# claims

claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:13ce5ec1ba9f1d856545
claim_id: claim:13ce5ec1ba9f1d856545
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
summary: In Homo sapiens, CD1a is abundantly expressed by Langerhans cells.
span_literal:
CD1a is abundantly expressed by human Langerhans cells (LCs) and thymocytes and is inducible by subsets of human DCs and innate lymphoid cells.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:0593e75193b9f5e406ac
claim_id: claim:0593e75193b9f5e406ac
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal:
Transcription factor 4 (TCF4) is essential for pDC development and phenotype maintenance, and the alteration of the balance between TCF4 and its inhibitor ID2 expression leads to the up-regulation of cDC-related genes.

summary:
In Homo sapiens, transcription factor 4 is essential for plasmacytoid dendritic cell development and phenotype maintenance, and its inhibitor ID2 leads to up-regulation of conventional dendritic cell-related genes.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:332b5d9ee1d35c8db76a
claim_id: claim:332b5d9ee1d35c8db76a
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal:
Here, we noted that the TCF4 expression level was low in skin activated DCs, coinciding with reduced levels of SPIB , BCL11A , and IRF8 , compared with skin BDCA-2 + CD123 hi DCs, while the ID2 level was high

summary:
In Homo sapiens, skin activated dendritic cells show low expression of TCF4, SPIB, BCL11A, and IRF8 and high expression of ID2 compared with BDCA-2-positive CD123-high dendritic cells.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:dd3638db5a930437962b
claim_id: claim:dd3638db5a930437962b
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
summary: In Homo sapiens, IRF4 remained at a high level in skin activated dendritic cells.
span_literal:
Meanwhile, IRF4 , which is highly expressed in certain cDC subsets ( Naik et al., 2015 ) and pDCs, remained at a high level in skin activated DCs


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:726ba9a8a627c94498dc
claim_id: claim:726ba9a8a627c94498dc
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
summary: In Homo sapiens, skin activated dendritic cells show decreased expression of RUNX2 and IRF7.
span_literal:
runt related transcription factor 2 (RUNX2) and its downstream signaling molecule IRF7, which are key regulators of IFN-I production ( Chopin et al., 2016 ; Sawai et al., 2013 ), were both decreased, while costimulatory marker genes were elevated in skin activated DCs


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:e0c65a2716e2a171fc90
claim_id: claim:e0c65a2716e2a171fc90
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
summary: In Homo sapiens, skin activated dendritic cells expressed very high levels of CCL22.
span_literal:
Notably, skin activated DCs expressed very high levels of CCL22, a chemoattractant for C-C chemokine receptor type 4 (CCR4)–expressing cells that facilitates migration into the skin


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:40c4dcb683b54fbd7dda
claim_id: claim:40c4dcb683b54fbd7dda
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal:
CCR7 directs the lymph node homing of DCs and was one of the most significantly up-regulated transcripts in skin activated DCs

summary:
In Homo sapiens, CCR7 was one of the most significantly up-regulated transcripts in skin activated dendritic cells.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:80ae84e03e397362713e
claim_id: claim:80ae84e03e397362713e
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal:
The ASDCs detected herein from skin blisters were highly activated, expressing CCL22 and CD83, and may be recruited into skin in response to inflammatory cues

summary:
In Homo sapiens, Axl-positive Siglec-6-positive dendritic cells detected from skin blisters express CCL22 and CD83.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:13ed5b53ad19a6347630
claim_id: claim:13ed5b53ad19a6347630
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal:
In addition, activated DCs derived from HDM-challenged skin blisters expressed a higher level of genes related to DC maturation, such as HLA-DPA1 and LAMP3 , which appear during DC maturation

summary:
In Homo sapiens, activated dendritic cells derived from house dust mite-challenged skin blisters expressed higher levels of HLA-DPA1 and LAMP3.


claim_key: hca:0260_10.1084_jem.20190811_d700cd1f81:claim:c1296dd832a8e039d85f
claim_id: claim:c1296dd832a8e039d85f
paper_key: hca:0260_10.1084_jem.20190811_d700cd1f81
span_literal:
Tang-Huau et al. (2018) recently conducted scRNA-seq analyses on ascites macrophages, ascites DCs, and tonsil DCs and described an activated cDC2 subset in the tonsil expressing high levels of genes similar to those found in skin BDCA-2 + CD123 int DCs, including CCR7 , CCL19 , LAMP3 , IDO1 , CD83 , and HLA class II

summary:
In Homo sapiens, an activated conventional dendritic cell type 2 subset in the tonsil expresses high levels of CCR7, CCL19, LAMP3, IDO1, and CD83.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:597d369bf205ac5cea13
claim_id: claim:597d369bf205ac5cea13
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
anti-CD205 antibody (green) marked cortical TEC (cTEC) and anti-CK5-14 (red) marked medullary TEC (mTEC)

summary:
In Homo sapiens, cortical thymic epithelial cells are marked by CD205 (LY75), while medullary thymic epithelial cells are marked by CK5-14.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:150f509c35da42f13227
claim_id: claim:150f509c35da42f13227
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
FACS plot visualising cTEC (EpCAM low CD205 + , 4.87%), mTEC (EpCAM high CD205 − , 11.1%) and TIC (EpCAM − CD205 − , 61.5%) in the CD45-negative population enriched for sorting

summary:
In Homo sapiens, cortical thymic epithelial cells are EpCAM low and CD205 positive, medullary thymic epithelial cells are EpCAM high and CD205 negative, and thymic interstitial cells are EpCAM negative and CD205 negative within the CD45-negative population.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:fd3bfe6c51da67ba01f7
claim_id: claim:fd3bfe6c51da67ba01f7
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
the mesenchymal marker CD90 (THY1) was also expressed by a large proportion (>60%) of mTEC and approximately all cTEC, as well as by TIC

summary:
In Homo sapiens, the mesenchymal marker CD90 (THY1) is expressed by medullary thymic epithelial cells, cortical thymic epithelial cells, and thymic interstitial cells.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:45b3d932b7f708682770
claim_id: claim:45b3d932b7f708682770
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
the mesenchymal marker CD90 (THY1) was also expressed by a large proportion (>60%) of mTEC and approximately all cTEC, as well as by TIC

summary:
In Homo sapiens, the mesenchymal marker CD90 (THY1) is expressed by cortical thymic epithelial cells.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:dafc06c54c27e40cb917
claim_id: claim:dafc06c54c27e40cb917
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
Area under the curve (AUC) summary intensity plots for the gene signatures of cTEC ( CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA and TP53AIP1 ), mTEC ( CD24, CDH1, CLDN3, EPCAM and HES6 ) and comTEC ( CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1 and ZEB1 ) clusters showing expression level for lineage specific genes in a purple scale.

summary:
In Homo sapiens, cortical thymic epithelial cells are characterized by the gene signature including CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA and TP53AIP1.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:1272e18966e3a22aa6df
claim_id: claim:1272e18966e3a22aa6df
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
Area under the curve (AUC) summary intensity plots for the gene signatures of cTEC ( CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA and TP53AIP1 ), mTEC ( CD24, CDH1, CLDN3, EPCAM and HES6 ) and comTEC ( CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1 and ZEB1 ) clusters showing expression level for lineage specific genes in a purple scale.

summary:
In Homo sapiens, medullary thymic epithelial cells are characterized by the gene signature including CD24, CDH1, CLDN3, EPCAM and HES6.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:b78f4cc62c81ec242924
claim_id: claim:b78f4cc62c81ec242924
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
Area under the curve (AUC) summary intensity plots for the gene signatures of cTEC ( CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA and TP53AIP1 ), mTEC ( CD24, CDH1, CLDN3, EPCAM and HES6 ) and comTEC ( CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1 and ZEB1 ) clusters showing expression level for lineage specific genes in a purple scale.

summary:
In Homo sapiens, common thymic epithelial cells (comTEC) are characterized by the gene signature including CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1 and ZEB1.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:c548e380544e8e3be618
claim_id: claim:c548e380544e8e3be618
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
Immunofluorescence of cultivated TIC demonstrates protein expression for TE7 and vimentin (VIM), as well as PDGFRβ, NG2 and Smooth Muscle Actin (αSMA)

summary:
In Homo sapiens, cultivated thymic interstitial cells express TE7, vimentin (VIM), PDGFRβ, NG2 (chondroitin sulfate proteoglycan 4), and smooth muscle actin (αSMA).


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:3a27814e7e1d8e3db9b0
claim_id: claim:3a27814e7e1d8e3db9b0
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
FACS analysis revealed that these TIC consistently expressed PDGFRα, PDGFRβ, CD90, CD146, and, to variable extents, NG2 and alkaline phosphatase (ALP), consistent with a perivascular phenotype

summary:
In Homo sapiens, thymic interstitial cells consistently express PDGFRα, PDGFRβ, CD90, CD146, and to variable extents NG2 and alkaline phosphatase (ALP), consistent with a perivascular phenotype.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:3a0cbbdbbde37e5ddce5
claim_id: claim:3a0cbbdbbde37e5ddce5
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
Heatmap and hierarchical clustering of samples according to expression of thymic identity genes ( SIX1, EYA1, PAX1 and PAX9 ), markers of thymic cortex ( CTSV, PRSS16 and LY75 ) and medulla ( CD24 and CDH1 ).

summary:
In Homo sapiens, markers of the thymic cortex include CTSV, PRSS16 and LY75, while markers of the thymic medulla include CD24 and CDH1.


claim_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30:claim:f07d357fafeeeaa43875
claim_id: claim:f07d357fafeeeaa43875
paper_key: hca:0261_10.1038_s41467-020-20082-7_77f7a74c30
span_literal:
Heatmap and hierarchical clustering of samples according to expression of thymic identity genes ( SIX1, EYA1, PAX1 and PAX9 ), markers of thymic cortex ( CTSV, PRSS16 and LY75 ) and medulla ( CD24 and CDH1 ).

summary:
In Homo sapiens, markers of the thymic medulla include CD24 and CDH1, expressed by medullary thymic epithelial cells.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:67dfe923482f29b194a6
claim_id: claim:67dfe923482f29b194a6
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
Markers that distinguish the different decidual fibroblast populations identify two clusters of perivascular cells (referred to as PV1 and PV2) that share expression of the smooth muscle marker (MGP) and are distinguished by different levels of MCAM, which is higher in PV1, and MMP11, which is higher in PV2

summary:
In Homo sapiens, perivascular cell 1 and perivascular cell 2 share expression of the smooth muscle marker MGP, with MCAM being higher in perivascular cell 1 and MMP11 being higher in perivascular cell 2.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:73c597391671ae84d17a
claim_id: claim:73c597391671ae84d17a
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
Markers that distinguish the different decidual fibroblast populations identify two clusters of perivascular cells (referred to as PV1 and PV2) that share expression of the smooth muscle marker (MGP) and are distinguished by different levels of MCAM, which is higher in PV1, and MMP11, which is higher in PV2

summary:
In Homo sapiens, perivascular cell 2 shares expression of MGP with perivascular cell 1, and is distinguished by higher expression of MMP11 compared to perivascular cell 1.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:c23bcec612ae355cc87b
claim_id: claim:c23bcec612ae355cc87b
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
There are three clusters of stromal cells (labelled dS1, dS2 and dS3), all of which express the WNT inhibitor DKK1.

summary:
In Homo sapiens, decidual stromal cell 1, decidual stromal cell 2, and decidual stromal cell 3 all express the WNT inhibitor DKK1.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:b708bd6db850f2a9de8b
claim_id: claim:b708bd6db850f2a9de8b
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
dS1 shares the expression of ACTA2 and TAGLNwith PV1 and PV2, and lacks expression of the classical decidual markers prolactin (PRL) and IGFBP1.

summary:
In Homo sapiens, decidual stromal cell 1 expresses ACTA2 and TAGLN but lacks expression of prolactin (PRL) and IGFBP1.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:bf2ca3ece15f60352970
claim_id: claim:bf2ca3ece15f60352970
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual stromal cell 2 expresses IGFBP1, IGFBP2, and IGFBP6.
span_literal:
By contrast, dS2 and dS3 express IGFBP1, IGFBP2 and IGFBP6 and share markers with two subsets of decidualized stromal cells that have recently been described in vitro 22 .


