oxytocin receptor) in ciliated cells.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:50017261a1045f86733d
claim_id: claim:50017261a1045f86733d
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
Ionocytes are the only non-immune cell to express appreciable levels of any chemokine receptor (CXCR4) .

summary:
In Homo sapiens, ionocytes are the only non-immune cell type to express appreciable levels of the chemokine receptor CXCR4.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:d1b2abaff05d40557f7d
claim_id: claim:d1b2abaff05d40557f7d
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
All three novel dendritic populations express CCR1 , which could mediate their attraction to veins ( CCL23 ), bronchial vessels ( CCL14 ), ciliated cells ( CCL15 ), and lymphocytes ( CCL5 ).

summary:
In Homo sapiens, the three novel dendritic cell populations (IGSF21-positive, EREG-positive, and TREM2-positive) express CCR1.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:32f4a6235a169b7075db
claim_id: claim:32f4a6235a169b7075db
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
summary: In Homo sapiens, MYRF is selectively expressed in alveolar type 1 cells, which also express AGER.
span_literal:
MYRF is selectively expressed in AT1 cells (arrowheads; 97% of MYRF + cells were AGER +, n=250 scored cells).


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:80434175de31c15a7f96
claim_id: claim:80434175de31c15a7f96
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
smFISH of alveolar section of adult human lung probed for PH disease gene KCNK3 (red) and pericyte marker COX4I2 (white) with DAPI counterstain (blue) and ECM autoflourescence (green). Note pericyte-specific expression (arrowheads, 91% of COX4I2+ pericytes were KCNK3 +, n=77).

summary:
In Homo sapiens, the pulmonary hypertension disease gene KCNK3 shows pericyte-specific expression, with 91% of COX4I2-positive pericytes also expressing KCNK3.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:ab707f78262d665fa71c
claim_id: claim:ab707f78262d665fa71c
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
smFISH of alveolar section of adult human lung probed for atrioventricular (AV) dysplasia gene ACVRL1 (red), endothelial marker CLDN5 (white) with DAPI counterstain. Note ACVRL1 CLDN5 double-positive capillaries (white arrowheads, 70% of CLDN5+ capillaries were ACVRL1 +, n=102)

summary:
In Homo sapiens, the atrioventricular dysplasia gene ACVRL1 is expressed in capillary endothelial cells, with 70% of CLDN5-positive capillaries also expressing ACVRL1.


claim_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2:claim:68a236e50af4edcc9b01
claim_id: claim:68a236e50af4edcc9b01
paper_key: hca:0026_10.1038_s41586-020-2922-4_1612ece6e2
span_literal:
smFISH of alveolar section of adult human lung probed for COPD/emphysema gene SERPINA1 and AT2 marker SFTPC , and DAPI. Note AT2-specific expression (arrowheads; 93% of AT2 cells were SERPINA1 +, n=176).

summary:
In Homo sapiens, the COPD/emphysema gene SERPINA1 shows alveolar type 2 cell-specific expression, with 93% of alveolar type 2 cells expressing SERPINA1, which also express the marker SFTPC.


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:41a1507b02aa3345bff6
claim_id: claim:41a1507b02aa3345bff6
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, alveolar type 2 cells express the lineage markers SFTPC and SFTPB.
span_literal:
including expression of the lineage markers SFTPC and SFTPB in AT2 cells, and CLIC5 and AGER in AT1 cells


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:1c4794f398e0dcc6df56
claim_id: claim:1c4794f398e0dcc6df56
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
span_literal:
We used expression of the DATP marker genes ( KRT8 , CLDN4 and CDKN1A) 25 to develop a DATP signature

summary:
In Homo sapiens, damage-associated transient progenitor cells are marked by expression of KRT8, CLDN4, and CDKN1A.


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:74b01ea8b29197019ac2
claim_id: claim:74b01ea8b29197019ac2
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, pathological fibroblasts are marked by expression of CTHRC1.
span_literal:
we identified expansion of recently described CTHRC1 + pathological fibroblasts 3 contributing to rapidly ensuing pulmonary fibrosis in COVID-19


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:72709d62ae8f4e729839
claim_id: claim:72709d62ae8f4e729839
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, pathological fibroblasts strongly express CTHRC1, COL1A1, and COL3A1.
span_literal:
pFBs strongly expressed CTHRC1 , a recently described hallmark gene that defines these cells, and genes of pathological ECM 3 , including COL1A1 and COL3A1


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:dd11c30aca06250ed42e
claim_id: claim:dd11c30aca06250ed42e
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, basal cells of the airway epithelium are marked by expression of KRT5 and TP63.
span_literal:
Among captured airway epithelial cells, we recovered four distinct trajectories: KRT5 + TP63 + basal ( n = 534), club ( n = 1,232), and goblet cells ( n = 1,757), and one trajectory with fewer cells ( n = 110) that was primarily found in COVID-19 lungs, which we identify as putative tuft-like cells


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:d97fd7e442e62859cc67
claim_id: claim:d97fd7e442e62859cc67
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
span_literal: IRF8 , B2M , MKI67 and TOP2A (‘cycling epithelium
summary:
In Homo sapiens, cycling epithelial cells are characterized by expression of IRF8, B2M, MKI67, and TOP2A.


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:1ce784cea90a58bbf631
claim_id: claim:1ce784cea90a58bbf631
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
span_literal:
a cluster showing high expression of the extracellular matrix (ECM) components COL6A3 , COL1A2 , and COL3A1 (‘ECM high epithelium’; n = 1,179)

summary:
In Homo sapiens, extracellular matrix high epithelial cells show high expression of COL6A3, COL1A2, and COL3A1.


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:93322fc26e8287d9caf6
claim_id: claim:93322fc26e8287d9caf6
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, tuft cells are marked by expression of CHAT or POU2F3 in the lung.
span_literal:
The numbers of tuft cells (CHAT + or POU2F3 + ) were increased threefold in the upper airways of individuals with COVID-19, and they were ectopically present in the lung parenchyma of COVID-19 but not control lungs


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:18de73671ef1a74e63ec
claim_id: claim:18de73671ef1a74e63ec
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
span_literal:
COVID-19 AT2 cells displayed decreased expression of ETV5 ( Fig. 3d ), a transcription factor that is required for maintaining AT2 cell identity.

summary:
In Homo sapiens, ETV5 is a transcription factor required for maintaining alveolar type 2 cell identity, and its expression is decreased in COVID-19 alveolar type 2 cells.


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:dfe74f7fa533f48f04a6
claim_id: claim:dfe74f7fa533f48f04a6
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, CAV1 is a marker of late alveolar type 1 cell maturation.
span_literal:
CAV1 , a marker of late AT1 maturation 24 , was expressed at significantly lower levels in AT1 cells from COVID-19 lungs


claim_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864:claim:29d2a2bd18552f169d92
claim_id: claim:29d2a2bd18552f169d92
paper_key: hca:0027_10.1038_s41586-021-03569-1_1910c01864
summary: In Homo sapiens, pathological fibroblasts are identified by high expression of COL1A1 and CTHRC1.
span_literal:
Cell clusters with high expression of COL1A1 and CTHRC1 were annotated as ‘pathological fibroblasts’ because they have been reported to contribute to the leading edge of fibrosis 3 .


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:311b07a0eac686f01f44
claim_id: claim:311b07a0eac686f01f44
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
We used expression of FDA approved biomarkers, MUC16 /CA125 and WFDC2 /HE4, to identify EC and OC cancer clusters

summary:
In Homo sapiens, MUC16 and WFDC2 are used as biomarkers to identify endometrial cancer and ovarian cancer clusters.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:dd8a93c547e2125c7c9e
claim_id: claim:dd8a93c547e2125c7c9e
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal: Expression of KIT /CD117 was used to identify GIST cancer clusters
summary:
In Homo sapiens, KIT is a positive marker used to identify gastro-intestinal stromal tumor cancer clusters.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:3141df0c73fb3cbc3aec
claim_id: claim:3141df0c73fb3cbc3aec
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal: malignant subclusters using the EC biomarkers MUC16 /CA125 and WFDC2
summary:
In Homo sapiens, MUC16 and WFDC2 are biomarkers used to identify ovarian cancer malignant subclusters.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:46b5c89419bc07052ae1
claim_id: claim:46b5c89419bc07052ae1
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
the hallmark mTOR pathway regulator RHEB is significantly upregulated in the subcluster labeled as 3-Ovarian cancer, that comes from Patient 7 diagnosed with endometrioid OC

summary:
In Homo sapiens, RHEB is significantly upregulated in the 3-Ovarian cancer subcluster from endometrioid ovarian cancer.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:b00e1834406b97b84b46
claim_id: claim:b00e1834406b97b84b46
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
there is increased IMPA2 expression in the malignant fraction of the EEC cohort and increased chromatin accessibility of a cancer-specific dRE within the IMAP2 locus

summary:
In Homo sapiens, IMPA2 expression is increased in the malignant fraction of the endometrioid endometrial cancer cohort.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:8d8ea712a71053fbe3bb
claim_id: claim:8d8ea712a71053fbe3bb
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
We also found three clear cancer-specific dREs linked to increased SOX9 expression in the malignant fraction of the EEC cohort

summary:
In Homo sapiens, SOX9 expression is increased in the malignant fraction of the endometrioid endometrial cancer cohort.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:b149c9337339cd76df53
claim_id: claim:b149c9337339cd76df53
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
we note that CD24 is highly expressed in the malignant fraction of the EEC cohort, and we highlight three cancer-specific dREs linked to CD24 expression

summary:
In Homo sapiens, CD24 is highly expressed in the malignant fraction of the endometrioid endometrial cancer cohort.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:4fc96eaacc62537d17a1
claim_id: claim:4fc96eaacc62537d17a1
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
PI3 , encoding peptidase inhibitor 3 (Elafin protein), is highly expressed in the malignant fraction

summary:
In Homo sapiens, PI3 (peptidase inhibitor 3) is highly expressed in the malignant fraction of the high-grade serous ovarian cancer cohort.


claim_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5:claim:e0cec2a4a2d3ee03a965
claim_id: claim:e0cec2a4a2d3ee03a965
paper_key: hca:0028_10.1016_j.molcel.2021.10.013_4a3d615da5
span_literal:
We also highlight two cancer-specific dREs that were strongly associated with increased LAPTM4B expression in the malignant fraction of the HGSOC patient cohort

summary:
In Homo sapiens, LAPTM4B expression is increased in the malignant fraction of the high-grade serous ovarian cancer patient cohort.


claim_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506:claim:474bcc2e572061f14ef4
claim_id: claim:474bcc2e572061f14ef4
paper_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506
summary: In Homo sapiens retina, PDE6A is a marker for rod photoreceptor cells.
span_literal:
we visualized the expression and gene body accessibility of the same set of markers ( PDE6A for rod, NETO1 for BC, ARR3 for cone, ONECUT1 for HC, RLBP1 for MG, RBPMS for RGC, TFAP2B for AC, GFAP for astrocyte, and CD74 for microglia)


claim_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506:claim:79c7a42ebb990a23e3bf
claim_id: claim:79c7a42ebb990a23e3bf
paper_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506
span_literal:
two OPN4 positive clusters in our dataset showed one-to-one matching to the two ipRGC clusters of the previous study, and their marker genes, EOMES and LMO2 , were also consistent

summary:
In Homo sapiens retina, OPN4, EOMES, and LMO2 are marker genes for intrinsically photosensitive retinal ganglion cells.


claim_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506:claim:ff42ce9c1376de1a5ff8
claim_id: claim:ff42ce9c1376de1a5ff8
paper_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506
summary: In Homo sapiens retina, MEIS2 is a marker gene for DB3b bipolar cells.
span_literal:
We were also able to identify marker genes of DB3b ( MEIS2 ) and DB5 ( QPCT ) for human and monkey BCs.


claim_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506:claim:e2fc881324b569108c65
claim_id: claim:e2fc881324b569108c65
paper_key: hca:0029_10.1016_j.xgen.2023.100298_96b489f506
summary: In Homo sapiens, RBFOX3 (NeuN) is highly expressed in a subset of neuronal cells.
span_literal:
NeuN is a nuclear envelope protein encoded by the RBFOX3 gene that has been reported to be highly expressed in a subset of neuronal cells.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:8ca8382b0ddecfda48db
claim_id: claim:8ca8382b0ddecfda48db
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
human intestinal stem cells (ISCs) significantly expressed classic markers LGR5 , ASCL2 , SLC12A2 , and RGMB

summary:
In Homo sapiens, intestinal stem cells significantly express the classic markers LGR5, ASCL2, SLC12A2, and RGMB.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:2065ed55e89e98eb4da6
claim_id: claim:2065ed55e89e98eb4da6
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
RARRES2 , a retinoid-response gene with no reported association to the gut epithelium, was enriched in colon ISCs, with low SI ISC

summary:
In Homo sapiens, RARRES2 is enriched in colon intestinal stem cells compared with small intestine intestinal stem cells.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:6da28a3a6949e6e38955
claim_id: claim:6da28a3a6949e6e38955
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal: LYZ was not unique to human PCs
summary:
In Homo sapiens, LYZ is expressed in Paneth cells but is not unique to them, with expression also seen in Bestrophin 4 positive cells and follicle-associated epithelium.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:f3ad1e168fd1adcf9e4c
claim_id: claim:f3ad1e168fd1adcf9e4c
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
summary: In Homo sapiens, LYZ shows high expression in follicle-associated epithelium.
span_literal:
LYZ was not unique to human PCs, with expression also seen in BEST4 + cells and high expression in FAE