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:871531d1265d5ba60678
claim_id: claim:871531d1265d5ba60678
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual stromal cell 3 expresses PRL and CYP11A1.
span_literal:
The dS3 subset expresses PRL as well as genes involved in steroid biosynthesis (for example, CYP11A1)


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:38ad61b975367ad7457d
claim_id: claim:38ad61b975367ad7457d
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
We identified three main dNK subsets (dNK1, dNK2 and dNK3), which all co-express the tissue-resident markers CD49A (also known as ITGA1) and CD9

summary:
In Homo sapiens, decidual natural killer cell 1, decidual natural killer cell 2, and decidual natural killer cell 3 all co-express the tissue-resident markers ITGA1 and CD9.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:76da0ad91540b96ef800
claim_id: claim:76da0ad91540b96ef800
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
We identified three main dNK subsets (dNK1, dNK2 and dNK3), which all co-express the tissue-resident markers CD49A (also known as ITGA1) and CD9

summary:
In Homo sapiens, decidual natural killer cell 2 co-expresses the tissue-resident markers ITGA1 and CD9.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:dc98345a0f8aa8cdd2da
claim_id: claim:dc98345a0f8aa8cdd2da
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
We identified three main dNK subsets (dNK1, dNK2 and dNK3), which all co-express the tissue-resident markers CD49A (also known as ITGA1) and CD9

summary:
In Homo sapiens, decidual natural killer cell 3 co-expresses the tissue-resident markers ITGA1 and CD9.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:a26467da2cec3e5eaaec
claim_id: claim:a26467da2cec3e5eaaec
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual natural killer cell 1 expresses ENTPD1, CYP26A1, and B4GALNT1.
span_literal:
dNK1 cells express CD39 (also known as ENTPD1), CYP26A1 and B4GALNT1, whereas the defining markers of dNK2 cells are ANXA1 and ITGB2; the latter is shared with dNK3 cells


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:9b18da573e7016932eca
claim_id: claim:9b18da573e7016932eca
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
dNK1 cells express CD39 (also known as ENTPD1), CYP26A1 and B4GALNT1, whereas the defining markers of dNK2 cells are ANXA1 and ITGB2; the latter is shared with dNK3 cells

summary:
In Homo sapiens, decidual natural killer cell 3 shares expression of ITGB2 with decidual natural killer cell 2.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:f17665b1d15c437fef2d
claim_id: claim:f17665b1d15c437fef2d
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
dNK3 cells express CD160, KLRB1 and CD103 (also known as ITGAE), but not the innate lymphocyte cell marker CD127 (also known as IL7R)

summary:
In Homo sapiens, decidual natural killer cell 3 expresses CD160, KLRB1, and ITGAE, but does not express the innate lymphocyte cell marker IL7R.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:676b1e17cfee9a997a58
claim_id: claim:676b1e17cfee9a997a58
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
We find that dNK1 cells express higher levels of KIRs that can bind to HLA-C molecules: inhibitory KIR2DL1, KIR2DL2 and KIR2DL3 and activating KIR2DS1 and KIR2DS4

summary:
In Homo sapiens, decidual natural killer cell 1 expresses higher levels of KIR2DL1, KIR2DL2, KIR2DL3, KIR2DS1, and KIR2DS4.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:6a240b9a99912f0fd9cd
claim_id: claim:6a240b9a99912f0fd9cd
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, LILRB1 is expressed only by the decidual natural killer cell 1 subset.
span_literal:
LILRB1, the receptor with high affinity for the dimeric form of HLA-G molecules, is expressed only by the dNK1 subset.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:cd807a047b284385cdc1
claim_id: claim:cd807a047b284385cdc1
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual natural killer cell 1 expresses KLRC2, KLRC3, and KLRC1.
span_literal:
Both dNK1 and dNK2—but not dNK3—express activating NKG2C (also known as KLRC2) and NKG2E (also known as KLRC3) as well as inhibitory NKG2A (also known as KLRC1) receptors for HLA-E molecules


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:eec2c08fd683fab17a94
claim_id: claim:eec2c08fd683fab17a94
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
dNK1 contains more cytoplasmic granules than dNK2 and dNK3, which is consistent with our scRNA-seq data that show higher levels of expression of PRF1, GNLY, GZMA and GZMB RNA in this subset

summary:
In Homo sapiens, decidual natural killer cell 1 shows higher levels of expression of PRF1, GNLY, GZMA, and GZMB.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:18cd48e9e10130390bc2
claim_id: claim:18cd48e9e10130390bc2
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual natural killer cell 1 expresses higher levels of CSF1.
span_literal:
dNK1 cells express higher levels of CSF1, the receptor of which (CSF1R) is expressed by EVT and macrophages


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:5893012f2601a112a370
claim_id: claim:5893012f2601a112a370
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal: By contrast, dNK2 and dNK3 express high levels of XCL1, and CCL5 is highly expressed by dNK3
summary:
In Homo sapiens, decidual natural killer cell 2 and decidual natural killer cell 3 express high levels of XCL1, and CCL5 is highly expressed by decidual natural killer cell 3.


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:774e372861e2f5ab06a4
claim_id: claim:774e372861e2f5ab06a4
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, extravillous trophoblast cells show high expression of CD274 (PDL1).
span_literal:
There is high expression of PDL1 (also known as CD274) in EVT, which we confirmed in situ by using immunohistochemistry on serial sections of decidua basalis (the site of trophoblast invasion) stained for PDL1 and HLA-G


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:9fe89ef24dc779f5e02a
claim_id: claim:9fe89ef24dc779f5e02a
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual natural killer cell 3 highly expresses KLRB1 and TIGIT.
span_literal:
These include KLRB1 and TIGIT, which are highly expressed by dNK3 cells, potentially binding CLEC2D and PVR, which are expressed by EVT


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:c112803c50e20d34a553
claim_id: claim:c112803c50e20d34a553
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, decidual natural killer cell 1 expresses ENTPD1.
span_literal:
The dNK1 subset expresses CD39 (which is encoded by ENTPD1), which—together with CD73 (which is encoded by NT5E)—converts ATP to adenosine to prevent immune activation 33


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:3734886292d91a0229c7
claim_id: claim:3734886292d91a0229c7
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
summary: In Homo sapiens, maternal macrophages (M3 cluster) express CD14, S100A9, CD163, CD68, and CSF1R.
span_literal:
with the exception of maternal macrophages (M3 cluster) that express CD14, S100A9, CD163, CD68 and CSF1R


claim_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8:claim:628b8ac33fbdc5492b7c
claim_id: claim:628b8ac33fbdc5492b7c
paper_key: hca:0262_10.1038_s41586-018-0698-6_e4aeb353b8
span_literal:
EVT have a unique human leukocyte antigen (HLA) profile: they do not express the dominant T cell ligands, class I HLA-A and HLA-B, or class II molecules 8 , 9 but do express HLA-G and HLA-E and polymorphic HLA-C class I molecules.

summary:
In Homo sapiens, extravillous trophoblast cells do not express HLA-A or HLA-B, but do express HLA-G, HLA-E, and HLA-C.


claim_key: hca:0263_10.1126_science.abq3061_cd915f6391:claim:aac885b6cf2851ab247b
claim_id: claim:aac885b6cf2851ab247b
paper_key: hca:0263_10.1126_science.abq3061_cd915f6391
span_literal:
Module 1 was up-regulated in AFib and contained inflammatory and profibrotic genes such as CCR2 , IL10 , ITGA9 , MMP9 , SPP1 , TIMP2 , and VIM

summary:
In Homo sapiens, mononuclear phagocytes and dendritic cells in atrial fibrillation up-regulate inflammatory and profibrotic genes including CCR2, IL10, ITGA9, MMP9, SPP1, TIMP2, and VIM.


claim_key: hca:0263_10.1126_science.abq3061_cd915f6391:claim:3ba9964db344fe904393
claim_id: claim:3ba9964db344fe904393
paper_key: hca:0263_10.1126_science.abq3061_cd915f6391
span_literal:
Module 1 genes SPP1 and CCR2 and the cell surface markers TREM2 and CD9 were among the top up-regulated genes in MP/DCs from patients with AFib

summary:
In Homo sapiens, SPP1, CCR2, TREM2, and CD9 are among the top up-regulated genes in mononuclear phagocytes and dendritic cells from patients with atrial fibrillation.


claim_key: hca:0263_10.1126_science.abq3061_cd915f6391:claim:d873ccf4926b666f05fb
claim_id: claim:d873ccf4926b666f05fb
paper_key: hca:0263_10.1126_science.abq3061_cd915f6391
span_literal:
TREM2 and CD9, which encode proteins that can be detected by cell surface staining ( 22 ), further distinguished the SPP1 + mac(c) cluster from other cells

summary:
In Homo sapiens, TREM2 and CD9 further distinguish the SPP1-positive macrophage cluster mac(c) from other cells.


claim_key: hca:0263_10.1126_science.abq3061_cd915f6391:claim:0f6af5b83b510774c765
claim_id: claim:0f6af5b83b510774c765
paper_key: hca:0263_10.1126_science.abq3061_cd915f6391
span_literal: The expanding mac(c) cluster was the dominant SPP1 source in atria of patients with AFib
summary:
In Homo sapiens, the expanding macrophage cluster mac(c) is the dominant SPP1 source in atria of patients with atrial fibrillation.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:a2b6d6842f298816e1cd
claim_id: claim:a2b6d6842f298816e1cd
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
Graph-based clustering of merged and normalized cells identified robust, discrete clusters of epithelial cells ( EPCAM+ , KRT8+ , and KRT18+ ), fibroblasts ( COL1A1+ ), endothelial cells ( CLDN5+ ), T cells ( CD3D+ ), B cells (CD79A+ ), and myeloid cells ( LYZ+ ) based on canonical marker genes

summary:
In Homo sapiens colorectal cancer, epithelial cells are identified by positive expression of EPCAM, KRT8, and KRT18.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:fb40340878fe9e3a0b72
claim_id: claim:fb40340878fe9e3a0b72
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
Graph-based clustering of merged and normalized cells identified robust, discrete clusters of epithelial cells ( EPCAM+ , KRT8+ , and KRT18+ ), fibroblasts ( COL1A1+ ), endothelial cells ( CLDN5+ ), T cells ( CD3D+ ), B cells (CD79A+ ), and myeloid cells ( LYZ+ ) based on canonical marker genes

summary:
In Homo sapiens colorectal cancer, endothelial cells are identified by positive expression of CLDN5.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:c842180d7a73d70d8344
claim_id: claim:c842180d7a73d70d8344
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal: CAF-S1s were identified by the expression of fibroblast-specific markers (FAP, PDPN, PDGFRA).
summary:
In Homo sapiens colorectal cancer, cancer-associated fibroblast S1 cells are identified by expression of FAP, PDPN, and PDGFRA.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:402c1b564e206e0e4ac5
claim_id: claim:402c1b564e206e0e4ac5
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
CAF-S1s were further divided into (a) myo-fibroblastic (myCAF) (enhanced expression of collagen-related genes (COL1A1 and COL1A2) and fibroblast markers (FAP, PDPN) and (b) inflammatory (iCAF) subtypes (express chemokines such as CXCL12)

summary:
In Homo sapiens colorectal cancer, myofibroblastic cancer-associated fibroblasts show enhanced expression of COL1A1, COL1A2, FAP, and PDPN.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:adf20c51c29f803bbf19
claim_id: claim:adf20c51c29f803bbf19
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
we identified all five distinct CAF-S1 subtypes in patients with CRC: ecm-myCAF ( GJB; ANTXR1 , and SDC1 ), wound-myCAF ( SEMA3C ; ANTXR1 and CD9 ), TGF ß -myCAF ( CST1 ; TGFß1 ; ANTXR1 and LAMP5 ), IL-iCAF ( SCARA5 ; DLK1 ), and detox-iCAF ( ADH1B ; GPC3 )

summary:
In Homo sapiens colorectal cancer, extracellular matrix myofibroblastic cancer-associated fibroblast is marked by GJB, ANTXR1, and SDC1.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:cacaa9778e199bbb0b28
claim_id: claim:cacaa9778e199bbb0b28
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
we identified all five distinct CAF-S1 subtypes in patients with CRC: ecm-myCAF ( GJB; ANTXR1 , and SDC1 ), wound-myCAF ( SEMA3C ; ANTXR1 and CD9 ), TGF ß -myCAF ( CST1 ; TGFß1 ; ANTXR1 and LAMP5 ), IL-iCAF ( SCARA5 ; DLK1 ), and detox-iCAF ( ADH1B ; GPC3 )

summary:
In Homo sapiens colorectal cancer, wound myofibroblastic cancer-associated fibroblast is marked by SEMA3C, ANTXR1, and CD9.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:00fb2a0798ce48a8957c
claim_id: claim:00fb2a0798ce48a8957c
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
we identified all five distinct CAF-S1 subtypes in patients with CRC: ecm-myCAF ( GJB; ANTXR1 , and SDC1 ), wound-myCAF ( SEMA3C ; ANTXR1 and CD9 ), TGF ß -myCAF ( CST1 ; TGFß1 ; ANTXR1 and LAMP5 ), IL-iCAF ( SCARA5 ; DLK1 ), and detox-iCAF ( ADH1B ; GPC3 )

summary:
In Homo sapiens colorectal cancer, transforming growth factor beta myofibroblastic cancer-associated fibroblast is marked by CST1, TGFB1, ANTXR1, and LAMP5.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:5d138d9b20e1ecdb4cf8
claim_id: claim:5d138d9b20e1ecdb4cf8
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
summary:
In Homo sapiens colorectal cancer, interleukin inflammatory cancer-associated fibroblast is marked by SCARA5 and DLK1.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:779ac8594ac74a33cee1
claim_id: claim:779ac8594ac74a33cee1
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
summary:
In Homo sapiens colorectal cancer, detoxification inflammatory cancer-associated fibroblast is marked by ADH1B and GPC3.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:f7f42959aac8e48ffb43
claim_id: claim:f7f42959aac8e48ffb43
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
The CAF-S4 population expressed pericyte markers ( RGS5 , CSPG4 , and PDGFRB ), CD248 (endosialin) and EPAS1 ( HIF2 ), implying that this CAF subtype is vessel-associated, with hypoxia likely contributing to invasion and metastasis as proposed by others

summary:
In Homo sapiens colorectal cancer, cancer-associated fibroblast S4 expresses pericyte markers RGS5, CSPG4, PDGFRB, CD248, and EPAS1.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:a7d228cd38de27f71d95
claim_id: claim:a7d228cd38de27f71d95
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
summary: In Homo sapiens colorectal cancer, dendritic cells are identified by positive expression of CD1C.
span_literal:
we re-clustered these cells and identified CD1C+ dendritic cells, tumor-associated macrophages (C1Q+ TAMs, MRC1+), monocytes ( S100A8+) and granulocyte clusters in all four datasets


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:c9841fc89c1350a1b077
claim_id: claim:c9841fc89c1350a1b077
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
we re-clustered these cells and identified CD1C+ dendritic cells, tumor-associated macrophages (C1Q+ TAMs, MRC1+), monocytes ( S100A8+) and granulocyte clusters in all four datasets

summary:
In Homo sapiens colorectal cancer, tumor-associated macrophages are identified by positive expression of C1Q and MRC1.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:bc6d25f6cb2ca624da27
claim_id: claim:bc6d25f6cb2ca624da27
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
Monocytes revealed proinflammatory phenotypes (1L1B, S100A8, S100A9), while TAMs showed anti-inflammatory (APOE, SEPP1, CD163) signatures

summary:
In Homo sapiens colorectal cancer, monocytes express proinflammatory markers IL1B, S100A8, and S100A9.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:5b94fb82d56d2e582d9f
claim_id: claim:5b94fb82d56d2e582d9f
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
Monocytes revealed proinflammatory phenotypes (1L1B, S100A8, S100A9), while TAMs showed anti-inflammatory (APOE, SEPP1, CD163) signatures

summary:
In Homo sapiens colorectal cancer, tumor-associated macrophages express anti-inflammatory markers APOE, SEPP1, and CD163.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:d06d0fd438c96d10259c
claim_id: claim:d06d0fd438c96d10259c
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
FOXP3 CD4+ Tregs expressing immune checkpoint markers (PD-1, LAG3, CTLA4) were among the most abundant T cells in the CRCTME compared to non-malignant tissue

summary:
In Homo sapiens colorectal cancer, FOXP3-positive CD4-positive regulatory T cells express immune checkpoint markers PDCD1, LAG3, and CTLA4.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:eaaf0f5e4adf815a1954
claim_id: claim:eaaf0f5e4adf815a1954
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
summary: In Homo sapiens colorectal cancer, CD8-positive GZMK T cells express GZMA, GZMH, IFNG, and CCL4.
span_literal:
CD8+GZMK and CD8+GZMB expressed granzymes (GZMA, GZMH), interferon-gamma (IFNG), perforin (PRF1 in CD8+GZMB), and CCL4, which have been shown to mediate effector functions


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:f55cd22597eda0718c3c
claim_id: claim:f55cd22597eda0718c3c
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
CD8+GZMK and CD8+GZMB expressed granzymes (GZMA, GZMH), interferon-gamma (IFNG), perforin (PRF1 in CD8+GZMB), and CCL4, which have been shown to mediate effector functions

summary:
In Homo sapiens colorectal cancer, CD8-positive GZMB T cells express GZMA, GZMH, IFNG, PRF1, and CCL4.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:c2be3502fe1d230a1986
claim_id: claim:c2be3502fe1d230a1986
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
This cell state displayed activation (CXCL13) and exhaustion (LAG3, HAVCR2, CD96) markers, which may account for their participation in the immune checkpoint inhibitor sensitivity of MSI-H colorectal cancers.

summary:
In Homo sapiens colorectal cancer, CD8-positive GZMB T cells display activation marker CXCL13 and exhaustion markers LAG3, HAVCR2, and CD96.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:3d4f15e071c75555b211
claim_id: claim:3d4f15e071c75555b211
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
span_literal:
CD8+GZMK cells, on the other hand, have been identified as pre-dysfunctional T cells that express pre-dysfunctional markers such as EOMES and KLRG1

summary:
In Homo sapiens colorectal cancer, CD8-positive GZMK T cells express pre-dysfunctional markers EOMES and KLRG1.


claim_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757:claim:ad5a9241a329151f519c
claim_id: claim:ad5a9241a329151f519c
paper_key: hca:0264_10.1186_s13059-022-02677-z_ec9d743757
summary: In Homo sapiens colorectal cancer, epithelial cells are marked by EPCAM, KRT8, and KRT18.
span_literal:
Depending on the presence of known marker genes the clusters were grouped as: epithelial cells ( EPCAM , KRT8 , and KRT18 ), fibroblasts ( COL1A1 , DCN , COL1A2 , and C1R ), endothelial cells (CD31+), myeloid cells ( LYZ , MARCO , CD68 , and FCGR3A ), CD4 T cells ( CD4 ), CD8 T cells ( CD8A and CD8B ), and B cells ( MZB1 )


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:7e85ca68433003e643ef
claim_id: claim:7e85ca68433003e643ef
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
These include SOX2 -derived KRT5 + basal-like cells 3 , 4 (Phenograph Cluster 13), which exhibited increased RAS signaling and mesenchymal gene enrichment associated with wound response, and SOX9 -expressing AEPs 5 (Phenograph Clusters 10–11), which were tumor-specific and predominantly derived (80%) from the neoadjuvant-treated primary tumor MSK-LX679

summary:
In Homo sapiens primary lung adenocarcinoma, basal-like cells are marked by positive expression of KRT5 and are derived from the SOX2 lineage.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:9755e66a655cda199b56
claim_id: claim:9755e66a655cda199b56
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
These include SOX2 -derived KRT5 + basal-like cells 3 , 4 (Phenograph Cluster 13), which exhibited increased RAS signaling and mesenchymal gene enrichment associated with wound response, and SOX9 -expressing AEPs 5 (Phenograph Clusters 10–11), which were tumor-specific and predominantly derived (80%) from the neoadjuvant-treated primary tumor MSK-LX679

summary:
In Homo sapiens primary lung adenocarcinoma, alveolar epithelial progenitors are marked by positive expression of SOX9.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:0e60e00081f397a935d8
claim_id: claim:0e60e00081f397a935d8
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
Nearly all carcinoma-specific cell types showed increased expression of transcription factors associated with progenitor cell function ( ID2 , SOX2 and SOX9 , Extended Data Fig. 7c ).

summary:
In Homo sapiens lung adenocarcinoma, carcinoma-specific cell types show increased expression of ID2, SOX2, and SOX9, transcription factors associated with progenitor cell function.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:aea1ca75ada6adf05858
claim_id: claim:aea1ca75ada6adf05858
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
NK cells and to a lesser extent, NKT cells, most abundantly expressed the surface receptors NKG7, NCR3, FCGR3A(CD16) and NCAM1(CD56) .

summary:
In Homo sapiens, natural killer cells most abundantly express the surface receptors NKG7, NCR3, FCGR3A, and NCAM1.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:4f5708c995577e5707e4
claim_id: claim:4f5708c995577e5707e4
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
NK cells and to a lesser extent, NKT cells, most abundantly expressed the surface receptors NKG7, NCR3, FCGR3A(CD16) and NCAM1(CD56) .

summary:
In Homo sapiens, natural killer T cells express the surface receptors NKG7, NCR3, FCGR3A, and NCAM1.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:0f9f6d73f331f6f5e7df
claim_id: claim:0f9f6d73f331f6f5e7df
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal: NKT cells were distinguished from NK cells by specific expression of CD3 .
summary:
In Homo sapiens, natural killer T cells are distinguished from natural killer cells by specific expression of CD3.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:71b3a03671f117ced110
claim_id: claim:71b3a03671f117ced110
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
summary: In Homo sapiens lung, epithelial cells abundantly express CDH1, SOX2, and SOX9.
span_literal:
epithelial cells abundantly expressed E-cadherin ( CDH1 ) as well as the lineage-determining transcription factors SOX2 and SOX9 .


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:928bb35a5bb628d4357a
claim_id: claim:928bb35a5bb628d4357a
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
Some mesenchymal cell types expressed platelet-derived growth factor receptor α ( PDGFRα ) and LGR5 , characteristically expressed in the Wnt-responsive alveolar niche 59 , 60 ; whereas others expressed PDGFRβ and neural/glial antigen 2, encoded by chondroitin sulfate proteoglycan 4 , CSPG4 , characteristic of pericytes.

summary:
In Homo sapiens lung, pericytes are characterized by expression of platelet-derived growth factor receptor beta (PDGFRβ) and CSPG4.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:998fc95177cbc72c9ce0
claim_id: claim:998fc95177cbc72c9ce0
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
Pulmonary endothelial cells were distinguished from other stromal cell types by their expression of vascular endothelial (VE)-cadherin ( CDH5 ) and the early endothelial cell marker CD34 .

summary:
In Homo sapiens lung, pulmonary endothelial cells are distinguished from other stromal cell types by expression of CDH5 and CD34.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:60940634e14b8520ebac
claim_id: claim:60940634e14b8520ebac
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
A subset of ITGAM(CD11B) + immature myeloid cells expressing both CSF1R and immunosuppressive IL10 were further distinguished as myeloid-derived suppressor cells (MDSCs), which have been shown to dampen inflammatory responses 66 , 67 .

summary:
In Homo sapiens, myeloid-derived suppressor cells are marked by positive expression of ITGAM, CSF1R, and IL10.


claim_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5:claim:422c166e119ef1fcefcd
claim_id: claim:422c166e119ef1fcefcd
paper_key: hca:0265_10.1038_s41591-019-0750-6_ba0c7c2ce5
span_literal:
The highest SOX2 -expressing cluster differentially upregulated the EMT marker vimentin ( VIM) and DKK1 , an autocrine WNT inhibitor associated with metastatic latency 16 , and downregulated E-cadherin ( CDH1 )

summary:
In Homo sapiens metastatic lung adenocarcinoma, the highest SOX2-expressing cluster upregulates VIM and DKK1 and downregulates CDH1.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:f48dc4cf57c883895302
claim_id: claim:f48dc4cf57c883895302
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal: DG cells such as SEMA5A ( Duan et al., 2014 ) and MAML2
summary:
In Homo sapiens hippocampus, dentate gyrus granule cell clusters express shared markers SEMA5A and MAML2.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:4495a4e29ed21e3cab84
claim_id: claim:4495a4e29ed21e3cab84
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal:
Clusters Gra.Neu1, Gra.Neu6, and Gra.Neu7 express IL1RAP and COL25A1 in addition to shared granule cell markers.