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:b0f27ec4643abe6e3571
claim_id: claim:b0f27ec4643abe6e3571
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
human scRNAseq studies have described a novel intestinal lineage, absent in mice, expressing BEST4 , SPIB , and CA7 , 5 with SI-specific CFTR 9 , 10 and colon-specific OTOP2

summary:
In Homo sapiens, Bestrophin 4 positive cells express BEST4, SPIB, and CA7, with small intestine-specific CFTR and colon-specific OTOP2.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:765ab4607ad33e327f8a
claim_id: claim:765ab4607ad33e327f8a
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal: DEGs included GUCA2A and GUCA2B 5 , which act as prohormones regulating satiety.
summary:
In Homo sapiens, Bestrophin 4 positive cells express GUCA2A and GUCA2B as differentially expressed genes.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:b2d866a0bb2758d3f41b
claim_id: claim:b2d866a0bb2758d3f41b
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal: CLCA1 , MUC2 , and TFF3 , with colonic GCs expressing higher WFDC2
summary:
In Homo sapiens, goblet cells express the classic markers CLCA1, MUC2, and TFF3, with colonic goblet cells expressing higher WFDC2.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:5be8d69be5592a80fbd8
claim_id: claim:5be8d69be5592a80fbd8
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
SUCNR1 , a G-protein–coupled receptor mediating SI IL25 release, 71 was negligible in the colon, suggesting SI and colon tuft cells differentially detect succinate-producing pathogens ( Figure 9 B and C ). Colonic tuft cells

summary:
In Homo sapiens, SUCNR1 is expressed in small intestine tuft cells but is negligible in colon tuft cells.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:c3458d271c047ed3a67e
claim_id: claim:c3458d271c047ed3a67e
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
summary: In Homo sapiens, colonic tuft cells express the umami taste receptor subunits TAS1R1 and TAS1R3.
span_literal:
Colonic tuft cells likely detect umami-chemosensory cues (eg, microbe-derived free amino acids) with heterodimeric umami taste receptor subunits TAS1R1 and TAS1R3


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:f9c5da91c27b67c17324
claim_id: claim:f9c5da91c27b67c17324
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
summary: In Homo sapiens, tuft cells express the lipopolysaccharide co-receptor CD14.
span_literal:
Expression of the LPS co-receptor CD14 across tuft cells 77 ( Figure 9 D ) supports this novel role in bacterial-related immune responses.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:e801db8e374ae001b45c
claim_id: claim:e801db8e374ae001b45c
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
SMOC2 , a murine ISC marker, 18 was expressed highest in PCs, with other markers shown as restricted to ISCs in mouse ( LGR5 , ASCL2 , RGMB ) expressed higher in human

summary:
In Homo sapiens, SMOC2 is expressed highest in Paneth cells, and LGR5, ASCL2, and RGMB are expressed higher in Paneth cells than expected.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:1cc97fb32f49d8cc16aa
claim_id: claim:1cc97fb32f49d8cc16aa
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
Mycophenolate mofetil (CellCept, Genentech, South San fransisco, CA) targets IMPDH2 and IMPDH1 were expressed in proliferative crypt populations and EECs, respectively.

summary:
In Homo sapiens, Inosine Monophosphate Dehydrogenase 2 is expressed in proliferative crypt cells and Inosine Monophosphate Dehydrogenase 1 is expressed in enteroendocrine cells.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:a438d826c07024d52ed1
claim_id: claim:a438d826c07024d52ed1
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
summary: In Homo sapiens, DHFR is expressed highest in transit amplifying and progenitor cells.
span_literal:
The methotrexate target DHFR was highest in TA and progenitor cells, while the tofacitinib (Xeljanz, Pfizer, New York, NY) target JAK1 had broader expression.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:9e5489189cbb43a54f0d
claim_id: claim:9e5489189cbb43a54f0d
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
We found CES2 , which metabolizes the cancer drug irinotecan into biologically active SN-38, 131 to be the highest-expressed phase I metabolism gene in the SI, with AE enrichment.

summary:
In Homo sapiens, CES2 is the highest-expressed phase I metabolism gene in the small intestine, with enrichment in absorptive enterocytes.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:602fbd65694b50853cf4
claim_id: claim:602fbd65694b50853cf4
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
summary: In Homo sapiens, Bestrophin 4 positive cells express Neuropeptide Y.
span_literal:
Bestrophin 4 (BEST4) + cells express Neuropeptide Y (NPY) and show maturational differences between the small intestine and colon.


claim_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9:claim:8738a5ad0e7ea7364020
claim_id: claim:8738a5ad0e7ea7364020
paper_key: hca:0030_10.1016_j.jcmgh.2022.02.007_2ccf593bb9
span_literal:
TRPM5 , ITPR2 , HTR3E , IL13RA1 , IL17RB ), with no connection found for 7 receptors ( GABRA4 , ADGRG6/GPR126 , SIGIRR , ITGB5 , KIT , PTPRJ , TLR9

summary:
In Homo sapiens, tuft cells uniquely express TRPM5, ITPR2, HTR3E, IL13RA1, IL17RB, GABRA4, ADGRG6, SIGIRR, ITGB5, KIT, PTPRJ, and TLR9.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:23c39f123c617c342cec
claim_id: claim:23c39f123c617c342cec
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Clusters 0 and 6 displayed high expression of Keratin 13 ( KRT13 ) and 19 ( KRT19 ) [ 17 , 18 ] as well as S100A8 and S100A9 [ 19 ], which pointed to conjunctival cell fates

summary:
In Homo sapiens, conjunctival cells are marked by high expression of KRT13, KRT19, S100A8, and S100A9.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:8590c27862fedcc08949
claim_id: claim:8590c27862fedcc08949
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Differential gene expression analysis indicated higher expression of KRT6A, KRT14 and KRT15 in cell cluster 0 compared to cell cluster 6 ( Figure S2B ), suggestive of a basal conjunctival epithelium

summary:
In Homo sapiens, basal conjunctival epithelial cells are marked by higher expression of KRT6A, KRT14, and KRT15.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:1ed0665e9de1a45389a8
claim_id: claim:1ed0665e9de1a45389a8
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Cluster 6 displayed higher expression of Mucin 4 ( MUC4 ) and 1 ( MUC1 ) as well as KRT4 , indicative of a superficial conjunctival epithelium

summary:
In Homo sapiens, superficial conjunctival epithelial cells are marked by higher expression of MUC4, MUC1, and KRT4.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:f49c111069d8216e81af
claim_id: claim:f49c111069d8216e81af
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
summary: In Homo sapiens, corneal and limbal epithelial cells display high expression of KRT12.
span_literal:
Cell clusters 1, 2, 4, 5, 7 and 10 displayed high expression of keratin 12 ( KRT12 ), whose expression is associated with corneal and limbal epithelium


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:6332106f9da366f3685b
claim_id: claim:6332106f9da366f3685b
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Cell cluster 1 displayed high expression of gap junction protein beta 6 ( GJB2 ), which is associated with a basal corneal epithelial phenotype

summary:
In Homo sapiens, basal corneal epithelial cells are marked by high expression of gap junction protein beta 2 (GJB2).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:e0248062417e60ad3806
claim_id: claim:e0248062417e60ad3806
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
summary: In Homo sapiens, basal corneal epithelial cells are marked by high expression of HES1 and HES5.
span_literal:
HES1 and HES5 , whose expression is confined to the basal and immediate suprabasal corneal epithelium [ 22 ], were also highly expressed in cluster 1


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:86d5129eb3d589723a5f
claim_id: claim:86d5129eb3d589723a5f
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Amphiregulin ( AREG) was the most highly expressed gene in cluster 2 ( Figure S1, S3A ). Its expression was confined to the most superficial part of corneal epithelium, ( Figure S3B ), leading to definition of this cluster as corneal superficial epithelium.

summary:
In Homo sapiens, corneal superficial epithelial cells are marked by high expression of amphiregulin (AREG).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:03f6b9dd263384e468a7
claim_id: claim:03f6b9dd263384e468a7
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
summary: In Homo sapiens, limbal superficial epithelial cells are marked by high expression of LYPD2.
span_literal:
Differential gene expression analysis indicated LYPD2 to be highly expressed in cluster 5 ( Figure S3A ); hence, IF with antibody raised against LYPD2 was carried out revealing low expression in the corneal epithelium ( Figure S3C ), but high expression in the limbal superficial epithelium, defining cluster 5 as limbal superficial epithelium


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:df9aae7e1250693c2f84
claim_id: claim:df9aae7e1250693c2f84
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
summary: In Homo sapiens, limbal progenitor cells are marked by high expression of KRT15.
span_literal:
KRT15, a limbal progenitor marker [ 23 , 24 ] was highly expressed in clusters 9 and 4 but not in cluster 10


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:d2ece7f148f605351d69
claim_id: claim:d2ece7f148f605351d69
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Through the differential gene expression analysis ( Figure S4A ), we were able to identify a unique marker for cluster 10, CPVL , which was not expressed in the other epithelial clusters

summary:
In Homo sapiens, limbal neural crest derived progenitor cells are marked by unique expression of CPVL.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:a5432b3814f1b49e963a
claim_id: claim:a5432b3814f1b49e963a
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
IF analysis revealed a large overlap in expression between the neural crest marker, MITF and the cluster 10 specific marker, CPVL ( Figure S5E , E’), confirming the LNCPs nature of this cell population.

summary:
In Homo sapiens, limbal neural crest derived progenitor cells are marked by expression of MITF and CPVL.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:1fe3d76327a05cdfa239
claim_id: claim:1fe3d76327a05cdfa239
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Cluster 9 showed an interesting transcriptional profile, exhibiting high expression of putative LPC markers including CXCL14, CEBPD, TP63, S100A2 and the more recently discovered marker, TXNIP [ 14 ]

summary:
In Homo sapiens, limbal progenitor cells are marked by high expression of CXCL14, CEBPD, TP63, S100A2, and TXNIP.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:a5051c30b2977630ae6a
claim_id: claim:a5051c30b2977630ae6a
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Fibulin 1 ( FBLN1 ), which forms part of the extracellular matrix (ECM) that regulates the LSCs niche [ 28 ], was highly expressed in clusters 8 and 16

summary:
In Homo sapiens, limbal fibroblasts and limbal stromal keratocytes are marked by high expression of fibulin 1 (FBLN1).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:f171617a13e11b28a104
claim_id: claim:f171617a13e11b28a104
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
A differential gene expression analysis between clusters 8 and 16, identified Osteoglycin ( OGN ) to be predominantly expressed in cluster 16 ( Figure S8D, E ). IF analysis ( Figure S8F-H ) showed a clear and distinct expression of OGN in the limbal, but not central cornea, hence we defined cluster 16 as limbal stromal keratocytes.

summary:
In Homo sapiens, limbal stromal keratocytes are marked by predominant expression of osteoglycin (OGN).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:cf07236c593dcc2a0c3b
claim_id: claim:cf07236c593dcc2a0c3b
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
High expression of Keratocan ( KERA ), encoding the keratan sulfate proteoglycan that is involved in corneal transparency [ 30 ], was found in cluster 3 and 12

summary:
In Homo sapiens, corneal stromal stem cells and corneal stroma keratocytes are marked by high expression of keratocan (KERA).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:10d3a5edc3b7eed37055
claim_id: claim:10d3a5edc3b7eed37055
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Differential gene expression analysis revealed Matrix Metallopeptidase 3 ( MMP3 ) expression in cluster 3, but not 12 ( Figure S9A ). IF localised the MMP3 immunopositive cells to the stroma of peripheral and central cornea ( Figure S9B-D ). All the MMP3-immunostained cells also showed expression of CD105 ( Figure S9E , E’), a marker of CSSCs [ 31 ], leading us to define cluster 3 as CSSCs.

summary:
In Homo sapiens, corneal stromal stem cells are marked by expression of matrix metallopeptidase 3 (MMP3) and CD105.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:a930842688c1f805650d
claim_id: claim:a930842688c1f805650d
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Clusters 15 and 17 were distinguished by the high expression of chemokine ligands ( CCL3 in cluster 15 and CCL5 in cluster 17) and were defined as immune cells I and II respectively

summary:
In Homo sapiens, immune cells type I are marked by high expression of CCL3 and immune cells type II are marked by high expression of CCL5.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:a08fd1b3d6acfd04f84e
claim_id: claim:a08fd1b3d6acfd04f84e
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
High expression of Transgelin ( TAGLN , also known as SM22α ; Fig. 1 B) and Actin Alpha 2 ( ACTA2 ; Figure S1 ) were found in cluster 13.