summary:
In Homo sapiens hippocampus, granule neuron clusters Gra.Neu1, Gra.Neu6, and Gra.Neu7 express IL1RAP and COL25A1.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:77e3b9079c0d54ed2ba2
claim_id: claim:77e3b9079c0d54ed2ba2
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal: Gra.Neu5 distinctly expresses a recently described neuronal stem cell marker LPAR1
summary:
In Homo sapiens hippocampus, granule neuron 5 distinctly expresses the neuronal stem cell marker LPAR1.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:32379cf0d22610a65e2e
claim_id: claim:32379cf0d22610a65e2e
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal:
These clusters were identified by the respective marker genes: NOS1 , CXCL14/CNR1, CALB2, SST, and SOX6

summary:
In Homo sapiens hippocampus, inhibitory neuronal clusters were identified by the respective marker genes NOS1, CXCL14, CNR1, CALB2, SST, and SOX6.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:0d42a5da58b9b216125c
claim_id: claim:0d42a5da58b9b216125c
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal:
The PVALB-positive interneurons were identified by robust SOX6 expression without co-expression of SST as SOX6 labels both SST and PVALB -positive interneurons

summary:
In Homo sapiens hippocampus, parvalbumin-positive interneurons were identified by robust SOX6 expression without co-expression of SST.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:e020410bb705c8fad557
claim_id: claim:e020410bb705c8fad557
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal: Astro1 was marked by a relatively higher expression of classical astrocyte markers such as GFAP.
summary:
In Homo sapiens hippocampus, astrocyte cluster Astro1 was marked by a relatively higher expression of the classical astrocyte marker GFAP.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:fa275d05c20dd3822987
claim_id: claim:fa275d05c20dd3822987
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal:
Astro2 expressed astrocyte markers including AQP4 ( Figure 1C ) and was characterized by higher expression of ATP1B3 and NR4A3

summary:
In Homo sapiens hippocampus, astrocyte cluster Astro2 expressed astrocyte markers including AQP4 and was characterized by higher expression of ATP1B3 and NR4A3.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:6984b543add07d64783c
claim_id: claim:6984b543add07d64783c
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal: oligodendrocytes ( MOG, MOBP, OPALIN
summary:
In Homo sapiens hippocampus, MOG, MOBP, and OPALIN are markers enriched in oligodendrocytes, while PCDH15 and FRMD4A are markers enriched in committed oligodendrocyte precursors.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:c3d353886e9a67efa155
claim_id: claim:c3d353886e9a67efa155
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal: committed oligodendrocyte precursors (COPs) ( PCDH15, FRMD4A
summary:
In Homo sapiens hippocampus, PCDH15 and FRMD4A are markers enriched in committed oligodendrocyte precursors.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:d59afaec37db2a33bdeb
claim_id: claim:d59afaec37db2a33bdeb
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal:
All of these three clusters express markers of homeostatic microglia, including P2RY12, and Micro1 expresses higher levels of EGR3, a gene enriched in pre-active state microglia

summary:
In Homo sapiens hippocampus, all three microglia clusters express markers of homeostatic microglia including P2RY12, and microglia cluster Micro1 expresses higher levels of EGR3, a gene enriched in pre-active state microglia.


claim_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c:claim:c59b64f534aeb23f5a48
claim_id: claim:c59b64f534aeb23f5a48
paper_key: hca:0266_10.1016_j.neuron.2021.05.003_0cca870e2c
span_literal:
All of these three clusters express markers of homeostatic microglia, including P2RY12, and Micro1 expresses higher levels of EGR3, a gene enriched in pre-active state microglia

summary:
In Homo sapiens hippocampus, microglia cluster Micro1 expresses higher levels of EGR3, a gene enriched in pre-active state microglia.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:215a37846217ad3607d4
claim_id: claim:215a37846217ad3607d4
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
We uncover a novel scar-associated TREM2 + CD9 + macrophage subpopulation, which expands in liver fibrosis, differentiates from circulating monocytes and is pro-fibrogenic.

summary:
In Homo sapiens, scar-associated macrophages are marked by positive expression of TREM2 and CD9, expanding in liver fibrosis.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:85ee1682a8e157184c12
claim_id: claim:85ee1682a8e157184c12
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
We also define novel ACKR1 + and PLVAP + endothelial cells which expand in cirrhosis, are topographically scar-restricted and enhance leucocyte transmigration.

summary:
In Homo sapiens, scar-associated endothelial cells are marked by positive expression of ACKR1 and PLVAP, expanding in liver cirrhosis.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:74c5ea8d8fb856d98bca
claim_id: claim:74c5ea8d8fb856d98bca
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Clusters MP(6) and MP(7) were enriched in CD163 , MARCO and TIMD4 ( Extended Data Fig. 4b ); tissue staining confirmed these as Kupffer cells (KC; resident liver macrophages), facilitating annotation of these clusters as KC(1) and KC(2) respectively ( Extended Data Fig. 4c ).

summary:
In Homo sapiens, Kupffer cells (resident liver macrophages) are enriched in CD163, MARCO, and TIMD4.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:4cd0504dce9e1708ad7e
claim_id: claim:4cd0504dce9e1708ad7e
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
A lack of TIMD4 expression distinguished KC(2) from KC(1) ( Extended Data Fig. 4b ); cell counting demonstrated TIMD4 + cell numbers to be equivalent between healthy and cirrhotic livers, but showed a loss of MARCO + cells, consistent with selective reduction in MARCO + TIMD4 - KC(2) in liver fibrosis ( Fig. 2c , Extended Data Fig. 4d, e ).

summary:
In Homo sapiens, Kupffer cell 2 is distinguished from Kupffer cell 1 by a lack of TIMD4 expression and is MARCO-positive and TIMD4-negative.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:1dd2ffb45526de1a673e
claim_id: claim:1dd2ffb45526de1a673e
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
summary: In Homo sapiens, scar-associated macrophages express the unique markers TREM2 and CD9.
span_literal:
Scar-associated clusters SAMΦ(1) and SAMΦ(2) expressed the unique markers TREM2 and CD9 ( Fig. 2d, e ).


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:729e5ab32bfe25c5f747
claim_id: claim:729e5ab32bfe25c5f747
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
These SAMΦ-defining signatures included genes such as TREM2 , IL1B , SPP1 , LGALS3 , CCR2 , and TNFSF12 , some of which are known to regulate the function of scar-producing myofibroblasts in fibrotic liver diseases 10 – 13 .

summary:
In Homo sapiens, scar-associated macrophages are defined by expression of TREM2, IL1B, SPP1, LGALS3, CCR2, and TNFSF12.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:5cd82e4aeced6e7a1ba8
claim_id: claim:5cd82e4aeced6e7a1ba8
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Module 1 contained multiple pro-fibrogenic genes including SPP1 , LGALS3 , CCL2 , CXCL8 , PDGFB and VEGFA 10 – 13 , and displayed ontology terms consistent with promoting tissue fibrosis and angiogenesis ( Fig. 3c, d ; Supplementary Table 10 ).

summary:
In Homo sapiens, scar-associated macrophages upregulate SPP1, LGALS3, CCL2, CXCL8, PDGFB, and VEGFA during monocyte-to-scar-associated macrophage differentiation.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:6364c707c729f47377b6
claim_id: claim:6364c707c729f47377b6
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Disease-specific endothelial cells Endo(6) and Endo(7), CD34 + PLVAP + VWA1 + and CD34 + PLVAP + ACKR1 + respectively ( Fig. 4a-c , Extended Data Fig. 8b ), expanded in cirrhotic liver tissue ( Fig. 4e ) and were restricted to the fibrotic niche ( Fig. 4d, e , Extended Data Fig. 8c ), allowing annotation as scar-associated endothelia SAEndo(1) and SAEndo(2) respectively.

summary:
In Homo sapiens, scar-associated endothelial cell 1 is marked by CD34, PLVAP, and VWA1, while scar-associated endothelial cell 2 is marked by CD34, PLVAP, and ACKR1, both expanding in cirrhotic liver.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:e8069d4eb106132927db
claim_id: claim:e8069d4eb106132927db
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Disease-specific endothelial cells Endo(6) and Endo(7), CD34 + PLVAP + VWA1 + and CD34 + PLVAP + ACKR1 + respectively ( Fig. 4a-c , Extended Data Fig. 8b ), expanded in cirrhotic liver tissue ( Fig. 4e ) and were restricted to the fibrotic niche ( Fig. 4d, e , Extended Data Fig. 8c ), allowing annotation as scar-associated endothelia SAEndo(1) and SAEndo(2) respectively.

summary:
In Homo sapiens, scar-associated endothelial cell 2 is marked by CD34, PLVAP, and ACKR1, expanding in cirrhotic liver.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:3ff517783ca80107a13a
claim_id: claim:3ff517783ca80107a13a
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
In contrast, CD34 - CLEC4M + Endo(1) (annotated as liver sinusoidal endothelial cells), were reduced in fibrotic livers ( Fig. 4b, e ).

summary:
In Homo sapiens, liver sinusoidal endothelial cells are marked by negative expression of CD34 and positive expression of CLEC4M.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:5684a5cf0026a71f4d28
claim_id: claim:5684a5cf0026a71f4d28
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Endo(6) (SAEndo(1)) cells expressed pro-fibrogenic genes including PDGFD , PDGFB , LOX , LOXL2 ; associated ontology terms included extracellular matrix organization (signature A; Extended Data Fig. 8g ).

summary:
In Homo sapiens, scar-associated endothelial cell 1 expresses pro-fibrogenic genes including PDGFD, PDGFB, LOX, and LOXL2.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:db06fbe0e9b2819cc8fc
claim_id: claim:db06fbe0e9b2819cc8fc
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
summary: In Homo sapiens, vascular smooth muscle cells are distinguished by MYH11 expression in the liver.
span_literal:
Cluster Mes(1), distinguished by MYH11 expression ( Fig. 5b , Extended Data Fig. 9a ), was identified as vascular smooth muscle cells (VSMC) ( Fig. 5c ).


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:ca8c7881a317632c653a
claim_id: claim:ca8c7881a317632c653a
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
summary: In Homo sapiens, hepatic stellate cells express high levels of RGS5 in the liver.
span_literal:
Cluster Mes(2) expressed high levels of RGS5 ( Fig. 5b , Extended Data Fig. 9a ), and RGS5 staining identified this population as hepatic stellate cells (HSC) ( Fig. 5c ).


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:75e68de593d98948e35b
claim_id: claim:75e68de593d98948e35b
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Cluster Mes(3) (distinguished by PDGFRA expression) expressed high levels of fibrillar collagens and pro-fibrogenic genes ( Fig. 5b, d , Extended Data Fig. 9a ).

summary:
In Homo sapiens, scar-associated mesenchymal cells are distinguished by PDGFRA expression in the liver.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:06a68dc6a9289cdc3e61
claim_id: claim:06a68dc6a9289cdc3e61
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
OSR1 expression distinguished cluster SAMesB ( Extended Data Fig. 9c ), and labelled a subpopulation of periportal cells in healthy liver and scar-associated cells in the fibrotic niche ( Extended Data Fig. 9e, f ).

summary:
In Homo sapiens, scar-associated mesenchymal cell subpopulation B is distinguished by OSR1 expression in the liver.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:82d9f675d2650fe73bd5
claim_id: claim:82d9f675d2650fe73bd5
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
SAEndo expressed high levels of non-canonical Notch ligands JAG1 , JAG2 and DLL4 interacting with Notch receptor NOTCH3 on SAMes ( Fig. 6e ).

summary:
In Homo sapiens, scar-associated endothelial cells express high levels of JAG1, JAG2, and DLL4, while scar-associated mesenchymal cells express NOTCH3.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:7c28a5907bf57be790b1
claim_id: claim:7c28a5907bf57be790b1
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
SAEndo expressed high levels of non-canonical Notch ligands JAG1 , JAG2 and DLL4 interacting with Notch receptor NOTCH3 on SAMes ( Fig. 6e ).

summary:
In Homo sapiens, scar-associated mesenchymal cells express NOTCH3, which interacts with ligands from scar-associated endothelial cells.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:721255fcd24fb0414f77
claim_id: claim:721255fcd24fb0414f77
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Additionally, SAMΦ expressed mesenchymal cell mitogens TNFSF12 and PDGFB , signaling to cognate receptors TNFRSF12A and PDGFRA on SAMes ( Fig. 6a ).

summary:
In Homo sapiens, scar-associated macrophages express TNFSF12 and PDGFB, signaling to TNFRSF12A and PDGFRA on scar-associated mesenchymal cells.