summary:
In Homo sapiens, fibroblastic corneal endothelial cells are marked by high expression of transgelin (TAGLN) and actin alpha 2 (ACTA2).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:4785b8919d16de0de6f8
claim_id: claim:4785b8919d16de0de6f8
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Clusters 11, 18 and 20 displayed high expression of the atypical chemokine receptor ( ACKR1 , also known as DARC, Fig. 1 B), whose expression is found on the endothelial cells of capillary and post-capillary venules

summary:
In Homo sapiens, endothelial cells of capillary and post-capillary venules are marked by high expression of atypical chemokine receptor 1 (ACKR1).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:d55f465a618a1ee0946a
claim_id: claim:d55f465a618a1ee0946a
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
IF revealed the presence of CDH19 immunopositive cells in the corneal endothelium ( Figure S11D-G ) and POSTN immunopositive cells in the blood vessels ( Figure S11H ), leading us to define clusters 20 and 11 as corneal endothelium and blood vessels, respectively.

summary:
In Homo sapiens, corneal endothelial cells are marked by CDH19 expression and blood vessel cells are marked by POSTN expression.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:09b92cc131932e0e38f8
claim_id: claim:09b92cc131932e0e38f8
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Cluster 14 showed high expression Hemoglobin Subunit Alpha 1 ( HBA1 ) and other genes present in red blood cells

summary:
In Homo sapiens, red blood cells are marked by high expression of hemoglobin subunit alpha 1 (HBA1).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:b4d74c58811df0a93f15
claim_id: claim:b4d74c58811df0a93f15
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
summary: In Homo sapiens, melanocytes are marked by high expression of TYRP1, PMEL, MLANA, MITF, and TYR.
span_literal:
Cluster 19 showed a high expression of pigmented cell markers including TYRP1, PMEL, MLANA, MITF and TYR ( Figs. 1B and S1 ), which led us to define this cluster as melanocytes.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:375e7bde09529dd721ac
claim_id: claim:375e7bde09529dd721ac
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Five markers namely GPHA2, CASP14, MMP10, MMP1 and AC093496.1 ( Lnc-XPC-2) were highly and predominantly expressed in cluster 9

summary:
In Homo sapiens, limbal progenitor cells are marked by high and predominant expression of GPHA2, CASP14, MMP10, MMP1, and AC093496.1 (Lnc-XPC-2).


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:75b3d95b54b78fc7c211
claim_id: claim:75b3d95b54b78fc7c211
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
span_literal:
Differential gene expression analysis identified several markers associated with limbal basal epithelium, including ITGA6 [ 57 ] , ITGB1 and VIM [ 58 ] in the additional cluster 1, defining it as cultured basal limbal epithelium

summary:
In Homo sapiens, cultured basal limbal epithelial cells are marked by expression of ITGA6, ITGB1, and VIM.


claim_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be:claim:7fae6c97bbe6e5d58666
claim_id: claim:7fae6c97bbe6e5d58666
paper_key: hca:0031_10.1016_j.jtos.2021.03.010_0c2fa1a2be
summary: In Homo sapiens, limbal suprabasal cells are marked by co-expression of KRT15 and CLDN4.
span_literal:
A dual plot gene expression heatmap showed the highest co-expression of KRT15 and CLDN4 in cell cluster 4 and to a lesser extent in cluster 0 ( Figure S6A ). IF with both antibodies showed the highest co-expression of these two markers in the suprabasal cells of the limbal crypt ( Figure S6B ), defining this cluster as limbal suprabasal cells.


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:c6cee6ff155579d9199c
claim_id: claim:c6cee6ff155579d9199c
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, carcinoma cells are marked by KRT8, KRT18, and EPCAM.
span_literal:
Cells from the malignant liver sites included carcinoma cells, marked by KRT8, KRT18, and EPCAM (Puram et al , 2017 ; Fig 1B )


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:2ca2793cca86c3543be2
claim_id: claim:2ca2793cca86c3543be2
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, scar-associated macrophages express the marker genes CD9, TREM2, CAPG, and GPNMB.
span_literal:
These cells express the marker genes CD9 and TREM2, a tumor suppressor in hepatocellular carcinoma (Tang et al , 2019 ), as well as the markers CAPG and GPNMB.


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:b929aa664263f9c7fcef
claim_id: claim:b929aa664263f9c7fcef
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, Kupffer cells express C1QB, MARCO, CD5L, and CD163.
span_literal:
Liver mononuclear phagocyte populations from the non‐malignant liver sites were composed of Kupffer cells, expressing C1QB, MARCO, CD5L, and CD163 (Appendix Fig S4 ).


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:a72e8c1923d998ee08aa
claim_id: claim:a72e8c1923d998ee08aa
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, regulatory T cells are marked by CTLA4 and FOXP3.
span_literal:
T cells from the malignant sites were predominantly composed of Tregs, marked by CTLA4 and FOXP3, whereas T‐cell populations from the non‐malignant sites were predominantly composed of cytotoxic T cells, expressing CCL5, GZMK, and NKG7 (Fig 2C ).


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:73f4ec1e35277619ae6d
claim_id: claim:73f4ec1e35277619ae6d
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, tissue monocytes 1 express FCN1 and S100A12.
span_literal:
tissue monocytes (TM1), expressing FCN1 and S100A12 (Ramachandran et al , 2019 ), and B cells (Fig 1C , Appendix Fig S4 ).


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:d2634259cf349fbcb55c
claim_id: claim:d2634259cf349fbcb55c
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, hepatic stellate cells are marked by retinol binding protein 1 (RBP1).
span_literal:
Hepatic stellate cells, marked by the retinol binding protein 1 (RBP1), and vascular smooth muscle cells, marked by Myosin‐11 (MYH11) (Ramachandran et al , 2019 ), were abundant in the non‐malignant liver sites (Fig 3A , Appendix Fig S1 C).


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:71cac210e6ed0e95115d
claim_id: claim:71cac210e6ed0e95115d
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
span_literal:
Cancer‐associated fibroblasts (CAFs), expressing extracellular matrix (ECM) genes such as COL1A1, LUM, and BGN, formed the larger cluster.

summary:
In Homo sapiens, cancer-associated fibroblasts express extracellular matrix genes such as COL1A1, LUM, and BGN.


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:a289512605af034ea3bf
claim_id: claim:a289512605af034ea3bf
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
summary: In Homo sapiens, pericytes are marked by RGS5 and CSPG4.
span_literal:
These markers included RGS5 and CSPG4, encoding the neuron‐glial antigen 2 protein (NG2) (Armulik et al , 2011 ).


claim_key: hca:0032_10.15252_msb.20209682_ea064ade0e:claim:40a56a0b11f9533a23db
claim_id: claim:40a56a0b11f9533a23db
paper_key: hca:0032_10.15252_msb.20209682_ea064ade0e
span_literal:
We found that some previously suggested markers of pericytes, such as DES (Nehls et al , 1992 ) and ANPEP (Kumar et al , 2017 ), were not specifically expressed in pericytes in the malignant human liver context (Dataset EV3 ).

summary:
In Homo sapiens, DES and ANPEP were not specifically expressed in pericytes in the malignant liver context.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:69b510428b6b699b63e5
claim_id: claim:69b510428b6b699b63e5
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
summary: In Homo sapiens, aquaporin 9 (AQP9) is a marker of principal cells in the epididymis.
span_literal:
One classical marker of principal cells in the mammalian epididymis is the water channel aquaporin 9 (AQP9)


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:18848edd84bd54d2e9cd
claim_id: claim:18848edd84bd54d2e9cd
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
The diagnostic marker for the ED is villin ( VIL1 ), which is apparently abundant in the ED epithelium but not seen in the caput epithelium in tissue sections

summary:
In Homo sapiens, villin (VIL1) is a positive marker of efferent duct epithelial cells and is not seen in the caput epididymis epithelium.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:0b388d01f16a6f14d635
claim_id: claim:0b388d01f16a6f14d635
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal: The most differentially express gene in this cluster is keratin 5
summary:
In Homo sapiens, keratin 5 (KRT5) is the most differentially expressed gene in basal cells of the epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:47e9c72d4c914a538ffd
claim_id: claim:47e9c72d4c914a538ffd
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Cluster 5 cells are spermatozoa based upon high expression of sperm proteins such as cilia and flagella associated protein 43 ( CFAP43 / WDR96 ) and the FOXJ1 transcription factor, which is diagnostic of ciliated cells.

summary:
In Homo sapiens, spermatozoa are identified by high expression of cilia and flagella associated protein 43 (CFAP43) and the FOXJ1 transcription factor.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:5570afee9ff331461a0c
claim_id: claim:5570afee9ff331461a0c
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Cluster 7 cells are clearly immune cells with multiple HLA peptides differentially expressed, suggestive of B-cells and the Fc Fragment of IgE Receptor Ig ( FCER1G ) gene, which encodes the Fc ε receptor that is strongly associated with monocytes and macrophages.

summary:
In Homo sapiens, immune cells in the epididymis differentially express multiple HLA peptides and FCER1G, with FCER1G being strongly associated with monocytes and macrophages.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:98bae784a8d4d3594483
claim_id: claim:98bae784a8d4d3594483
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
The most differentially over-expressed genes in cluster 0 include those encoding multiple antimicrobial peptides, including β defensins (DEFB118 [ Fig S2C and D ], 119 [ Fig 2C ], 121 and 123, all of which map to the 20q11 defensin gene cluster) and DEFB128 (at 20p13), and sperm-associated antigen 11A and 11B (SPAG11A/B [ Fig 3A–F ]).

summary:
In Homo sapiens, principal cells in the caput epididymis differentially overexpress DEFB118, DEFB119, DEFB121, DEFB123, DEFB128, SPAG11A, and SPAG11B.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:29cd78877a408d9afc8e
claim_id: claim:29cd78877a408d9afc8e
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also abundant in cluster 0 cells are transcripts for cystatin 11 ( CST11 ) a type 2 cysteine protease inhibitor

summary:
In Homo sapiens, cystatin 11 (CST11) transcripts are abundant in principal cells of the caput epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:0c17105061a69657850f
claim_id: claim:0c17105061a69657850f
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Adhesion G protein-coupled receptor G2 ( ADGR2 also known GPR64) and the serine protease inhibitor serpin family F member 2 ( SERPINF2 ), which are both androgen-responsive genes in human epididymis epithelial cells ( Yang et al, 2018 ), are also significantly over-expressed in cluster 0 cells.

summary:
In Homo sapiens, adhesion G protein-coupled receptor G2 (ADGRG2) and serpin family F member 2 (SERPINF2) are significantly overexpressed in principal cells of the caput epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:9faf48639e79b6cf782d
claim_id: claim:9faf48639e79b6cf782d
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also of note in this cluster are several lipocalins ( LCN6 , 8 , and 12 ), LCN8 is reported to be an epididymis specific lipocalin

summary:
In Homo sapiens, lipocalin 6 (LCN6), lipocalin 8 (LCN8), and lipocalin 12 (LCN12) are differentially expressed in principal cells of the caput epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:57d389e27fb4002deb47
claim_id: claim:57d389e27fb4002deb47
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
cluster 1 cells show differential expression of a different group of well characterized caput epididymis markers including epididymal protein 3A and 3B encoded by ( EDDM3A / 3B ) and cysteine-rich secretory protein 1 ( CRISP1 )

summary:
In Homo sapiens, apical and narrow cells in the caput epididymis differentially express epididymal secretory protein E3-alpha (EDDM3A), epididymal secretory protein E3-beta (EDDM3B), and cysteine-rich secretory protein 1 (CRISP1).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:98b2ef2392213667cb79
claim_id: claim:98b2ef2392213667cb79
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also abundant in cluster 1 cells are whey acidic protein four-disulfide core domain protein 8 and 9 ( WFDC8 / 9 )

summary:
In Homo sapiens, whey acidic protein four-disulfide core domain protein 8 (WFDC8) and whey acidic protein four-disulfide core domain protein 9 (WFDC9) are abundant in apical and narrow cells of the caput epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:073d762b1191640b0b3f
claim_id: claim:073d762b1191640b0b3f
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Transcripts from the Paired Box gene 2 transcription factor gene ( PAX2 ), which is known to direct a transcriptional network in urogenital cells including the epididymis cells ( Browne et al, 2018 , 2019 ) is also abundant in cluster 1.

summary:
In Homo sapiens, paired box gene 2 (PAX2) transcripts are abundant in apical and narrow cells of the caput epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:7b0573616fd8689c0939
claim_id: claim:7b0573616fd8689c0939
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Similarly over-expressed in cluster 1 cells are a group of β defensins. However, these are encoded by different genes than those seen in cluster 0 cells and include DEFB132 , DEFB129 , and DEFB127 , which map to the defensin gene cluster on chromosome 20p13, and DEFB110, DEFB134, and DEFB131, which are encoded by defensin gene clusters on three different chromosomes (6, 8, and 4, respectively).

summary:
In Homo sapiens, apical and narrow cells in the caput epididymis overexpress DEFB132, DEFB129, DEFB127, DEFB110, DEFB134, and DEFB131.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:9416015447b430d7dc03
claim_id: claim:9416015447b430d7dc03
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
In addition to the classical marker of basal cells in many epithelia, keratin 5 ( KRT5 ) ( Leir et al, 2020 ) ( Fig 6A and C ), which is the most DEG, the list of the top 25 DEGs show many that encode proteins involved in the cytoskeleton and extracellular matrix (Table S2).

summary:
In Homo sapiens, keratin 5 (KRT5) is a classical marker and the most differentially expressed gene in basal cells of the epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:f68063ab575335093900
claim_id: claim:f68063ab575335093900
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Among these are claudin 1 ( CLD1 ) ( Gregory et al, 2001 ), fibronectin ( FN1 ), integrin alpha 2 ( ITGA2 ), LIM domain and actin-binding protein 1 ( LIMA1 ), dystonin ( DST ), and keratin 17 ( KRT17 )

summary:
In Homo sapiens, basal cells in the epididymis differentially express claudin 1 (CLDN1), fibronectin 1 (FN1), integrin subunit alpha 2 (ITGA2), LIM domain and actin-binding protein 1 (LIMA1), dystonin (DST), and keratin 17 (KRT17).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:cd7abb0c727f580c079b
claim_id: claim:cd7abb0c727f580c079b
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also of note in cluster 3 are abundant transcripts from the TP63 gene ( Fig 6A, D, and E ), which encodes the p63 transcription factor, known as a marker of stem/progenitor cells in other epithelia such as the airway

summary:
In Homo sapiens, TP63 transcripts are abundant in basal cells of the epididymis, and TP63 is known as a marker of stem/progenitor cells.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:fd20afce9f291847a99c
claim_id: claim:fd20afce9f291847a99c
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Notable among DEGs in this group (Table S2) are vimentin ( VIM ) ( Fig 2C ), encoding the cytoskeletal intermediate filament protein found in non-epithelial cells such as mesenchymal cells, bone marrow stromal cell antigen 2 ( BST2 ) and myosin light chain 9 ( MYL9 ), a myosin regulatory subunit with a role in both smooth muscle and non-muscle cells.

summary:
In Homo sapiens, stromal/muscle cells in the epididymis differentially express vimentin (VIM), bone marrow stromal cell antigen 2 (BST2), and myosin light chain 9 (MYL9).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:28d99bf44f23fdd84624
claim_id: claim:28d99bf44f23fdd84624
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Other DEGs in this cluster include a number that encode proteins involved in actin filament polymerization and smooth muscle biology, for example, thymosin beta 4 X-linked ( TMSB4X ), gelsolin ( GSN ), and transgelin ( TAGLN ).

summary:
In Homo sapiens, stromal/muscle cells in the epididymis differentially express thymosin beta 4 X-linked (TMSB4X), gelsolin (GSN), and transgelin (TAGLN).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:0de20eb6ec2cb5bc76e8
claim_id: claim:0de20eb6ec2cb5bc76e8
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Differential expression of matrix gla protein ( MGP ) and SPARC-like protein 1 ( SPARCL1 ) also indicates that this cluster of cells may include blood vessel derivatives.

summary:
In Homo sapiens, stromal/muscle cells in the epididymis differentially express matrix gla protein (MGP) and SPARC-like protein 1 (SPARCL1).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:7bca0d1993ff441a300e
claim_id: claim:7bca0d1993ff441a300e
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
At the top of the DEG list is calcyphosine ( CAPS ), which encodes a calcium-binding protein with a predicted role in regulating ion transport.

summary:
In Homo sapiens, calcyphosine (CAPS) is the top differentially expressed gene in spermatozoa of the epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:73093c9fba3292f885b8
claim_id: claim:73093c9fba3292f885b8
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also among the DEGs is adenylate kinase ( AK1 ), which has a key role in energy metabolism, consistent with the motility requirements of sperm, and cation channel sperm associated auxiliary subunit delta ( CATSPERD ) a component of the CatSper complex involved in hyperactivation of sperm, which is required for sperm mobility.

summary:
In Homo sapiens, spermatozoa differentially express adenylate kinase 1 (AK1) and cation channel sperm associated auxiliary subunit delta (CATSPERD).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:cc9ae2b5b3f89561f551
claim_id: claim:cc9ae2b5b3f89561f551
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Another DEG with a predicted role in sperm motility role is tubulin polymerization promoting protein family member 3 ( TPPP3 ), the regulator of microtubule dynamics and bundling.

summary:
In Homo sapiens, tubulin polymerization promoting protein family member 3 (TPPP3) is a differentially expressed gene in spermatozoa.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:f332ad7e36b3cb081d0b
claim_id: claim:f332ad7e36b3cb081d0b
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Other DEGs with a role in the structure of motile cilia include radial spoke head component 1 ( RSPH1 ), the primary cilia formation ( PIFO ) gene, which has a role in cilia disassembly, multiple coiled-coil domain-containing protein genes such as cilia and flagella-associated protein 53 ( CFAP53 /formerly CCDC11 ) and 43 ( CFAP43 , also known as WDR96).

summary:
In Homo sapiens, spermatozoa differentially express radial spoke head component 1 (RSPH1), primary cilia formation gene (PIFO), cilia and flagella-associated protein 53 (CFAP53), and cilia and flagella-associated protein 43 (CFAP43).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:7fa3097233e44db057eb
claim_id: claim:7fa3097233e44db057eb
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Consistent with the importance of cilia in these cells is the identification of the forkhead box J1 ( FOXJ1 ) transcription factor as a DEG.

summary:
In Homo sapiens, forkhead box J1 (FOXJ1) is a differentially expressed gene in spermatozoa of the epididymis.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:90cdc5ac50f5bf0281d0
claim_id: claim:90cdc5ac50f5bf0281d0
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also relevant to sperm function is dynein light chain roadblock-type 2 ( DYNLRB2 ), which encodes an accessory component of the cellular motor dynein that facilitates movement of cargo along intracellular microtubules.

summary:
In Homo sapiens, dynein light chain roadblock-type 2 (DYNLRB2) is a differentially expressed gene in spermatozoa.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:0412d005043f860af442
claim_id: claim:0412d005043f860af442
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
known markers of spermatogenesis were also identified as DEGs, such as meiosis-specific nuclear structural 1 ( MNS1 ) and rhophilin-associated tail protein 1 like ( ROPN1L ).

summary:
In Homo sapiens, meiosis-specific nuclear structural 1 (MNS1) and rhophilin-associated tail protein 1 like (ROPN1L) are differentially expressed genes in spermatozoa.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:7830d3e6f6cf54e5aae1
claim_id: claim:7830d3e6f6cf54e5aae1
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
For example, at the top of the DEG list are several subunits of the vacuolar ATPase, including cytosolic ATPase H+ transporting V1 subunits G3, A and B ( ATP6V1G3 [ Fig 7A and C ], ATP6V1A , and ATP6V1B1 ) and transmembrane ATPase H+ transporting V0 subunit D2 ( ATP6V0D2 ) and A4 ( ATP6V0A4 ).

summary:
In Homo sapiens, clear cells in the epididymis differentially express ATP6V1G3, ATP6V1A, ATP6V1B1, ATP6V0D2, and ATP6V0A4.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:b8e09576aa7fffb307ca
claim_id: claim:b8e09576aa7fffb307ca
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
However, also among the most significant DEGs is FOXI1 ( Fig 7G ) and though of lower significance, but still among DEGs, are both CFTR ( Fig 7F ) and the gene encoding the α subunit of the epithelial sodium channel ( SCNN1A ).

summary:
In Homo sapiens, clear cells in the epididymis differentially express forkhead box I1 (FOXI1), CFTR, and the alpha subunit of the epithelial sodium channel (SCNN1A).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:06c31793012f807d3b8e
claim_id: claim:06c31793012f807d3b8e
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
At the top of the DEG list (Table S2) are several HLA molecules including Class II MHC molecules HLA-DRA.1 , DPA1.1 , DPB1.1 , DRB1.1 , and DQB1.1 indicative of antigen-presenting cells.

summary:
In Homo sapiens, immune cells in the epididymis differentially express HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1, and HLA-DQB1, indicative of antigen-presenting cells.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:73fb3d580e8f84f349c3
claim_id: claim:73fb3d580e8f84f349c3
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Based on additional DEGs, including CD22, which mediates B-cell interactions, together with the absence of T-lymphocyte–specific DEGs suggests the cluster contains a majority of B cells.

summary:
In Homo sapiens, CD22 is a differentially expressed gene in immune cells of the epididymis, mediating B cell interactions.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:146362c71606baf1b293
claim_id: claim:146362c71606baf1b293
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Also present are macrophages/monocytes as evidenced by the DEG Fc fragment of IgE receptor Ig ( FCER1G ), which is a macrophage/monocyte marker not expressed on B cells.

summary:
In Homo sapiens, Fc fragment of IgE receptor Ig (FCER1G) is a marker of macrophages/monocytes in the epididymis and is not expressed on B cells.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:27f92b2bf6592e4f0856
claim_id: claim:27f92b2bf6592e4f0856
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
Other abundant transcripts in ED cells include asparaginase and isoaspartyl peptidase 1 ( ASRGL1 ) a gene associated with prostate cancer ( Pudova et al, 2019 ), the estrogen receptor ( ESR1 , Fig 5C ) and FXYD domain containing ion transport regulator 2 ( FXYD2 ) that encodes the sodium/potassium-transporting ATPase subunit γ, which is involved in renal transport

summary:
In Homo sapiens, efferent duct cells differentially express asparaginase and isoaspartyl peptidase 1 (ASRGL1), estrogen receptor 1 (ESR1), and FXYD domain containing ion transport regulator 2 (FXYD2).


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:881473a3d0d3be415704
claim_id: claim:881473a3d0d3be415704
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
summary: In Homo sapiens, principal cells in the caput epididymis express little or no CFTR mRNA.
span_literal:
Here, we show that in the caput epididymis, most principal cells, which are the most abundant surface epithelial cell type, express little or no CFTR mRNA.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:a0f5fe6893f903bae88d
claim_id: claim:a0f5fe6893f903bae88d
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
In contrast, clear cells (cluster 6), which express high levels of genes encoding the V-ATPase hydrogen pump along with ENaC, the epithelial sodium channel, are also the primary location of abundant CFTR.

summary:
In Homo sapiens, clear cells in the epididymis express high levels of V-ATPase, epithelial sodium channel (ENaC), and abundant CFTR.


claim_key: hca:0033_10.26508_lsa.202000744_340b92b825:claim:4468a850deebc58e25c6
claim_id: claim:4468a850deebc58e25c6
paper_key: hca:0033_10.26508_lsa.202000744_340b92b825
span_literal:
The scRNA-seq data presented here shows TP63 is a highly significant DEG among the basal cells in cluster 3, with a subpopulation having very high expression levels.

summary:
In Homo sapiens, TP63 is a highly significant differentially expressed gene in basal cells of the epididymis.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:abb8ef22187d0456e97d
claim_id: claim:abb8ef22187d0456e97d
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
triple-negative BC cell lines (11 out of 15) show a basal-like phenotype with the expression of at least one of keratin 5, 14 or 17

summary:
In Homo sapiens, triple-negative breast cancer cell lines show a basal-like phenotype with expression of at least one of keratin 5 (KRT5), keratin 14 (KRT14), or keratin 17 (KRT17).


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:8e4820236628113f53a8
claim_id: claim:8e4820236628113f53a8
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
triple-negative subtype B (TNB) cell lines also expressing vimentin (VIM) and Collagen Type VI Alpha Chains (COL6A1, COL6A2, COL6A3)

summary:
In Homo sapiens, triple-negative subtype B breast cancer cell lines express vimentin (VIM) and Collagen Type VI Alpha Chains (COL6A1, COL6A2, COL6A3).