claim_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445:claim:4bb9cec4e96cc75fb917
claim_id: claim:4bb9cec4e96cc75fb917
paper_key: hca:0267_10.1038_s41586-019-1631-3_36f09e3445
span_literal:
Additionally, SAMΦ expressed mesenchymal cell mitogens TNFSF12 and PDGFB , signaling to cognate receptors TNFRSF12A and PDGFRA on SAMes ( Fig. 6a ).

summary:
In Homo sapiens, scar-associated mesenchymal cells express TNFRSF12A and PDGFRA, receiving signals from scar-associated macrophages.


claim_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0:claim:e9455085c4d1094da4d9
claim_id: claim:e9455085c4d1094da4d9
paper_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0
span_literal:
A novel transcription factor AEBP1 was identified as a crucial cardiac fibrosis regulator in ACTA2 + myofibroblasts.

summary:
In Homo sapiens, AEBP1 was identified as a crucial cardiac fibrosis regulator in ACTA2-positive myofibroblasts.


claim_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0:claim:2b2fc278b41dfd60909e
claim_id: claim:2b2fc278b41dfd60909e
paper_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0
span_literal:
Furthermore, a subset of tissue-resident macrophage, CXCL8 hi CCR2 + HLA-DR hi macrophage was particularly identified in severely fibrotic area, which interacted with activated endothelial cell via DARC , that potentially facilitate leukocyte recruitment and infiltration in human heart failure.

summary:
In Homo sapiens, a subset of tissue-resident macrophage expressing high CXCL8, CCR2, and high HLA-DR was identified in severely fibrotic area of the heart, interacting with activated endothelial cell via DARC.


claim_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0:claim:25650f803d54d46d394e
claim_id: claim:25650f803d54d46d394e
paper_key: hca:0268_10.1007_s00395-021-00897-1_9d51738bc0
span_literal:
Furthermore, a subset of tissue-resident macrophage, CXCL8 hi CCR2 + HLA-DR hi macrophage was particularly identified in severely fibrotic area, which interacted with activated endothelial cell via DARC , that potentially facilitate leukocyte recruitment and infiltration in human heart failure.

summary:
In Homo sapiens, activated endothelial cell interacted with tissue-resident macrophage via DARC in human heart failure.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:d84f13e7c77a28196a8a
claim_id: claim:d84f13e7c77a28196a8a
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
span_literal: RPCs expressed PAX6 and SOX2 transcription factors, which are key regulators of neuronal fate,
summary:
In Homo sapiens, retinal progenitor cells express PAX6 and SOX2, which are key regulators of neuronal fate.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:a41a1acb992341464466
claim_id: claim:a41a1acb992341464466
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
summary: In Homo sapiens, retinal progenitor cells express LHX2, VSX2, and ASCL1 as markers.
span_literal:
LHX2 , required for maintenance of open chromatin during retinogenesis 46 and gliogenesis, 47 and the RPC markers VSX2 and ASCL1


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:110577c6f0a5acd029b1
claim_id: claim:110577c6f0a5acd029b1
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
span_literal: The G2/M phase marker MKi67 was predominantly expressed by cells in RPC1, RPC2, and RPC5.
summary:
In Homo sapiens, the G2/M phase marker MKI67 is predominantly expressed by retinal progenitor cell 1, retinal progenitor cell 2, and retinal progenitor cell 5.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:af871c1ee0485901773f
claim_id: claim:af871c1ee0485901773f
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
span_literal:
The S phase marker PCNA was distributed more broadly; however, the majority of PCNA -positive cells were identified in RPC clusters 1, 2, 4, and 5

summary:
In Homo sapiens, the S phase marker PCNA is predominantly expressed in retinal progenitor cell 1, retinal progenitor cell 2, retinal progenitor cell 4, and retinal progenitor cell 5.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:89ad0fa563205460ab8b
claim_id: claim:89ad0fa563205460ab8b
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
span_literal:
Based on previous work, RGCs were classified by the expression of the following genes: POU4F2 , ISL1 , RBPMS , SNCG , GAP43 , NEFL/M, ELAVL4 , EOMES , and DCX .

summary:
In Homo sapiens, retinal ganglion cells are classified by the expression of POU4F2, ISL1, RBPMS, SNCG, GAP43, NEFL, NEFM, ELAVL4, EOMES, and DCX.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:a2b8f5c963c1cfa96745
claim_id: claim:a2b8f5c963c1cfa96745
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
span_literal:
The low levels of ATOH7 expression in RGC1 and RGC3, in conjunction with the fact that cells in these subpopulations expressed markers of differentiated RGCs, such as SNCG , RBPMS , GAP43 , and NEFM

summary:
In Homo sapiens, retinal ganglion cell 1 and retinal ganglion cell 3 express low levels of ATOH7 and express markers of differentiated retinal ganglion cells such as SNCG, RBPMS, GAP43, and NEFM.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:b6400f10936978c132a3
claim_id: claim:b6400f10936978c132a3
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
span_literal:
The low levels of ATOH7 expression in RGC1 and RGC3, in conjunction with the fact that cells in these subpopulations expressed markers of differentiated RGCs, such as SNCG , RBPMS , GAP43 , and NEFM

summary:
In Homo sapiens, retinal ganglion cell 3 expresses low levels of ATOH7 and expresses markers of differentiated retinal ganglion cells such as SNCG, RBPMS, GAP43, and NEFM.


claim_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589:claim:bcafb9f472cf4901f451
claim_id: claim:bcafb9f472cf4901f451
paper_key: hca:0269_10.1016_j.xgen.2022.100142_dd45161589
summary: In Homo sapiens, retinal progenitor cell 1 expresses the proliferative marker MKI67.
span_literal:
RPC1 was selected as the root of the trajectories due to the expression of the proliferative marker MKI67


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:6a3b7d81ada110058abe
claim_id: claim:6a3b7d81ada110058abe
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
span_literal:
there was a distinct cluster of myeloid progenitors (MP) expressing CD34 , low levels of SPINK2 and PTPRC , but not HOXA genes, which are required to generate definitive HSC

summary:
In Homo sapiens, myeloid progenitors express CD34, low levels of SPINK2 and PTPRC, but not HOXA genes, distinguishing them from definitive hematopoietic stem cells.


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:6ce422ff1aa9afbc8051
claim_id: claim:6ce422ff1aa9afbc8051
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
span_literal: cDC2 expressed bonafide DC markers (e.g., HLA-DR , CD1C , CLEC10A )
summary:
In Homo sapiens, conventional dendritic cell type 2 expresses HLA-DR, CD1C, and CLEC10A as bonafide dendritic cell markers.


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:960063a2476a96643b2d
claim_id: claim:960063a2476a96643b2d
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
summary: In Homo sapiens, CCR7-positive dendritic cells express CCR7 and LAMP3 and lack CD14.
span_literal:
The small subpopulation annotated as CCR7 + DCs showed a strong and specific prediction using a foetal thymus 21 CCR7 DC LR model (Supplementary Fig. 8 ) and the expected marker expression (e.g., CCR7 , LAMP3 and lack of CD14 ; Fig. 5b, c and Supplementary Fig. 9D ).


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:6b4b8e169c6717a91264
claim_id: claim:6b4b8e169c6717a91264
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
span_literal:
We observed positive cells for DC markers (CD1C, CD209, CD11c, HLA-DR, CD86) and low levels of the macrophage marker CD14, thus validating the DC phenotype

summary:
In Homo sapiens, dendritic cells are positive for CD1C, CD209, CD11c, HLA-DR, and CD86, and show low levels of the macrophage marker CD14.


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:a7531b266422a4eaaa28
claim_id: claim:a7531b266422a4eaaa28
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
span_literal:
Monocytes from the PRKCB KO cell line after the DC differentiation protocol had a myeloid-derived suppressor profile, including low expression of HLA-DR and CD74 with high levels of CCL2 and MMP9

summary:
In Homo sapiens, myeloid-derived suppressor cells are characterized by low expression of HLA-DR and CD74 and high levels of CCL2 and MMP9.


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:94ee77e69d20ae460b4f
claim_id: claim:94ee77e69d20ae460b4f
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
span_literal:
LSP1 and ICAM1 KOs monocytes from the DC protocol had a transcriptomic profile with intermediate monocytes features. They were characterised by the upregulation of the HLA genes and downregulation of the S100 gene family

summary:
In Homo sapiens, intermediate monocytes are characterized by upregulation of HLA genes and downregulation of the S100 gene family.


claim_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96:claim:453b1e6183b9bd4fd674
claim_id: claim:453b1e6183b9bd4fd674
paper_key: hca:0270_10.1038_s41467-022-30557-4_ba2c76ba96
summary: In Homo sapiens, macrophages are positive for CD14 and CD64.
span_literal:
By day31 + 7 there was an enrichment in macrophages, representing a total of 94.1% of cells (Fig. 3c ), which was consistent with the CD14 + /CD64 + cells analysed by FACS


claim_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5:claim:25b1a644ee15645c4354
claim_id: claim:25b1a644ee15645c4354
paper_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5
summary: In Homo sapiens salivary gland, B lymphocytes are marked by MS4A1.
span_literal:
B lymphocytes ( MS4A1 ), T helper (T h ) cells ( CD40LG ) and two cytotoxic T c subtypes (T cells ( CD8A )—subtype 1 ( EOMES and GMZA , exhausted type) and subtype 2 ( SPRY1 and ITAG1 , tissue-resident memory type).


claim_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5:claim:49d1f02ee752fa830d4d
claim_id: claim:49d1f02ee752fa830d4d
paper_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5
summary:
In Homo sapiens salivary gland, cytotoxic T cell subtype 1 (exhausted type) is marked by EOMES and GMZA.


claim_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5:claim:0cc1824093eaa12477ab
claim_id: claim:0cc1824093eaa12477ab
paper_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5
summary:
In Homo sapiens salivary gland, cytotoxic T cell subtype 2 (tissue-resident memory type) is marked by SPRY1 and ITAG1.


claim_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5:claim:a05542db72ea837a8c6f
claim_id: claim:a05542db72ea837a8c6f
paper_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5
summary: In Homo sapiens gingiva, cytotoxic T cells are marked by CD8A.
span_literal:
Among T cells, cytotoxic T cells (T c ; CD8A ), helper T cells (T h ; CD40LG ), regulatory T cells (T reg ; LAIR2), γδ T cells (γδ; KLRC4 ), mucosal-associated invariant T (MAIT) cells ( IL23R) ) and a cycling subset ( KI67 ) were cataloged.


claim_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5:claim:5dfcaea13fcb8e804563
claim_id: claim:5dfcaea13fcb8e804563
paper_key: hca:0271_10.1038_s41591-021-01296-8_efdcdd17f5
summary: In Homo sapiens gingiva, Basal 1 epithelial cells are defined by enriched expression of CXCL14.
span_literal:
Four basal epithelial cell populations (Basal 1–4) were discovered, defined by enriched expression of CXCL14 , KRT19 , COL7A1 and DSC2/3 , respectively.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:84776a5237aa96c84671
claim_id: claim:84776a5237aa96c84671
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
summary: In Homo sapiens, type II pneumocytes co-express ACE2 and TMPRSS2.
span_literal:
We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:5f1f491c302f8ab5fce8
claim_id: claim:5f1f491c302f8ab5fce8
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
summary: In Homo sapiens, type II pneumocytes express ACE2 and TMPRSS2.
span_literal:
Here, we found that ACE2 and TMPRSS2 were primarily expressed within type II pneumocytes and ciliated cells, in line with our analysis of the NHP-derived cells


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:7cfaf72c18be88d5a15b
claim_id: claim:7cfaf72c18be88d5a15b
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
In type II pneumocytes (identified by unique expression of surfactant proteins SFTPC , SFTPB , and SFTPA1 ), we found 1.4% of cells expressing ACE2 (FDR-adjusted p = 1.35E−21), 34.2% expressing TMPRSS2 (FDR-adjusted p < 1E−300), and 0.8% co-expressing both.

summary:
In Homo sapiens, type II pneumocytes are identified by unique expression of SFTPC, SFTPB, and SFTPA1, and express ACE2 and TMPRSS2.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:e4d62f78b714e0918d25
claim_id: claim:e4d62f78b714e0918d25
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
We found significant enrichment of BATF among ACE2 + TMPRSS2 + cells (FDR-adjusted p = 3.25E−7), which has been demonstrated previously to be upregulated by type I and type II IFNs

summary:
In Homo sapiens, ACE2-positive TMPRSS2-positive type II pneumocytes show significant enrichment of BATF.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:5e8e65f3802ab4973dae
claim_id: claim:5e8e65f3802ab4973dae
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
summary: In Homo sapiens, TRIM28 is co-expressed with ACE2 and TMPRSS2 in type II pneumocytes.
span_literal:
Of note, we also observed TRIM28 co-expressed with ACE2 and TMPRSS2 among type II pneumocytes in this dataset (FDR-adjusted p = 2.34E−9), which might play a role in potentiating an IFN response in lung epithelial cells


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:81869dcd1d53d55e072d
claim_id: claim:81869dcd1d53d55e072d
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
summary: In Homo sapiens, absorptive enterocytes selectively express ACE2.
span_literal:
we confirmed a large abundance of ACE2 + cells with selective expression within absorptive enterocytes (29.7% ACE2 + , FDR-adjusted p = 2.46E−100)


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:ee36164f0678cbfd6860
claim_id: claim:ee36164f0678cbfd6860
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
We observed significant enrichment of ACE2 expression in apical epithelial cells and, to a lesser extent, ciliated cells compared with all cell types recovered from surgically resected mucosa (1% of apical epithelial cells, FDR-adjusted p = 4.55E−6, n.s. in ciliated cells)

summary:
In Homo sapiens, apical epithelial cells of the nasal mucosa show significant enrichment of ACE2 expression.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:2e3f93dced972b5d05d2
claim_id: claim:2e3f93dced972b5d05d2
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
Cluster 7 secretory cells are marked by S100P , LYPD2 , PSCA , CEACAM5 , and STEAP4 ; encompass some MUC5AC goblet cells; and contain the most significantly enriched ACE2 and TMPRSS2 expression (4% express ACE2 , FDR-adjusted p = 7.32E−28; 28% express TMPRSS2 , FDR-adjusted p = 2.15E−132; Table S6 ).

summary:
In Homo sapiens, secretory goblet cluster 7 cells are marked by S100P, LYPD2, PSCA, CEACAM5, STEAP4, and MUC5AC, and show enriched ACE2 and TMPRSS2 expression.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:f56872098abc2933cea4
claim_id: claim:f56872098abc2933cea4
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
Notably, we observed significant upregulation of ADAR , GBP2 , OAS1 , JAK1 , and DUOX2 (FDR adjusted, all p < 0.02) within ACE2 + TMPRSS2 + cells, potentially indicative of IFN signaling

summary:
In Homo sapiens, ACE2-positive TMPRSS2-positive secretory cells of the nasal mucosa show significant upregulation of ADAR, GBP2, OAS1, JAK1, and DUOX2.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:8b159dc20d19fafe322b
claim_id: claim:8b159dc20d19fafe322b
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
Strikingly, ACE2 was most upregulated in samples from influenza-virus-infected individuals within bystander goblet or squamous cells not directly infected by virus

summary:
In Homo sapiens, ACE2 is most upregulated in bystander goblet cells and squamous cells during influenza virus infection.


claim_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837:claim:07f438ead6091f3279d6
claim_id: claim:07f438ead6091f3279d6
paper_key: hca:0272_10.1016_j.cell.2020.04.035_15a2d05837
span_literal:
Strikingly, ACE2 was most upregulated in samples from influenza-virus-infected individuals within bystander goblet or squamous cells not directly infected by virus

summary:
In Homo sapiens, ACE2 is most upregulated in bystander squamous cells during influenza virus infection.


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:6f40b9cb7c024165cdab
claim_id: claim:6f40b9cb7c024165cdab
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
span_literal:
As expected from prior literature, the AT2 cells showed highest ACE2 expression in the lung both in terms of their CPM values

summary:
In Homo sapiens, alveolar type 2 cells in the lung showed the highest ACE2 (angiotensin-converting enzyme 2) expression among lung cell types.


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:90e48d56eb75abc76083
claim_id: claim:90e48d56eb75abc76083
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
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

summary:
In Homo sapiens, TMPRSS2 (transmembrane protease serine 2) expression in the lung was strong with specificity for alveolar type 2 cells.


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:2c48c2bacd8ef21e0323
claim_id: claim:2c48c2bacd8ef21e0323
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
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

summary:
In Homo sapiens, FOXN4-positive cells were identified as a rare cell type in human bronchial epithelial cells, marked by FOXN4 expression.


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:ee56af25347cfed3ba67
claim_id: claim:ee56af25347cfed3ba67
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
span_literal:
ACE2 were comparable or 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 (angiotensin-converting enzyme 2) is most strongly expressed in transient secretory cells (secretory3) among human bronchial epithelial cell types.


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:62bb297a5255eb447707
claim_id: claim:62bb297a5255eb447707
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
span_literal:
Interestingly, the cell population enriched for ACE2 + cells was also the one most strongly expressing TMPRSS2

summary:
In Homo sapiens, the transient secretory cell population enriched for ACE2 (angiotensin-converting enzyme 2) also most strongly expresses TMPRSS2 (transmembrane protease serine 2) in bronchial epithelial cells.


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:7b4745e9c9c7e1df4ee8
claim_id: claim:7b4745e9c9c7e1df4ee8
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
span_literal:
Interestingly, also transient secretory cells in the HBECs showed an intermediate expression of FURIN

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


claim_key: hca:0273_10.15252_embj.20105114_43aa56d0ae:claim:0ccbdf34cde99f8cb10f
claim_id: claim:0ccbdf34cde99f8cb10f
paper_key: hca:0273_10.15252_embj.20105114_43aa56d0ae
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 vulnerable for SARS‐CoV‐2 infection.

summary:
In Homo sapiens, about 40% of ACE2 (angiotensin-converting enzyme 2)-positive transient secretory cells co-express the protease TMPRSS2 (transmembrane protease serine 2).


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:eb6352004b51bb999c42
claim_id: claim:eb6352004b51bb999c42
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal: mucous acini (M-Acinar; C2), characterized by high expression of MUC5B , TFF3 , and BPIFB2
summary:
In Homo sapiens, mucous acinar cells of the minor salivary gland are characterized by high expression of MUC5B, TFF3, and BPIFB2.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:ddbd96773a9457ef8f88
claim_id: claim:ddbd96773a9457ef8f88
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
C6 and C17 were characterized by enriched expression of ductal markers ( KRT19 , KRT7 , and WFDC2 ) and basal ductal makers ( KRT14 and KRT5)

summary:
In Homo sapiens, ductal cells of the minor salivary gland are characterized by enriched expression of KRT19, KRT7, and WFDC2, while basal ductal cells express KRT14 and KRT5.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:d4c696d1b06f84b2c794
claim_id: claim:d4c696d1b06f84b2c794
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
C16 displayed high expression of canonical myoepithelial cells (MECs) markers, such as TAGLN , ACTA2 , and KRT14

summary:
In Homo sapiens, myoepithelial cells of the minor salivary gland display high expression of TAGLN, ACTA2, and KRT14.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:21a15d45df24a2449d9d
claim_id: claim:21a15d45df24a2449d9d
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal: SMCs (C15), as identified by expression of ACTA2 , MYH1 , and MYL9
summary:
In Homo sapiens, smooth muscle cells of the minor salivary gland are identified by expression of ACTA2, MYH1, and MYL9.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:1699fe4e97fdffa0fc4f
claim_id: claim:1699fe4e97fdffa0fc4f
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
The presence of PECAM , CDH5 , and AQP1 in C5 and C19 identified these clusters as endothelial cells.

summary:
In Homo sapiens, endothelial cells of the minor salivary gland are identified by expression of PECAM, CDH5, and AQP1.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:3db6eaf1bda32a501153
claim_id: claim:3db6eaf1bda32a501153
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
An additional population which not only expresses PECAM1 , but also LYVE1 and PROX1 was identified as LEC (C20).

summary:
In Homo sapiens, lymphatic endothelial cells of the minor salivary gland express PECAM1, LYVE1, and PROX1.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:0f52f969294afa39a64b
claim_id: claim:0f52f969294afa39a64b
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
multiple immune cell populations expressing PTPRC were observed including myeloid cells (C11), T cells (C7), and plasma cells (C9, C12, and C18).

summary:
In Homo sapiens, immune cells of the minor salivary gland, including myeloid cells, T cells, and plasma cells, express PTPRC.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:870bde61f5ddccf81e0d
claim_id: claim:870bde61f5ddccf81e0d
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal: the ZG16B gene was enriched in serous and seromucous acinar cells.
summary:
In Homo sapiens, ZG16B gene expression is enriched in serous acinar cells of the minor salivary gland.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:6c5ef36c8901575207a8
claim_id: claim:6c5ef36c8901575207a8
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal: the ZG16B gene was enriched in serous and seromucous acinar cells.
summary:
In Homo sapiens, ZG16B gene expression is enriched in seromucous acinar cells of the minor salivary gland.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:d99f03fb719659c46dc7
claim_id: claim:d99f03fb719659c46dc7
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
both the expression level and distribution pattern of the ZG16B gene are similar to MUC7, a known serous acinar marker

summary:
In Homo sapiens, MUC7 is a known marker of serous acinar cells, and ZG16B shows a similar expression pattern in these cells.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:0b8878e25274479c5b5a
claim_id: claim:0b8878e25274479c5b5a
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
ZG16B protein exhibited strong co-expression with MUC7 in serous acinar cells in MSG sections of HVs. In contrast, no expression was observed in ductal cells, marked by KRT19 staining

summary:
In Homo sapiens, ZG16B and MUC7 are co-expressed in serous acinar cells of the minor salivary gland, while ductal cells, marked by KRT19, do not express ZG16B.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:1b579417a49be75923c3
claim_id: claim:1b579417a49be75923c3
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
ZG16B protein exhibited strong co-expression with MUC7 in serous acinar cells in MSG sections of HVs. In contrast, no expression was observed in ductal cells, marked by KRT19 staining

summary:
In Homo sapiens, ductal cells of the minor salivary gland are marked by KRT19 and do not express ZG16B.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:3881803ca5392e4c85e5
claim_id: claim:3881803ca5392e4c85e5
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
Single-cell RNA-seq analysis of healthy MSG localized ZG16B expression to two discrete acinar cell populations.

summary:
In Homo sapiens, single-cell RNA-seq analysis of healthy minor salivary gland localized ZG16B expression to two discrete acinar cell populations.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:9efcdcdd037415a15ba1
claim_id: claim:9efcdcdd037415a15ba1
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
ZG16B was expressed predominantly in serous and seromucous acinar cells co-expressing MUC7, suggesting that it could be involved in establishing and maintaining exocytosis of serous secretions.

summary:
In Homo sapiens, ZG16B is expressed predominantly in serous and seromucous acinar cells that co-express MUC7 in the salivary gland.


claim_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1:claim:6de7df5d7c007655e431
claim_id: claim:6de7df5d7c007655e431
paper_key: hca:0274_10.1016_j.isci.2021.103592_3ec037cca1
span_literal:
ZG16B was expressed predominantly in serous and seromucous acinar cells co-expressing MUC7, suggesting that it could be involved in establishing and maintaining exocytosis of serous secretions.

summary:
In Homo sapiens, ZG16B is expressed predominantly in seromucous acinar cells that co-express MUC7 in the salivary gland.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:67df301d2de972ac74e0
claim_id: claim:67df301d2de972ac74e0
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal: non-classical monocytes marked by FCGR3A (encoding CD16a) and low expression of CD14
summary:
In Homo sapiens, non-classical monocytes are marked by positive expression of FCGR3A and low expression of CD14.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:5def84e2733909a17f08
claim_id: claim:5def84e2733909a17f08
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
A distinct subset of CD14 + monocytes (cluster 1) ( Figure 2 A) marked by high expression of HLA-DRA , HLA-DRB1 , and co-stimulatory molecule CD83 ( Figure S2 D), the engagement of which has been linked to prolonged expansion of antigen-specific T cells ( Hirano et al., 2006 ), was selectively detected in mild COVID-19 ( Figure 2 C).

summary:
In Homo sapiens, HLA-DR-high CD83-high activated inflammatory monocytes in mild COVID-19 are marked by high expression of HLA-DRA, HLA-DRB1, and CD83.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:8a1d84b219dbb50872fe
claim_id: claim:8a1d84b219dbb50872fe
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal: Both cluster 1 and cluster 2 expressed high levels of ISGs IFI6 and ISG15 ( Figure S2 D).
summary:
In Homo sapiens, HLA-DR-high activated inflammatory monocytes (clusters 1 and 2) express high levels of interferon-stimulated genes IFI6 and ISG15.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:b032c4a2c9376cf9e9d2
claim_id: claim:b032c4a2c9376cf9e9d2
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
In patients with severe COVID-19, monocytes showed low expression of HLA-DR and high expression of alarmins S100A8/9/12 (cluster 3, Figures 2 A–2C and S2 D).