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:b621eb46f8df0e2baa6d
claim_id: claim:b621eb46f8df0e2baa6d
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
the non-tumorigenic MCF12A cell line lacks expression of ESR1, PGR and HER2 and displays a basal-like phenotype characterized by the expression of all basal-like marker genes including keratin 5, 14, 17 and TP63, in agreement with the literature

summary:
In Homo sapiens, the non-tumorigenic MCF12A cell line lacks expression of estrogen receptor 1 (ESR1), progesterone receptor (PGR), and Erb-B2 Receptor Tyrosine Kinase 2 (HER2), and expresses basal-like markers including KRT5, KRT14, KRT17, and TP63.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:f2223d2f2ad436acb237
claim_id: claim:f2223d2f2ad436acb237
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
clusters in the luminal island ([Figure 1G](433590v4_fig1.tif)) were associated to genes involved in cancer progression (BCAS330,31 cluster 2), dissemination (SCGB2A232,33 cluster 6), proliferation (DRAIC34,35 cluster 1), migration and invasion (CLCA236,37 cluster 8 and PIP38 cluster 18)

summary:
In Homo sapiens, luminal breast cancer cluster 2 is marked by BCAS3, cluster 6 by SCGB2A2, cluster 1 by DRAIC, cluster 8 by CLCA2, and cluster 18 by PIP.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:b70d51c25017ec2128a4
claim_id: claim:b70d51c25017ec2128a4
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
clusters in the luminal island ([Figure 1G](433590v4_fig1.tif)) were associated to genes involved in cancer progression (BCAS330,31 cluster 2), dissemination (SCGB2A232,33 cluster 6), proliferation (DRAIC34,35 cluster 1), migration and invasion (CLCA236,37 cluster 8 and PIP38 cluster 18)

summary:
In Homo sapiens, luminal breast cancer cluster 6 is marked by SCGB2A2, associated with cancer dissemination.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:68ab1933ec2926b4f6ad
claim_id: claim:68ab1933ec2926b4f6ad
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
clusters in the luminal island ([Figure 1G](433590v4_fig1.tif)) were associated to genes involved in cancer progression (BCAS330,31 cluster 2), dissemination (SCGB2A232,33 cluster 6), proliferation (DRAIC34,35 cluster 1), migration and invasion (CLCA236,37 cluster 8 and PIP38 cluster 18)

summary:
In Homo sapiens, luminal breast cancer cluster 1 is marked by DRAIC, associated with cancer proliferation.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:5fbad6d0f28ea90e6b99
claim_id: claim:5fbad6d0f28ea90e6b99
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
summary:
In Homo sapiens, luminal breast cancer cluster 8 is marked by CLCA2, associated with cancer migration and invasion.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:e23e3ebcf2d2c583d09f
claim_id: claim:e23e3ebcf2d2c583d09f
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
summary:
In Homo sapiens, luminal breast cancer cluster 18 is marked by PIP, associated with cancer migration and invasion.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:95c317bf8f18ee496dc3
claim_id: claim:95c317bf8f18ee496dc3
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
one subset of triple-negative patients strongly expresses the protease kallikrein-10 (KLK10), which has been associated with poor prognosis, poor response to tamoxifen treatment

summary:
In Homo sapiens, a subset of triple-negative breast cancer patients strongly expresses kallikrein-10 (KLK10), which has been associated with poor prognosis.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:465b0e2ef681dcfc7fd6
claim_id: claim:465b0e2ef681dcfc7fd6
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
a second subset is characterised by actin gamma 2 expression (ACTG2), which has been linked in BC to cell proliferation

summary:
In Homo sapiens, a second subset of triple-negative breast cancer patients is characterized by actin gamma 2 (ACTG2) expression.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:6a945fbeb01adeed78a2
claim_id: claim:6a945fbeb01adeed78a2
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
span_literal:
Luminal cell lines highly express luminal epithelium genes, but neither basal epithelial nor stromal markers

summary:
In Homo sapiens, luminal breast cancer cell lines highly express luminal epithelium genes but lack basal epithelial and stromal markers.


claim_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb:claim:c69f0ab2ff73262b409e
claim_id: claim:c69f0ab2ff73262b409e
paper_key: hca:0035_10.1101_2021.03.02.433590_8f70c6deeb
summary: In Homo sapiens, the HER2 overexpressing cell lines JIMT1 and HCC1954 express keratin 5 (KRT5).
span_literal:
two out of five HER2 overexpressing (HER2+) cell lines (JIMT1 and HCC1954) in the atlas are in the triple-negative “archipelago” and express keratin 5 (KRT5)


claim_key: hca:0036_10.1016_j.cell.2021.10.024_2ce0b899c4:claim:a11e01df62efd41513d8
claim_id: claim:a11e01df62efd41513d8
paper_key: hca:0036_10.1016_j.cell.2021.10.024_2ce0b899c4
span_literal:
we discovered DA cCREs at loci encoding marker genes of pre-natal myocytes including MYH3 and MYH8 , the heavy chains of embryonic and neonatal myosin respectively, as well as markers of type I (slow) and type II (fast) twitch adult myocytes including MYH6/MYH7 and MYH1/MYH2 respectively

summary:
In Homo sapiens, MYH3 and MYH8 are marker genes of pre-natal myocytes, while MYH6 and MYH7 are markers of type I (slow) twitch adult skeletal myocytes, and MYH1 and MYH2 are markers of type II (fast) twitch adult skeletal myocytes.


claim_key: hca:0036_10.1016_j.cell.2021.10.024_2ce0b899c4:claim:de22280592ae6ee5f9c9
claim_id: claim:de22280592ae6ee5f9c9
paper_key: hca:0036_10.1016_j.cell.2021.10.024_2ce0b899c4
span_literal:
Notably, cardiac fibroblasts were accessible at loci encoding cardiac developmental transcription factors GATA4 and TBX20

summary:
In Homo sapiens, cardiac fibroblasts show chromatin accessibility at loci encoding the cardiac developmental transcription factors GATA4 and TBX20.


claim_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e:claim:4265cf6d6ba061e377df
claim_id: claim:4265cf6d6ba061e377df
paper_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e
span_literal: PCDH15 and MEGF11 for OPCs
summary:
In Homo sapiens entorhinal cortex, oligodendrocyte progenitor cells are marked by PCDH15 and MEGF11.


claim_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e:claim:65597ba547075e139447
claim_id: claim:65597ba547075e139447
paper_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e
summary: In Homo sapiens entorhinal cortex, KCNQ3 was identified as a novel marker gene for microglia.
span_literal:
our analyses identified several putative novel specific cell-type marker genes (Supplementary Table 2 ), including KCNQ3 in microglia


claim_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e:claim:bec68c8f96090e453958
claim_id: claim:bec68c8f96090e453958
paper_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e
summary: In Homo sapiens entorhinal cortex, ADGRV1 was identified as a novel astrocyte-specific marker gene.
span_literal:
We also identified a novel astrocyte-specific gene, ADGRV1 , which encodes the nervous system-restricted calcium-binding G-protein-coupled receptor GPR98, mutations in which cause Usher disease


claim_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e:claim:2409a5e8f56e369f53e4
claim_id: claim:2409a5e8f56e369f53e4
paper_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e
span_literal:
several previously described microglia-specific GWAS genes, including INPP5D , HLA−DRB5 , PLCG2 , HLA−DRB1 , CSF3R , and MS4A6A , showed highly specific expression in microglia

summary:
In Homo sapiens entorhinal cortex, INPP5D, HLA-DRB5, PLCG2, HLA-DRB1, CSF3R, and MS4A6A showed highly specific expression in microglia.


claim_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e:claim:a48f73d4ab8e893dd50b
claim_id: claim:a48f73d4ab8e893dd50b
paper_key: hca:0037_10.1038_s41593-019-0539-4_24ef44df9e
summary: In Homo sapiens entorhinal cortex, RIN3 and TBXAS1 were detected as microglia-specific genes.
span_literal:
we detected two microglia-specific GWAS genes not previously associated with microglia, RIN3 and TBXAS1


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:675f51aa3943398f1743
claim_id: claim:675f51aa3943398f1743
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
Some of the visceral samples included cells that appeared to be endometrial in origin ( PRLR +), likely due to endometriosis.

summary:
In Homo sapiens, endometrial cells in visceral adipose tissue are positive for PRLR (prolactin receptor).


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:ecc18066cd146b02cfe5
claim_id: claim:ecc18066cd146b02cfe5
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
We identified six distinct subpopulations of human ASPCs in subclustered scRNA-seq and sNuc-seq samples, all of which express the common marker gene PDGFRA

summary:
In Homo sapiens, all adipose stem and progenitor cell subpopulations express the common marker gene PDGFRA.


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:aff37ef5138d19ebea91
claim_id: claim:aff37ef5138d19ebea91
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
summary: In Homo sapiens, adipose stem and progenitor cell 2 is characterized by high expression of ALDH1A3.
span_literal:
mASPC2 and hASPC2 are both characterized by high expression of Aldh1a3/ALDH1A3 , and strongly resemble previously identified early multipotent progenitor cells that reside in the reticular interstitium of the fat pad


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:91831cf67369fdde87fa
claim_id: claim:91831cf67369fdde87fa
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
summary: In Homo sapiens, adipose stem and progenitor cell 4 expresses EPHA3.
span_literal:
Similarly, mASPC4 and hASPC4 express Epha3/EPHA3 and likely represent the anti-adipogenic Areg population reported by Schwalie et. al.


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:41153349f44778514b3a
claim_id: claim:41153349f44778514b3a
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
summary: In Homo sapiens, macrophages in white adipose tissue are positive for CD14.
span_literal:
Analysis of human immune cells from scRNA-seq and sNuc-seq samples again revealed expected cell types, including multiple subpopulations of monocytes, macrophages ( CD14 +), dendritic cells (DCs), B and T lymphocytes, and NK cells ( CD96 +), mast cells ( CPA3 +), and neutrophils ( CSF3R +)


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:74d5378564719812fc19
claim_id: claim:74d5378564719812fc19
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
summary:
In Homo sapiens, neutrophils in white adipose tissue are positive for CSF3R (colony stimulating factor 3 receptor).


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:a333db6d29e8e2cf560b
claim_id: claim:a333db6d29e8e2cf560b
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
summary: In Homo sapiens, dendritic cell subpopulation 1 in white adipose tissue is positive for CLEC9A.
span_literal:
DC subpopulations 1 and 2 resemble previously reported CLEC9A + and CD1C + populations from blood, respectively


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:bfa806e10e15a7fd8346
claim_id: claim:bfa806e10e15a7fd8346
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
Lymphocytes also resemble previously reported B cell, T Cell, and NK cell populations from human WAT, including CTLA4 + hTregs

summary:
In Homo sapiens, regulatory T cells in white adipose tissue are positive for CTLA4 (cytotoxic T-lymphocyte associated protein 4).


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:a136eb1f967a0c2282d7
claim_id: claim:a136eb1f967a0c2282d7
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
One particularly interesting adipocyte subpopulation is hAd6, which selectively expresses genes typically associated with thermogenesis, such as EBF2 , ESRRG , and PPARGC1A

summary:
In Homo sapiens, adipocyte subpopulation hAd6 selectively expresses EBF2, ESRRG, and PPARGC1A, genes typically associated with thermogenesis.


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:068e661133d1695e84b5
claim_id: claim:068e661133d1695e84b5
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
Thus, the adipokines adiponectin and adipsin ( CFD ) are most highly expressed in hAd3, and insulin signaling components like INSR , IRS1 and IRS2 are most highly expressed in hAd5

summary:
In Homo sapiens, adipocyte subpopulation hAd3 most highly expresses the adipokine adipsin (CFD), and adipocyte subpopulation hAd5 most highly expresses insulin signaling components INSR, IRS1, and IRS2.


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:111a7f3c3c978ae5a386
claim_id: claim:111a7f3c3c978ae5a386
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
Thus, the adipokines adiponectin and adipsin ( CFD ) are most highly expressed in hAd3, and insulin signaling components like INSR , IRS1 and IRS2 are most highly expressed in hAd5

summary:
In Homo sapiens, adipocyte subpopulation hAd5 most highly expresses insulin signaling components INSR, IRS1, and IRS2.


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:469cb18694e1797b5141
claim_id: claim:469cb18694e1797b5141
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
hAd3 was associated with “triglyceride biosynthesis” and included higher expression of DGAT2 , SREBF1 , and PNPLA3

summary:
In Homo sapiens, adipocyte subpopulation hAd3 has higher expression of DGAT2, SREBF1, and PNPLA3, associated with triglyceride biosynthesis.


claim_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981:claim:9d505f625d4f9ee7c2a0
claim_id: claim:9d505f625d4f9ee7c2a0
paper_key: hca:0038_10.1038_s41586-022-04518-2_c7bd3c9981
span_literal:
The hAd4 cluster expresses the highest amounts of several fatty acid desaturases, including ELOVL5 and FADS3

summary:
In Homo sapiens, adipocyte subpopulation hAd4 expresses the highest amounts of fatty acid desaturases including ELOVL5 and FADS3.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:2703bf46664ce921f380
claim_id: claim:2703bf46664ce921f380
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal: MSCs were characterized by the higher expression of FRZB, NOTCH3 , THY1 , and MYH11
summary:
In Homo sapiens dental pulp, mesenchymal stem cells are characterized by higher expression of FRZB, NOTCH3, THY1, and MYH11.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:d74dd05091a4edd074a9
claim_id: claim:d74dd05091a4edd074a9
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Fibroblasts were characterized by the expression of collagen-coding genes (e.g., COL1A1 ; logFC = 0.91 and adjusted p value <0.001) and MDK (logFC = 1.44 and adjusted p value <0.001), a gene whose expression is restricted to the dental mesenchyme during mouse odontogenesis ( Mitsiadis et al., 1995 ), as well as by the reduced expression of FRZB (logFC = −0.76 and adjusted p value <0.001; Figures 1 B–1D).

summary:
In Homo sapiens dental pulp, fibroblasts are characterized by expression of COL1A1 and MDK and by reduced expression of FRZB.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:6de00ff548bdd57ceca0
claim_id: claim:6de00ff548bdd57ceca0
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Odontoblasts were characterized by the expression of dentin sialophosphoprotein ( DSPP ) ( Figure 1 I) and dentin matrix acidic phosphoprotein 1 ( DMP1 ), genes encoding for phosphoproteins that constitute essential components of the dentin matrix

summary:
In Homo sapiens dental pulp, odontoblasts are characterized by expression of dentin sialophosphoprotein (DSPP) and dentin matrix acidic phosphoprotein 1 (DMP1).