summary:
In Homo sapiens, HLA-DR-low S100A-high monocytes in severe COVID-19 show low expression of HLA-DR and high expression of S100A8, S100A9, and S100A12.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:f701c7725b31c0188573
claim_id: claim:f701c7725b31c0188573
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
Immature neutrophils (cluster 6) expressed CD24 , PGLYRP1 , DEFA3 , and DEFA4 , whereas neutrophil cluster 5 expressed FCGR3B (CD16b), CXCL8 , and LCN2 (lipocalin 2) ( Figures 2 C and S2 A).

summary:
In Homo sapiens, immature neutrophils express CD24, PGLYRP1, DEFA3, and DEFA4, whereas mature neutrophils express FCGR3B, CXCL8, and LCN2.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:7a348c4420b863bb9749
claim_id: claim:7a348c4420b863bb9749
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
Cluster 2 monocytes expressed high levels of SELL (CD62L) and CD163 ( HLA-DR lo CD163 hi ) ( Figure 4 B), associated with anti-inflammatory macrophage functions ( Fischer-Riepe et al., 2020 ; MacParland et al., 2018 ), as well as pre-maturation markers like MPO and PLAC8

summary:
In Homo sapiens, HLA-DR-low CD163-high monocytes express high levels of SELL, CD163, MPO, and PLAC8.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:377c0a365c45eda18de8
claim_id: claim:377c0a365c45eda18de8
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
we identified clusters 4 and 6 as CD81 + SPN (CD43) + FUT4 (CD15) + CD63 + CEACAM8 (CD66b) + pro-neutrophils, clusters 3 and 5 as ITGAM (CD11b) + CEACAM8 (CD66b) + CD101 +/− pre-neutrophils, and the remaining clusters as mature neutrophils ( Figure S4 A).

summary:
In Homo sapiens, pro-neutrophils are marked by CD81, SPN, FUT4, CD63, and CEACAM8, while pre-neutrophils are marked by ITGAM, CEACAM8, and CD101.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:20c1ab79e1d6b8f380a1
claim_id: claim:20c1ab79e1d6b8f380a1
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
summary: In Homo sapiens, mature neutrophils express FCGR3B and MME as markers.
span_literal:
Clusters 0, 1, and 2 (originally in cluster 4 in Figure 2 A) expressed mature neutrophil markers FCGR3B (CD16) and MME (CD10) ( Figure S4 A).


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:a7ee907f8e885ff38b4f
claim_id: claim:a7ee907f8e885ff38b4f
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal: LDN in cluster 1 expressed numerous ISGs ( ISG15 , IFITM1/3 , and RSAD2
summary:
In Homo sapiens, interferon-stimulated gene-expressing low-density neutrophils (cluster 1) express ISG15, IFITM1, IFITM3, and RSAD2, while pro-neutrophils express MPO, ELANE, and PRTN3.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:5533c18a6f8b1554ab41
claim_id: claim:5533c18a6f8b1554ab41
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal: pro-neutrophils) expressed genes (e.g., MPO , ELANE , and PRTN3
summary:
In Homo sapiens, pro-neutrophils express MPO, ELANE, and PRTN3, genes involved in neutrophil extracellular trap formation.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:c469375b5827d72ebafc
claim_id: claim:c469375b5827d72ebafc
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
summary: In Homo sapiens, pre-neutrophils express PADI4, a co-factor in NETosis.
span_literal:
Both pre-neutrophil clusters expressed PADI4 , another co-factor in NETosis ( Leshner et al., 2012 ) ( Figure 5 D).


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:44c0e54fadec1f4ac6c1
claim_id: claim:44c0e54fadec1f4ac6c1
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
summary: In Homo sapiens, pre-neutrophils and pro-neutrophils express CD24, OLFM4, LCN2, and BPI.
span_literal:
pre-neutrophils (clusters 3 and 5) and pro-neutrophils expressed genes including CD24 , OLFM4 , LCN2 , and BPI


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:7b63cca39c101a79e57a
claim_id: claim:7b63cca39c101a79e57a
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
Finally, known inhibitors of T cell activation, namely CD274 (PD-L1) and Arginase 1 ( ARG1 ) ( Bronte et al., 2003 ; Li et al., 2018 ) were highly expressed in neutrophils in COVID-19 patients ( Figure 5 E).

summary:
In Homo sapiens, neutrophils in COVID-19 patients highly express CD274 (PD-L1) and ARG1 (Arginase 1), known inhibitors of T cell activation.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:5c4eba25542fee7ba9bd
claim_id: claim:5c4eba25542fee7ba9bd
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
Collectively, the neutrophil compartment in peripheral blood of severe COVID-19 patients is characterized by the appearance of LDN, FUT4 (CD15) + CD63 + CD66b + pro-neutrophils, and ITGAM (CD11b) + CD101 + pre-neutrophils, reminiscent of emergency myelopoiesis, as well as CD274 (PD-L1) + ZC3H12A + mature neutrophils reminiscent of gMDSC-like cells, which might exert suppressive or anti-inflammatory functions.

summary:
In Homo sapiens, pro-neutrophils in severe COVID-19 are characterized by FUT4, CD63, and CEACAM8 expression, pre-neutrophils by ITGAM and CD101, and mature neutrophils by CD274 and ZC3H12A expression.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:6b4f9c6c097d5f8a2985
claim_id: claim:6b4f9c6c097d5f8a2985
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
Collectively, the neutrophil compartment in peripheral blood of severe COVID-19 patients is characterized by the appearance of LDN, FUT4 (CD15) + CD63 + CD66b + pro-neutrophils, and ITGAM (CD11b) + CD101 + pre-neutrophils, reminiscent of emergency myelopoiesis, as well as CD274 (PD-L1) + ZC3H12A + mature neutrophils reminiscent of gMDSC-like cells, which might exert suppressive or anti-inflammatory functions.

summary:
In Homo sapiens, pre-neutrophils in severe COVID-19 are characterized by ITGAM and CD101 expression.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:77167c27b359388d35a1
claim_id: claim:77167c27b359388d35a1
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal:
Collectively, the neutrophil compartment in peripheral blood of severe COVID-19 patients is characterized by the appearance of LDN, FUT4 (CD15) + CD63 + CD66b + pro-neutrophils, and ITGAM (CD11b) + CD101 + pre-neutrophils, reminiscent of emergency myelopoiesis, as well as CD274 (PD-L1) + ZC3H12A + mature neutrophils reminiscent of gMDSC-like cells, which might exert suppressive or anti-inflammatory functions.

summary:
In Homo sapiens, mature neutrophils in severe COVID-19 express CD274 (PD-L1) and ZC3H12A, reminiscent of granulocytic myeloid-derived suppressor cell-like cells.


claim_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307:claim:673850a6fa7ea6b19b81
claim_id: claim:673850a6fa7ea6b19b81
paper_key: hca:0275_10.1016_j.cell.2020.08.001_8e5789b307
span_literal: monocytes showed low expression of HLA-DR, and high levels of MAFB , PLBD1 , and CD163
summary:
In Homo sapiens, monocytes in severe COVID-19 show low expression of HLA-DR and high expression of MAFB, PLBD1, and CD163, associated with anti-inflammatory macrophage functions.


claim_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5:claim:37396850d9591e34081a
claim_id: claim:37396850d9591e34081a
paper_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5
span_literal:
Androgen receptor ( AR ) and progesterone receptor ( PGR ) gene expression levels increased during cardiomyocyte maturation, although expression levels did not differ between male and female cardiomyocytes

summary:
In Homo sapiens, androgen receptor (AR) and progesterone receptor (PGR) gene expression levels increase during cardiomyocyte maturation.


claim_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5:claim:2a43a7e23ec3ee048e16
claim_id: claim:2a43a7e23ec3ee048e16
paper_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5
span_literal:
The gene encoding the glucocorticoid receptor nuclear receptor subfamily 3 group C member 1 ( NR3C1 ), was downregulated in cardiomyocytes during cardiac maturation

summary:
In Homo sapiens, nuclear receptor subfamily 3 group C member 1 (NR3C1) is downregulated in cardiomyocytes during cardiac maturation.


claim_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5:claim:c078e4965a6651fef1c2
claim_id: claim:c078e4965a6651fef1c2
paper_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5
span_literal:
Single-cell analysis confirmed upregulation of PGR in human cardiomyocytes during postnatal maturation, whereas AR expression was below the threshold of detection in our snRNA-seq analysis

summary:
In Homo sapiens, progesterone receptor (PGR) is upregulated in cardiomyocytes during postnatal maturation, whereas androgen receptor (AR) expression was below the threshold of detection by single-nucleus RNA sequencing.


claim_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5:claim:5e7b24bd8532dd6d4f22
claim_id: claim:5e7b24bd8532dd6d4f22
paper_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5
span_literal:
cardiomyocyte maturation was associated with transcriptional repression and loss of chromatin accessibility around the promoters of TNNI1 and BMP5

summary:
In Homo sapiens, cardiomyocyte maturation is associated with transcriptional repression of TNNI1 and BMP5.


claim_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5:claim:dc7923f2d6e421d6e1e9
claim_id: claim:dc7923f2d6e421d6e1e9
paper_key: hca:0276_10.1161_circulationaha.120.051921_99b9da8ca5
span_literal:
transcriptional activation and gain of accessibility around the promoters of the metabolic genes PDK4 and PFKFB2

summary:
In Homo sapiens, cardiomyocyte maturation is associated with transcriptional activation of the metabolic genes PDK4 and PFKFB2.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:f352593a946fc9c8e3b5
claim_id: claim:f352593a946fc9c8e3b5
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
span_literal:
we relied on clustering and recognized marker genes for MG, namely SLC1A3 , RLBP1 , SLN , SOX2 , NFIA , CRYM , CLU , and LINC00461 , as outlined in a prior study

summary:
In Homo sapiens, Müller glial cells are identified by the marker genes SLC1A3, RLBP1, SLN, SOX2, NFIA, CRYM, CLU, and LINC00461.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:7c0f045fdf74a64cbe80
claim_id: claim:7c0f045fdf74a64cbe80
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
span_literal: upon OTX2 activation, NRPCs predominantly differentiate into photoreceptors and BCs
summary:
In Homo sapiens, OTX2 activation in neurogenic retinal progenitor cells drives differentiation into photoreceptors and bipolar cells.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:8fd03d86c2ae61d20e3f
claim_id: claim:8fd03d86c2ae61d20e3f
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
span_literal: OTX2 expression exclusively in NRPCs that adopt a BC, rod, or cone fate
summary:
In Homo sapiens, OTX2 is expressed exclusively in neurogenic retinal progenitor cells that adopt a bipolar cell, rod, or cone fate.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:8268f664797162dbfa33
claim_id: claim:8268f664797162dbfa33
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
span_literal:
ALDH1A1 and ALDH1A3 , which are involved in RA synthesis, are enriched in peripheral PRPCs whereas CYP26A1 , which functions in RA degradation, is highly expressed in macular PRPCs

summary:
In Homo sapiens, ALDH1A1 and ALDH1A3 are enriched in peripheral primary retinal progenitor cells, whereas CYP26A1 is highly expressed in macular primary retinal progenitor cells.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:01ea6fa7221807f43453
claim_id: claim:01ea6fa7221807f43453
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
span_literal:
ALDH1A1 and ALDH1A3 , which are involved in RA synthesis, are enriched in peripheral PRPCs whereas CYP26A1 , which functions in RA degradation, is highly expressed in macular PRPCs

summary:
In Homo sapiens, CYP26A1 is highly expressed in macular primary retinal progenitor cells compared to peripheral primary retinal progenitor cells.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:5461551d816c9a1fa4d2
claim_id: claim:5461551d816c9a1fa4d2
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
span_literal:
only CNGB3 and PDE6H exhibit significantly higher expression levels in macular cones compared to peripheral cones

summary:
In Homo sapiens, CNGB3 and PDE6H exhibit significantly higher expression levels in macular cone photoreceptors compared to peripheral cone photoreceptors.