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:305b8cd9a951e4e27b03
claim_id: claim:305b8cd9a951e4e27b03
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal: A first cluster was characterized by the expression of EDN1/CLDN5 and represented arterial ECs
summary:
In Homo sapiens dental pulp, arterial endothelial cells are characterized by expression of EDN1 and CLDN5.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:6678c5ef77d54b899778
claim_id: claim:6678c5ef77d54b899778
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
A second endothelial cluster was characterized by the expression of ACKR1/CD234 ( Figures 1 I and S4 ) and represented postcapillary and collecting venules.

summary:
In Homo sapiens dental pulp, postcapillary and collecting venule endothelial cells are characterized by expression of ACKR1/CD234.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:373dfd338781c3505f5c
claim_id: claim:373dfd338781c3505f5c
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
The third main endothelial cluster was characterized by the expression of the insulin receptor ( INSR ) and RGCC

summary:
In Homo sapiens dental pulp, the third endothelial cell cluster is characterized by expression of insulin receptor (INSR) and RGCC.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:9139530366e5f32f4862
claim_id: claim:9139530366e5f32f4862
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
summary: In Homo sapiens dental pulp, T cells are characterized by expression of PTPRC and CD3E.
span_literal:
This cluster mostly consisted of T cells and macrophages, characterized by the expression of PTPRC , CD3E , and CSF1R


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:3ad28dce0c4259846c89
claim_id: claim:3ad28dce0c4259846c89
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
ScCs formed two clearly distinct clusters of SOX10 + cells, identified as myelinating MBP + -ScCs and non-myelinating GFRA3 + -ScCs

summary:
In Homo sapiens dental pulp, Schwann cells express SOX10, with myelinating Schwann cells expressing MBP and non-myelinating Schwann cells expressing GFRA3.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:ca7f2cfb6a95ad4517b8
claim_id: claim:ca7f2cfb6a95ad4517b8
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
ScCs formed two clearly distinct clusters of SOX10 + cells, identified as myelinating MBP + -ScCs and non-myelinating GFRA3 + -ScCs

summary:
In Homo sapiens dental pulp, non-myelinating Schwann cells are characterized by expression of GFRA3.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:33cd882884b4ebd083db
claim_id: claim:33cd882884b4ebd083db
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
summary: In Homo sapiens dental pulp, epithelial cells express KRT14, KRT5, and stratifin (SFN).
span_literal:
These epithelial cells express keratin-coding genes such as KRT14 and KRT5 , as well as s tratifin ( SFN )


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:f9b335dda5feabf69a83
claim_id: claim:f9b335dda5feabf69a83
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
We finally identified a population of erythrocytes that is characterized by the presence of the beta- hemoglobin-coding transcript HBB .

summary:
In Homo sapiens dental pulp, erythrocytes are characterized by expression of the beta-hemoglobin-coding transcript HBB.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:c430f489cda9089d37b2
claim_id: claim:c430f489cda9089d37b2
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
summary: In Homo sapiens periodontium, mesenchymal stem cells express FRZB, NOTCH3, MYH11, and THY1.
span_literal:
We detected a cluster of MSCs expressing FRZB , NOTCH3 , MYH11 , and THY1 (logFC of 1.83, 1.24, 1.47, and 1.61, respectively, and adjusted p value <0.001, compared to other cells in the periodontium; Figures 2 B and 2C).


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:8c366af3dfd305062ea3
claim_id: claim:8c366af3dfd305062ea3
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
summary: In Homo sapiens periodontium, fibroblasts are defined by expression of MDK and COL1A1.
span_literal:
The fibroblastic compartment was defined by cells expressing MDK (logFC = 1.25 and adjusted p value < 0.001; Figure 2 C) and collagen-coding genes such as COL1A1 ( Figures 2 B and 2C; logFC = 3.42 and adjusted p value < 0.001).


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:803795d527355694dd18
claim_id: claim:803795d527355694dd18
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
The periodontium was characterized by the presence of PTPRC + immune cells, including T cells ( CD3E + /CD3D + ), B cells ( MZB1 + ), monocytes, and macrophages (CSF1R + )

summary:
In Homo sapiens periodontium, immune cells express PTPRC, T cells express CD3E and CD3D, B cells express MZB1, and macrophages express CSF1R.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:c7b7caad4802436c7e1d
claim_id: claim:c7b7caad4802436c7e1d
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Epithelial cells formed different subclusters, characterized by the expression of epithelial genes such as KRT14 and ODAM , signaling molecules such as WNT10A , and specific sets of interleukin-coding genes such as IL1A and IL1B

summary:
In Homo sapiens periodontium, epithelial cells are characterized by expression of KRT14, ODAM, WNT10A, IL1A, and IL1B.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:ca36f1307db6d58fe0f3
claim_id: claim:ca36f1307db6d58fe0f3
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Both compartments contained two main MSC clusters characterized by increased expression of MYH11 (logFC = 2.00 and p value <0.001) and THY1 (logFC = 1.63 and p value <0.001), respectively, when compared to all other clusters

summary:
In Homo sapiens dental pulp and periodontium, two main mesenchymal stem cell clusters are characterized by increased expression of MYH11 and THY1, respectively.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:22559ac21218b4ea919b
claim_id: claim:22559ac21218b4ea919b
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
We detected a second THY1 -positive (and MYH11 -negative) MSC cluster, with increased expression of CCL2 (logFC = 3.46 and p value <0.001 when compared to other clusters; Figures 3 B and 3D).

summary:
In Homo sapiens, a CCL2-positive mesenchymal stem cell subcluster is THY1-positive and MYH11-negative, with increased expression of CCL2.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:9310920b7d76d1a6e435
claim_id: claim:9310920b7d76d1a6e435
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
summary: In Homo sapiens, the CCL2-positive mesenchymal stem cell cluster expresses TNC (tenascin C).
span_literal:
The CCL2 + MSC cluster also expressed genes associated with the remodeling of the extracellular matrix, such as TNC (tenascin C)


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:2715c85d22f86cd7e7ce
claim_id: claim:2715c85d22f86cd7e7ce
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
ACTA2 , RERGL , and PLN (phospholamban) are particularly enriched in the MYH11 + MSC subcluster, while DCN (decorin) and STEAP4 are highly expressed in the THY1 + MSC subcluster.

summary:
In Homo sapiens, ACTA2, RERGL, and PLN (phospholamban) are enriched in the MYH11-positive mesenchymal stem cell subcluster, while DCN (decorin) and STEAP4 are highly expressed in the THY1-positive mesenchymal stem cell subcluster.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:b4661b39ee2adbf80379
claim_id: claim:b4661b39ee2adbf80379
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
ACTA2 , RERGL , and PLN (phospholamban) are particularly enriched in the MYH11 + MSC subcluster, while DCN (decorin) and STEAP4 are highly expressed in the THY1 + MSC subcluster.

summary:
In Homo sapiens, DCN (decorin) and STEAP4 are highly expressed in the THY1-positive mesenchymal stem cell subcluster.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:891cf2e0d9986fd2b3bc
claim_id: claim:891cf2e0d9986fd2b3bc
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
MCAM/CD164 is a classical marker of MSCs in dental and non-dental tissues ( Shi and Gronthos, 2003 ).

summary:
In Homo sapiens, MCAM/CD146 is a classical marker of mesenchymal stem cells in dental and non-dental tissues.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:af471cda44b3cd5642a3
claim_id: claim:af471cda44b3cd5642a3
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal: RGS5 expression marks the perivascular NOTCH3 + MSCs in the dental pulp ( Lovschall et al., 2007 ).
summary:
In Homo sapiens dental pulp, RGS5 expression marks perivascular NOTCH3-positive mesenchymal stem cells.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:e23069f35f8efb55654e
claim_id: claim:e23069f35f8efb55654e
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Most MSCs populations express ID4 , which codes for a transcription factor that inhibits cell differentiation ( Junankar et al., 2015 ; Patel et al., 2015 ).

summary:
In Homo sapiens, most mesenchymal stem cell populations express ID4, a transcription factor that inhibits cell differentiation.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:3b6b5ebac0b4cc41062f
claim_id: claim:3b6b5ebac0b4cc41062f
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
THY1 / CD90 is a general marker of human mesenchymal stem cells, and it is vastly used to sort human dental pulp stem cells ( Dominici et al., 2006 ; Ledesma-Martinez et al., 2016 ; Sharpe, 2016 ).

summary:
In Homo sapiens, THY1/CD90 is a general marker of mesenchymal stem cells and is used to sort dental pulp stem cells.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:0fffb7ab9e2de1358074
claim_id: claim:0fffb7ab9e2de1358074
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
MSCs in the human dental pulp and periodontium are characterized by the expression of FRZB , NOTCH3 , THY1 , and MYH11

summary:
In Homo sapiens, mesenchymal stem cells in the dental pulp and periodontium are characterized by expression of FRZB, NOTCH3, THY1, and MYH11.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:7db7913845601722a040
claim_id: claim:7db7913845601722a040
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Both dental pulp and periodontium MSCs can be subdivided into subpopulations characterized by the expression of the same specific markers MYH11 , THY1 , and CCL2 .

summary:
In Homo sapiens, dental pulp and periodontium mesenchymal stem cells can be subdivided into subpopulations characterized by expression of MYH11, THY1, and CCL2.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:4e05bd2bb604a14cfab4
claim_id: claim:4e05bd2bb604a14cfab4
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
summary: In Homo sapiens, dental pulp mesenchymal stem cells strongly express KRT18.
span_literal:
Surprisingly, dental pulp MSCs strongly expressed KRT18 , a gene previously reported to be exclusively expressed in cells of single-layered and pseudostratified epithelia (logFC = 1.46, p value < 0.001; Table S1 , Figure S10 ).


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:4e3ee8c995b2212c83b1
claim_id: claim:4e3ee8c995b2212c83b1
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
In contrast to the periodontal MSCs, dental pulp MSCs expressed higher levels of CXCL14 and RARRES1 (logFC = 2.04 and 1.00, respectively, and p values < 0.001; Figure 3 H; Table S1 ).

summary:
In Homo sapiens, dental pulp mesenchymal stem cells express higher levels of CXCL14 and RARRES1 compared to periodontal mesenchymal stem cells.


claim_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60:claim:1b3fe2a433d5a8c44e2a
claim_id: claim:1b3fe2a433d5a8c44e2a
paper_key: hca:0039_10.1016_j.isci.2021.102405_1f6d3fbc60
span_literal:
Periodontal MSCs were also characterized by higher expression of SPARC /o steonectin , a secreted molecule fundamental for the regulation of periodontal homeostasis and collagen content (logFC = 1.00 and p value < 0.001; Figure 3 H; Tables S1 and S6 ).

summary:
In Homo sapiens, periodontal mesenchymal stem cells are characterized by higher expression of SPARC/osteonectin.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:e28bbb8b72166d4e3254
claim_id: claim:e28bbb8b72166d4e3254
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Flow-cytometry-based marker profiling and gene expression portraits have identified three major epithelial cell types in the breast, including basal/stem (CD49f+/EpCAM−), luminal progenitors (CD49f+/EpCAM+), and mature luminal (CD49f−/EpCAM+) cells.

summary:
In Homo sapiens breast, basal/stem cells are positive for CD49f (ITGA6) and negative for EpCAM, luminal progenitor cells are positive for both CD49f and EpCAM, and mature luminal cells are negative for CD49f and positive for EpCAM.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:e78dd83fec2bb35bfde3
claim_id: claim:e78dd83fec2bb35bfde3
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
summary: In Homo sapiens breast, TP63 and NFIB are enriched transcription factors in basal/stem cells.
span_literal:
Cell-type enriched transcription factor networks, such as TP63/NFIB , ELF5/EHF , and FOXA1/ESR1 , control gene expression patterns in basal/stem, luminal progenitor, and mature luminal cells, respectively.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:4625d4cb852057c94d63
claim_id: claim:4625d4cb852057c94d63
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Cell-type enriched transcription factor networks, such as TP63/NFIB , ELF5/EHF , and FOXA1/ESR1 , control gene expression patterns in basal/stem, luminal progenitor, and mature luminal cells, respectively.

summary:
In Homo sapiens breast, ELF5 and EHF are enriched transcription factors in luminal progenitor cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:5c5881d5457d2dc2de29
claim_id: claim:5c5881d5457d2dc2de29
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
summary: In Homo sapiens normal breast, basal/stem cell cluster 5 expresses higher levels of NDUFA4L2.
span_literal:
For example, cluster 5 expressed higher levels of NDUFA4L2 , a mitochondrial NADPH dehydrogenase ( Figure 2 A).


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:68302aef04f9c5ad09ae
claim_id: claim:68302aef04f9c5ad09ae
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
This cluster also expressed higher levels of CD36 , a lipid transporter associated with breast cancer metastasis, as well as Vimentin , a marker of basal cells.

summary:
In Homo sapiens normal breast, basal/stem cell cluster 5 expresses higher levels of CD36 and Vimentin.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:6eae11b5d6642ec8acdf
claim_id: claim:6eae11b5d6642ec8acdf
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
For example, although all luminal progenitor cells expressed secreted fizzled related protein 1 ( SFRP1 ), a modulator of Wnt signaling, 28 genes such as SLP1 , ANXA1 , RARRES1 , KLK5 , and KRT15 were enriched in cluster 2.

summary:
In Homo sapiens normal breast, all luminal progenitor cells express SFRP1, and luminal progenitor cluster 2 is enriched for SLP1, ANXA1, RARRES1, KLK5, and KRT15.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:82526309a257cb05f9b0
claim_id: claim:82526309a257cb05f9b0
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
For example, although all luminal progenitor cells expressed secreted fizzled related protein 1 ( SFRP1 ), a modulator of Wnt signaling, 28 genes such as SLP1 , ANXA1 , RARRES1 , KLK5 , and KRT15 were enriched in cluster 2.

summary:
In Homo sapiens normal breast, luminal progenitor cluster 2 is enriched for SLP1, ANXA1, RARRES1, KLK5, and KRT15.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:98a1d60b143c2d20fc57
claim_id: claim:98a1d60b143c2d20fc57
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal: KRT14 and KRT17 expression was enriched in cluster 2, but not in cluster 0.
summary:
In Homo sapiens normal breast, luminal progenitor cluster 2 is enriched for KRT14 and KRT17, whereas luminal progenitor cluster 0 is not.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:1affd7a7076a748c5599
claim_id: claim:1affd7a7076a748c5599
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal: Cluster 10 was KRT14 positive and enriched for the expression of GLYATL2 .
summary:
In Homo sapiens normal breast, luminal progenitor cluster 10 is positive for KRT14 and enriched for GLYATL2.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:3f08828d79f0e3643af6
claim_id: claim:3f08828d79f0e3643af6
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Cluster 11 was enriched for the expression of multiple genes, including TOP2A , NUSAP1 , UBE2C , TPX2 , SPC25 , MKI67 , CDK1 , CENPF , and CCNA2 ( Figures 1 D and 2 B).

summary:
In Homo sapiens normal breast, luminal progenitor cluster 11 is enriched for TOP2A, NUSAP1, UBE2C, TPX2, SPC25, MKI67, CDK1, CENPF, and CCNA2.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:7259f4b6c592c5120f69
claim_id: claim:7259f4b6c592c5120f69
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal: Cluster 12 was characterized by elevated expression of MEG3 , IGF1 , and PTGDS .
summary:
In Homo sapiens normal breast, luminal progenitor cluster 12 is characterized by elevated expression of MEG3, IGF1, and PTGDS.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:b30afae7028374f3d5db
claim_id: claim:b30afae7028374f3d5db
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal: All three of these clusters expressed ESR1 and pioneering factors FOXA1 and GATA3 .
summary:
In Homo sapiens normal breast, mature luminal cell clusters (clusters 1, 3, and 4) express ESR1, FOXA1, and GATA3.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:4637126fd0e61790de34
claim_id: claim:4637126fd0e61790de34
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
XBP1 and STC2 , ESR 1 target genes, 30 were uniformly expressed at higher levels in all three of these clusters ( Figure 3 A).

summary:
In Homo sapiens normal breast, mature luminal cell clusters uniformly express higher levels of XBP1 and STC2.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:3dc055622ef9cef29ded
claim_id: claim:3dc055622ef9cef29ded
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
In fact, while the expression level of SFRP1 was able to distinguish luminal progenitors from mature luminal cells, expression levels of XBP 1 and STC2 were able to distinguish mature luminal cells from luminal progenitors.

summary:
In Homo sapiens normal breast, SFRP1 expression distinguishes luminal progenitor cells from mature luminal cells, and XBP1 and STC2 expression distinguishes mature luminal cells from luminal progenitor cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:d26370d2bae20fac2baa
claim_id: claim:d26370d2bae20fac2baa
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
In fact, while the expression level of SFRP1 was able to distinguish luminal progenitors from mature luminal cells, expression levels of XBP 1 and STC2 were able to distinguish mature luminal cells from luminal progenitors.

summary:
In Homo sapiens normal breast, XBP1 and STC2 expression distinguishes mature luminal cells from luminal progenitor cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:a3ad0c03cdc04a5c66c9
claim_id: claim:a3ad0c03cdc04a5c66c9
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
summary: In Homo sapiens normal breast, mature luminal cluster 3 is enriched for ANKRD30A.
span_literal:
Cluster 3 was enriched for ANKRD30A , whereas cluster 4 was enriched for PIP , MUCL1 , TAT , and TSPAN8 .


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:c1a9b993ab095013b21f
claim_id: claim:c1a9b993ab095013b21f
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Cluster 3 was enriched for ANKRD30A , whereas cluster 4 was enriched for PIP , MUCL1 , TAT , and TSPAN8 .

summary:
In Homo sapiens normal breast, mature luminal cluster 4 is enriched for PIP, MUCL1, TAT, and TSPAN8.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:68102a34654d373dd6c9
claim_id: claim:68102a34654d373dd6c9
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
ALDH1A3 expression, which has been suggested to identify breast cancer stem cells, 32 was expressed mainly in N4, N14, and N16 clusters of luminal progenitor cells ( Figure 4 B).

summary:
In Homo sapiens normal breast, ALDH1A3 is expressed mainly in luminal progenitor cell clusters N4, N14, and N16.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:96cd2799305932131ec0
claim_id: claim:96cd2799305932131ec0
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Among genes that define basal/stem, luminal progenitor, and luminal mature cells, as expected, CD117 (KIT) expression was restricted to luminal progenitor cells, 5 whereas ESR1 and FOXA1 expression was restricted to luminal mature cell clusters ( Figure S2 ).

summary:
In Homo sapiens normal breast, CD117 (KIT) expression is restricted to luminal progenitor cells, whereas ESR1 and FOXA1 expression is restricted to luminal mature cell clusters.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:227fabff436be16bb383
claim_id: claim:227fabff436be16bb383
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Among genes that define basal/stem, luminal progenitor, and luminal mature cells, as expected, CD117 (KIT) expression was restricted to luminal progenitor cells, 5 whereas ESR1 and FOXA1 expression was restricted to luminal mature cell clusters ( Figure S2 ).

summary:
In Homo sapiens normal breast, ESR1 and FOXA1 expression is restricted to luminal mature cell clusters.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:4d3bed1b7bd6d9958b06
claim_id: claim:4d3bed1b7bd6d9958b06
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
EHF and ELF5 expression showed strong signals in subclusters N14 and N16, which could be alveolar progenitor cells, as these two transcription factors play a major role in alveolar differentiation during pregnancy.

summary:
In Homo sapiens normal breast, EHF and ELF5 show strong expression in subclusters N14 and N16, which could be alveolar progenitor cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:b5b4b3824fa03bb1169b
claim_id: claim:b5b4b3824fa03bb1169b
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Cluster 15 is likely composed of myoepithelial cells, as this cluster expressed higher levels of ACTA2 and KRT17 , previously described markers of myoepithelial cells ( Figure S2 ).

summary:
In Homo sapiens normal breast, cluster 15, likely composed of myoepithelial cells, expresses higher levels of ACTA2 and KRT17, previously described markers of myoepithelial cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:d11a131d82b029834ba4
claim_id: claim:d11a131d82b029834ba4
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
N0 and N2 are likely enriched for stemness-associated genes as well, as these cells expressed higher levels of EGFR and CD44 and low levels of various keratins, 36 and likely different from the rest of the luminal progenitor cells, as they expressed very low levels of CD49f and EpCAM.

summary:
In Homo sapiens normal breast, clusters N0 and N2 express higher levels of EGFR and CD44 and low levels of various keratins, CD49f, and EpCAM.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:7226d723a0108671d66e
claim_id: claim:7226d723a0108671d66e
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
A closer look at genes enriched in each cluster and their signature genes revealed that XBP1 is expressed predominantly in luminal mature cells, whereas SFRP1 is expressed predominantly in luminal progenitor cells.

summary:
In Homo sapiens normal breast, XBP1 is expressed predominantly in luminal mature cells, whereas SFRP1 is expressed predominantly in luminal progenitor cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:48c71f15f1e44b647f28
claim_id: claim:48c71f15f1e44b647f28
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
A closer look at genes enriched in each cluster and their signature genes revealed that XBP1 is expressed predominantly in luminal mature cells, whereas SFRP1 is expressed predominantly in luminal progenitor cells.

summary:
In Homo sapiens normal breast, SFRP1 is expressed predominantly in luminal progenitor cells, whereas XBP1 is expressed predominantly in luminal mature cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:151f977471ddb673f222
claim_id: claim:151f977471ddb673f222
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Multiple genes are enriched in basal cell clusters, including CLDN5 (N5 and N7), CD36 (N7), and CD93 (N5, N13, and N22).

summary:
In Homo sapiens normal breast, multiple genes are enriched in basal cell clusters, including CLDN5, CD36, and CD93.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:4ee457dfc6853c8fd31d
claim_id: claim:4ee457dfc6853c8fd31d
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
This cluster as well as its counterpart in the first analysis (C9), although representing <2% of epithelial cells, is characterized by expression of cell cycle markers MKI67 and TK1 (p = 3.83E−13) and mitotic spindle checkpoint protein ZWINT (p = 4.62E−17).

summary:
In Homo sapiens normal breast, luminal progenitor cluster N19 is characterized by expression of MKI67, TK1, and ZWINT.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:de27ce68aba537ab06e4
claim_id: claim:de27ce68aba537ab06e4
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
The N8 cluster expresses the highest level of ESR1 as well as its pioneer factors FOXA1 , GATA3 , and also TBX3 .

summary:
In Homo sapiens normal breast, mature luminal cluster N8 expresses the highest level of ESR1 as well as FOXA1, GATA3, and TBX3.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:2e32277b77437aba73dd
claim_id: claim:2e32277b77437aba73dd
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Among these four clusters, N2 and N8, but not N12 and N17, expressed FOXA1 , GATA3 , and TBX3 ( Table S3 ).

summary:
In Homo sapiens normal breast, mature luminal clusters N2 and N8 express FOXA1, GATA3, and TBX3, whereas mature luminal clusters N12 and N17 do not.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:2d992e883f897d168c79
claim_id: claim:2d992e883f897d168c79
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Among these four clusters, N2 and N8, but not N12 and N17, expressed FOXA1 , GATA3 , and TBX3 ( Table S3 ).

summary:
In Homo sapiens normal breast, mature luminal clusters N12 and N17 do not express FOXA1, GATA3, and TBX3.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:55edc257b3d557c3c4a6
claim_id: claim:55edc257b3d557c3c4a6
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Consistent with an earlier report, 34 RANK (TNFRSF11A) expression was restricted to a few luminal progenitor cells, whereas its ligand RANKL (TNFSF11) expression was observed in progesterone-receptor-positive mature luminal cells ( Figure S2 ).

summary:
In Homo sapiens normal breast, RANK (TNFRSF11A) expression is restricted to luminal progenitor cells, whereas RANKL (TNFSF11) expression is observed in progesterone-receptor-positive mature luminal cells.


claim_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408:claim:3fb2cb33d5cb86e6e14e
claim_id: claim:3fb2cb33d5cb86e6e14e
paper_key: hca:0040_10.1016_j.xcrm.2021.100219_d37660c408
span_literal:
Consistent with an earlier report, 34 RANK (TNFRSF11A) expression was restricted to a few luminal progenitor cells, whereas its ligand RANKL (TNFSF11) expression was observed in progesterone-receptor-positive mature luminal cells ( Figure S2 ).

summary:
In Homo sapiens normal breast, RANKL (TNFSF11) expression is observed in progesterone-receptor-positive mature luminal cells.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:eb4cc67322da86f8c6fc
claim_id: claim:eb4cc67322da86f8c6fc
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
The surrounding alveolar mesenchyme contains myofibroblasts (myoFB) characterized by alpha smooth muscle actin ( ACTA2 ), contraction of which forms septal ridges that are vital for alveologenesis.

summary:
In Homo sapiens, myofibroblasts in the alveolar mesenchyme are characterized by alpha smooth muscle actin (ACTA2).


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:4d3fe40c2b2d8532a261
claim_id: claim:4d3fe40c2b2d8532a261
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, epithelial cells are marked by EPCAM and CDH1.
span_literal:
Initially, major cell types were identified based on Cicero-linked gene activity scores, 16 which connect open regulatory regions to genes and serve as an estimation of gene expression, and corresponding peaks in promoter regions of canonical markers (epithelial – EPCAM, CDH1 ; mesenchymal – COL6A3, PDGFRA ; endothelial – PECAM1 ; immune – PTPRC )


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:43ab88c55aca23359ceb
claim_id: claim:43ab88c55aca23359ceb
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, mesenchymal progenitors are positive for NFIB, ZEB2, DACH1, ID3, and EBF1.
span_literal:
Annotated clusters represented expected cell types, except for a cluster we labeled as mesenchymal progenitors (Mes.Prog, NFIB + , ZEB2 + , DACH1 + , ID3 + , EBF1 + ) in both human and mouse.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:25e91b655ba9903d951c
claim_id: claim:25e91b655ba9903d951c
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, airway epithelial cells are positive for ELF3 and GRHL2.
span_literal:
Epithelial compartments consisted of airway (AW, ELF3 + , GRHL2 + ), alveolar type 2 (AT2, SFTPA1 + , ABCA3 + ), alveolar type I (AT1, HOPX + , PDPN + , AGER + ), and clusters with both AT1 and AT2 signatures labeled as AT1.AT2.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:ff6f2ad5534445017a17
claim_id: claim:ff6f2ad5534445017a17
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, matrix fibroblasts are positive for COL6A3, PDGFRA, and WNT2.
span_literal:
Matrix fibroblasts (MFB, COL6A3 + , PDGFRA + , WNT2 + ), myofibroblasts (MyoFB, ACTA2 + ), and pericytes (Peri, PDGRB + ) were identified in the stromal populations.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:ab3e23a01567abd7909e
claim_id: claim:ab3e23a01567abd7909e
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
In human endothelial clusters (Endo, PECAM1 + ), we also identified lymphatic cells (Lymph, TBX1 + ) that did not clearly separate out in mouse at this level of resolution.

summary:
In Homo sapiens lung, endothelial cells are positive for PECAM1 and lymphatic cells are positive for TBX1.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:91c234b9a9be46bfe8ae
claim_id: claim:91c234b9a9be46bfe8ae
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, alveolar progenitor cells are positive for AXIN2.
span_literal:
AXIN2 + Alv.Prog cells contained regulatory elements related to NAV2 , which plays a role in cellular growth and migration, and FZD2, a receptor for bronchoalveolar stem cells with a role in stem cell maintenance and differentiation


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:1caa7c425584f627bf6d
claim_id: claim:1caa7c425584f627bf6d
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, alveolar type 1 cells are marked by PDPN, RTKN2, VEGFA, GPRC5A, and MYRF.
span_literal:
AT1 clusters were active near canonical marker PDPN along with more contemporary markers: RTKN2, VEGFA, GPRC5A, and MYRF


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:094fd7f856ea14e28110
claim_id: claim:094fd7f856ea14e28110
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal: The myoFB_1 cluster demonstrated highest gene activity for PDGFRA and myoFB_2 for ACTA2
summary:
In Homo sapiens lung, myofibroblast 1 demonstrates highest gene activity for PDGFRA and myofibroblast 2 for ACTA2.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:beb17ef513e3ab5d6b83
claim_id: claim:beb17ef513e3ab5d6b83
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
Both myoFB clusters contained activity associated with myosin light chain kinase ( MYLK ), elastin ( ELN) , transforming growth factor beta induced ( TGFBI ), and latent transforming growth factor beta binding protein 1 ( LTBP1 ) genes

summary:
In Homo sapiens lung, myofibroblasts show gene activity for myosin light chain kinase (MYLK), elastin (ELN), transforming growth factor beta induced (TGFBI), and latent transforming growth factor beta binding protein 1 (LTBP1).


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:ed137dc6d5f5f4960a82
claim_id: claim:ed137dc6d5f5f4960a82
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
MyoFB_2 displayed additional myosin heavy chain 11 ( MYH11 ) and myocardin ( MYOCD ) gene activity along with SRF TF activity

summary:
In Homo sapiens lung, myofibroblast 2 displays gene activity for myosin heavy chain 11 (MYH11) and myocardin (MYOCD) along with serum response factor (SRF) transcription factor activity.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:d895eda852ad6a873980
claim_id: claim:d895eda852ad6a873980
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
summary: In Homo sapiens lung, myofibroblast 1 shows chromatin accessibility near IGF1.
span_literal:
MyoFB_1 was accessible near IGF1 which stimulates the proliferation and differentiation of lung fibroblasts into myoFBs.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:bddedde824eb480ce9b6
claim_id: claim:bddedde824eb480ce9b6
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
In the myoFB_1 cluster, differential TF analysis revealed highest activity of myocyte enhancer factor 2A ( MEF2A ) which is involved in muscle development, cell growth, and ECM remodeling

summary:
In Homo sapiens lung, myofibroblast 1 shows highest transcription factor activity of myocyte enhancer factor 2A (MEF2A).


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:ef43faa1cddbd373a106
claim_id: claim:ef43faa1cddbd373a106
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
PIEZO2 , a mechanically activated channel that converts physical stress into chemical signals for cellular communication, 70 , 71 , 72 was the most significant DA gene in human D1 MFB_1

summary:
In Homo sapiens lung, PIEZO2 is the most significant differentially accessible gene in matrix fibroblast 1 at day 1 of life.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:e8aee681bd00d30caa63
claim_id: claim:e8aee681bd00d30caa63
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
In summary, PIEZO2 was identified as a novel marker gene for a matrix FB subtype at human D1, its expression is likely regulated by a bHLH TF, and Piezo2 was not active in mouse matrix FBs across all sampled time points suggesting a species-specific difference in early developmental response pathways to stretch.

summary:
In Homo sapiens lung, PIEZO2 was identified as a novel marker gene for a matrix fibroblast subtype at day 1 of life.


claim_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd:claim:e428394eb00500d2e913
claim_id: claim:e428394eb00500d2e913
paper_key: hca:0041_10.1016_j.xgen.2022.100108_d4824b85dd
span_literal:
Fgf18 labels myoFBs during alveolar septation, 53 and adult small airway myoFBs are associated with decreased lung function in chronic obstructive pulmonary disease.

summary:
In Homo sapiens lung, fibroblast growth factor 18 (FGF18) labels myofibroblasts during alveolar septation.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:83a876c1bf5cf74fcb58
claim_id: claim:83a876c1bf5cf74fcb58
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Trophoblasts share expression of KRT7 and PERP across all subtypes and can be further subclassified into VCT, SCT, and EVT by sublineage markers such as PARP1 , ERVFRD-1 , and HLA-G , respectively

summary:
In Homo sapiens, trophoblasts share expression of KRT7 and PERP, with villous cytotrophoblasts marked by PARP1, syncytiotrophoblasts marked by ERVFRD-1, and extravillous trophoblasts marked by HLA-G.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:62994b1fa5ad8d9f9a20
claim_id: claim:62994b1fa5ad8d9f9a20
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, CGA is primarily expressed by syncytiotrophoblasts and extravillous trophoblasts.
span_literal:
CGA , which codes for the common α subunit of the hormones hCG (human chorionic gonadotropin), LH (luteinizing hormone), FSH (follicle-stimulating hormone), and TSH (thyroid-stimulating hormone), is primarily expressed by SCTs and EVTs.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:a3cf980ff7a3253c2dc1
claim_id: claim:a3cf980ff7a3253c2dc1
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
The aromatase CYP19A , which converts androgens to estrogens, is specifically expressed by SCTs, whereas HSD3B1 , which is essential for the production of progesterone for pregnancy maintenance, is mainly expressed by EVTs and SCTs.

summary:
In Homo sapiens, CYP19A is specifically expressed by syncytiotrophoblasts, while HSD3B1 is mainly expressed by extravillous trophoblasts and syncytiotrophoblasts.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:45a4e358e62fc207fb1b
claim_id: claim:45a4e358e62fc207fb1b
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
SCTs also express the transforming growth factor–β superfamily member GDF15 , which is elevated in maternal plasma during pregnancy and dysregulated in preeclampsia and diabetic pregnancies

summary:
In Homo sapiens, syncytiotrophoblasts express GDF15, a transforming growth factor-beta superfamily member.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:a80b808f93da4d136bc0
claim_id: claim:a80b808f93da4d136bc0
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, SLC27A2 is specifically expressed by villous cytotrophoblasts.
span_literal:
SLC27A2 was specifically expressed by VCTs, SLC22A11 was expressed by both SCTs and VCTs, SLC13A4 and SLC52A1 were highly expressed by SCTs but showed negligible expression in other placental cell types, whereas SLCO4A1 was predominantly expressed by EVTs.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:44c51d7a5cc447d121a1
claim_id: claim:44c51d7a5cc447d121a1
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
SLC27A2 was specifically expressed by VCTs, SLC22A11 was expressed by both SCTs and VCTs, SLC13A4 and SLC52A1 were highly expressed by SCTs but showed negligible expression in other placental cell types, whereas SLCO4A1 was predominantly expressed by EVTs.

summary:
In Homo sapiens, SLC22A11 is expressed by both syncytiotrophoblasts and villous cytotrophoblasts. In Homo sapiens, SLC13A4 and SLC52A1 are highly expressed by syncytiotrophoblasts.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:4b16b1148917fb593b15
claim_id: claim:4b16b1148917fb593b15
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
We also observed that LCMT1-AS2 , an antisense noncoding RNA to LCMT1 , and INSL4 , an insulin family hormone, were abundantly and specifically expressed by SCTs.

summary:
In Homo sapiens, LCMT1-AS2 and INSL4 are abundantly and specifically expressed by syncytiotrophoblasts.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:8445c49c717c4be39eda
claim_id: claim:8445c49c717c4be39eda
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal: We characterized EVTs by the expression of HLA-G , DIO2 , and LAIR2
summary:
In Homo sapiens, extravillous trophoblasts are characterized by the expression of HLA-G, DIO2, and LAIR2.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:e77dfb3031614d619d22
claim_id: claim:e77dfb3031614d619d22
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, HTRA4 is a novel marker of extravillous trophoblasts.
span_literal:
but we also found novel EVT markers, including the serine peptidase HTRA4 , previously reported to be up-regulated in the early onset but not late onset of preeclampsia along with increased levels in maternal serum


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:81106923e1e78bacb2ac
claim_id: claim:81106923e1e78bacb2ac
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, MFAP5 is specifically expressed by extravillous trophoblasts.
span_literal:
The extracellular matrix (ECM) glycoprotein MFAP5 , a component of microfibrils shown to induce cell motility and invasion of cancer cells ( 13 ), was also specifically expressed by EVTs, consistent with a role in EVT invasion and mobility.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:f9cbaf2a3814972b419a
claim_id: claim:f9cbaf2a3814972b419a
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
Last, we identified EVTs and VECs as the primary sources of prostaglandin catabolizing enzyme HPGD .

summary:
In Homo sapiens, extravillous trophoblasts and vascular endothelial cells are the primary sources of HPGD.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:ddaef94167fa8615ea3e
claim_id: claim:ddaef94167fa8615ea3e
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
summary: In Homo sapiens, EGFL6 is specifically expressed by placental fibroblasts.
span_literal:
Last, the placenta-specific EGFL6 gene, known to promote endothelial cell migration and angiogenesis, was also FB-specifically expressed.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:1021eb453899ea7cfe36
claim_id: claim:1021eb453899ea7cfe36
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
FB1 and FB3 showed a characteristic resemblance to myofibroblasts by expressing DES , MFAP4 , OGN , and S100A4 genes.

summary:
In Homo sapiens, placental fibroblast 1 and fibroblast 3 express DES, MFAP4, OGN, and S100A4, resembling myofibroblasts.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:953201a2551deaf5b032
claim_id: claim:953201a2551deaf5b032
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
FB1 and FB3 showed a characteristic resemblance to myofibroblasts by expressing DES , MFAP4 , OGN , and S100A4 genes.

summary:
In Homo sapiens, placental fibroblast 3 expresses DES, MFAP4, OGN, and S100A4, resembling myofibroblasts.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:017d06b6c7795b5e2762
claim_id: claim:017d06b6c7795b5e2762
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal: FB3 additionally expressed proinflammatory genes such as IL6 , PTGDS , CFD , CXCL2 , and BDKRB1 .
summary:
In Homo sapiens, placental fibroblast 3 additionally expresses proinflammatory genes IL6, PTGDS, CFD, CXCL2, and BDKRB1.


claim_key: hca:0042_10.1126_sciadv.aau4788_744a251f24:claim:9d113de212e5f35b8f8e
claim_id: claim:9d113de212e5f35b8f8e
paper_key: hca:0042_10.1126_sciadv.aau4788_744a251f24
span_literal:
FB2s are characterized by the unique expression of REN and AGTR1 , genes implicated in the regulation of blood pressure, sodium, and fluid homeostasis, as well as IGFBP7 and AREG .

summary:
In Homo sapiens, placental fibroblast 2 is characterized by unique expression of REN, AGTR1, IGFBP7, and AREG.