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:80a1f4465df0bd16a194
claim_id: claim:80a1f4465df0bd16a194
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
summary: In Homo sapiens, LYST shows high expression in developing bipolar cells and photoreceptors.
span_literal:
LYST , which is associated with CHS (Chediak–Higashsyndrome), shows high expression in developing BCs


claim_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d:claim:2001d6af79b5556e1395
claim_id: claim:2001d6af79b5556e1395
paper_key: hca:0277_10.1038_s41467-024-50853-5_ed4f7a095d
summary: In Homo sapiens, LYST shows high expression in developing photoreceptors.
span_literal:
LYST , which is associated with CHS (Chediak–Higashsyndrome), shows high expression in developing BCs and photoreceptors


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:98db2e76b4e54bc68e14
claim_id: claim:98db2e76b4e54bc68e14
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
Most cells (>90%) were luminal MECs (luMECs) expressing lactalbumin alpha and casein beta and positive for keratin 8 and keratin 18 .

summary:
In Homo sapiens, luminal mammary epithelial cells express lactalbumin alpha, casein beta, keratin 8, and keratin 18.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:59b020e1451f41219e59
claim_id: claim:59b020e1451f41219e59
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
No expression of pluripotency markers POU class 5 homeobox 1 ( POU5F1 , encoding OCT4) SRY-box transcription factor 2 ( SOX2 ) or nanog homeobox ( NANOG ), was observed.

summary:
In Homo sapiens, human milk-derived mammary epithelial cells show no expression of the pluripotency markers POU class 5 homeobox 1, SRY-box transcription factor 2, or nanog homeobox.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:f7bea817604e50706813
claim_id: claim:f7bea817604e50706813
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
indicating a negligible basal/stem cell population (epithelial cell adhesion molecule (EPCAM) /integrin subunit alpha 6(CD49f) , 0.07%) and a small progenitor population (EPCAM + /CD49f + , 1.1%).

summary:
In Homo sapiens, the basal/stem cell population in human milk is negative for epithelial cell adhesion molecule and integrin subunit alpha 6, while the progenitor population is positive for epithelial cell adhesion molecule and integrin subunit alpha 6.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:5f7fad70e6f3f8b0535c
claim_id: claim:5f7fad70e6f3f8b0535c
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
indicating a negligible basal/stem cell population (epithelial cell adhesion molecule (EPCAM) /integrin subunit alpha 6(CD49f) , 0.07%) and a small progenitor population (EPCAM + /CD49f + , 1.1%).

summary:
In Homo sapiens, the progenitor population in human milk is positive for epithelial cell adhesion molecule and integrin subunit alpha 6.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:31dd87788d319b1c6cca
claim_id: claim:31dd87788d319b1c6cca
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
summary: In Homo sapiens, luminal mammary epithelial cells express KRT8 and KRT18.
span_literal:
The vast majority of cells were KRT8 & KRT18 expressing luMECs, found in all clusters except 3 and 6.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:b9711949cf233fe592c7
claim_id: claim:b9711949cf233fe592c7
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal: KRT8 + / KRT18 + cells expressed high levels of lactalbumin alpha ( LALBA ) & casein beta ( CSN2 )
summary:
In Homo sapiens, KRT8-positive/KRT18-positive luminal mammary epithelial cells express high levels of lactalbumin alpha (LALBA) and casein beta (CSN2).


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:863bd5c02cd4126f3842
claim_id: claim:863bd5c02cd4126f3842
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
Clusters 3 and 6 contained the only cells expressing protein tyrosine phosphatase receptor type C ( PTPRC ), which encodes the hematopoietic and immune cell marker CD45

summary:
In Homo sapiens, hematopoietic and immune cells express protein tyrosine phosphatase receptor type C (PTPRC), which encodes CD45.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:dd111cdd6447a58bd127
claim_id: claim:dd111cdd6447a58bd127
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
we did not detect transcripts encoding OCT4 ( POU class 5 homeobox 1, POU5F1 ), SOX2 or NANOG in our scRNA-seq dataset

summary:
In Homo sapiens, human milk-derived cells do not express POU class 5 homeobox 1 (POU5F1), SRY-box transcription factor 2 (SOX2), or nanog homeobox (NANOG).


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:ecab54673baa5f9bc75b
claim_id: claim:ecab54673baa5f9bc75b
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
we examined expression of progenitor markers CD44 molecule (Indian blood group), CD55 molecule (Cromer blood group), aldehyde dehydrogenase 1 family member A3, integrin subunit alpha 6, which encodes CD49f, and CD14 molecule ( CD44, CD55, ALDH1A3, ITGA6 and CD14 , respectively)

summary:
In Homo sapiens, mammary progenitor cells are marked by CD44 molecule, CD55 molecule, aldehyde dehydrogenase 1 family member A3, integrin subunit alpha 6, and CD14 molecule.


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:715695d393b498feb2fd
claim_id: claim:715695d393b498feb2fd
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
Cells in the progenitor subcluster also showed high expression of genes previously reported to indicate mammary stem-ness in milk-derived cells ( keratin 5 ( KRT5 ), prominen 1 ( PROM1 , encoding CD133), nestin ( NES ), integrin subunit beta 1 ( ITGB1 , encoding CD29), kruppel like factor 4 ( KLF4 )

summary:
In Homo sapiens, mammary progenitor cells show high expression of keratin 5 (KRT5), prominin 1 (PROM1), nestin (NES), integrin subunit beta 1 (ITGB1), and Kruppel like factor 4 (KLF4).


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:a9aac6e0601eab7b01a9
claim_id: claim:a9aac6e0601eab7b01a9
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
Transmembrane 4 L six family member 1 ( TM4SF1 ), tumor associated calcium signal transducer 2 ( TACSTD2 ), tumor necrosis factor receptor superfamily member 12A ( TNFRSF12A ), and possibly claudin 4 ( CLDN4 ) encode cell surface markers in progenitor luMECs.

summary:
In Homo sapiens, progenitor luminal mammary epithelial cells express cell surface markers transmembrane 4 L six family member 1 (TM4SF1), tumor associated calcium signal transducer 2 (TACSTD2), tumor necrosis factor receptor superfamily member 12A (TNFRSF12A), and claudin 4 (CLDN4).


claim_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6:claim:dddf1922b22f2f984ff1
claim_id: claim:dddf1922b22f2f984ff1
paper_key: hca:0278_10.1007_s10911-020-09466-z_d1b799dcf6
span_literal:
Cell surface markers encoded by lymphocyte antigen 6 family member D ( LY6D ) and neurotrophic receptor tyrosine kinase 2 ( NTRK2 ) could potentially be used to isolate the majority of luMECs during flow sorting

summary:
In Homo sapiens, luminal mammary epithelial cells express lymphocyte antigen 6 family member D (LY6D) and neurotrophic receptor tyrosine kinase 2 (NTRK2).


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:e3c18e955cb503d4677f
claim_id: claim:e3c18e955cb503d4677f
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
The upper group of cells in Fig. 2 b highly express CLEC9A and XCR1 , indicating its identify of cDC1, whereas the lower group of cells in Fig. 1 b highly express CD1C and ZEB2 , indicating its identity of cDC2 (Fig. 2 c).

summary:
In Homo sapiens, conventional dendritic cell type 1 (cDC1) is marked by high expression of CLEC9A and XCR1, whereas conventional dendritic cell type 2 (cDC2) is marked by high expression of CD1C and ZEB2.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:c142aba303344424e9cd
claim_id: claim:c142aba303344424e9cd
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
The upper group of cells in Fig. 2 b highly express CLEC9A and XCR1 , indicating its identify of cDC1, whereas the lower group of cells in Fig. 1 b highly express CD1C and ZEB2 , indicating its identity of cDC2 (Fig. 2 c).

summary:
In Homo sapiens, conventional dendritic cell type 2 (cDC2) is marked by high expression of CD1C and ZEB2.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:c544d5c33e0c93127b35
claim_id: claim:c544d5c33e0c93127b35
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
Cluster 2 genes were highly expressed in cDC1, including CLEC9A , XCR1 and transcriptional factor IRF8, enriched for integrin signaling pathway and IFN-gamma pathway.

summary:
In Homo sapiens, conventional dendritic cell type 1 (cDC1) highly expresses CLEC9A, XCR1, and the transcription factor IRF8.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:c4f310ae468c955f965e
claim_id: claim:c4f310ae468c955f965e
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
Cluster 3 genes were highly expressed in cDC2s, including the surface marker CD1c and transcription factor CEBPB and ZEB2, enriched for IL1/4/5 signaling pathway and Toll-like receptor signaling pathway.

summary:
In Homo sapiens, conventional dendritic cell type 2 (cDC2) highly expresses the surface marker CD1c and the transcription factors CEBPB and ZEB2.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:a3ce64f2a32ddffcd5bd
claim_id: claim:a3ce64f2a32ddffcd5bd
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
cDC1 dependent transcriptional factors include IRF8 [ 10 ], ID2 [ 11 ], BATF3 [ 10 , 12 ], NFIL3 [ 13 ].

summary:
In Homo sapiens, conventional dendritic cell type 1 (cDC1) development depends on the transcription factors IRF8, ID2, BATF3, and NFIL3.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:8976fdcb32923a196bbc
claim_id: claim:8976fdcb32923a196bbc
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal: cDC2 dependent transcriptional factors include IRF4 [ 14 , 15 ], KLF4 [ 16 ], ZEB2 [ 17 ].
summary:
In Homo sapiens, conventional dendritic cell type 2 (cDC2) development depends on the transcription factors IRF4, KLF4, and ZEB2.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:44dea0e467ac61de48b7
claim_id: claim:44dea0e467ac61de48b7
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
Among the 16 MR TFs, IRF8 and IRF4 were known to be specific to cDC1s and cDC2s, respectively [ 10 , 14 , 15 ].

summary:
In Homo sapiens, IRF8 is specific to conventional dendritic cell type 1 (cDC1) and IRF4 is specific to conventional dendritic cell type 2 (cDC2).


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:7af368f87e7d37fe3b1f
claim_id: claim:7af368f87e7d37fe3b1f
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
Indeed, our single RNAseq data indicates that expression of IRF8 was high in most cDC1s and low in most cDC2s (Fig. 4 e) whereas expression of IRF4 was low in most cDC1s and high in most cDC2s (Fig. 4 e).

summary:
In Homo sapiens, IRF8 expression is high in conventional dendritic cell type 1 (cDC1) and low in conventional dendritic cell type 2 (cDC2), whereas IRF4 expression is low in cDC1 and high in cDC2.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:cb81af5f1a961d723488
claim_id: claim:cb81af5f1a961d723488
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
Indeed, our single RNAseq data indicates that expression of IRF8 was high in most cDC1s and low in most cDC2s (Fig. 4 e) whereas expression of IRF4 was low in most cDC1s and high in most cDC2s (Fig. 4 e).

summary:
In Homo sapiens, IRF4 expression is high in conventional dendritic cell type 2 (cDC2) and IRF8 expression is low in cDC2, compared to conventional dendritic cell type 1 (cDC1).


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:0ee365d31848c11ea5cb
claim_id: claim:0ee365d31848c11ea5cb
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
CD172a(SIRPA) is a surface marker that can distinguish the two pre-cDC subsets, with higher expression indicating pre-commitment to cDC2 and lower expression indicating pre-commitment to cDC1 [ 5 ].

summary:
In Homo sapiens, SIRPA (CD172a) is a surface marker with higher expression in precursor conventional dendritic cell type 2 (pre-cDC2) and lower expression in precursor conventional dendritic cell type 1 (pre-cDC1).


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:7a83c97eeed1f712ba2e
claim_id: claim:7a83c97eeed1f712ba2e
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal:
Cluster 1 genes were highly expressed in pre-cDCs and low in cDCs, including key genes like SOX4 and TCF4, enriched for development pathways like EGF-EGFR1 signaling pathway and mitotic pathway .

summary:
In Homo sapiens, precursor conventional dendritic cells (pre-cDCs) highly express SOX4 and TCF4 compared to conventional dendritic cells.


claim_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c:claim:822a9c250be236bcd05a
claim_id: claim:822a9c250be236bcd05a
paper_key: hca:0279_10.1186_s12860-019-0199-y_bf14d4299c
span_literal: Maintaining of IRF8 high expression level is required for cDC1 identity [ 10 ].
summary:
In Homo sapiens, maintaining high expression of IRF8 is required for conventional dendritic cell type 1 (cDC1) identity.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:34e988a65970ada74512
claim_id: claim:34e988a65970ada74512
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
NPCs were identified as cell population 4 on the basis of CITED1 , SIX1 , LYPD1 , and DAPL1 expression

summary:
In Homo sapiens, nephron progenitor cells were identified on the basis of CITED1, SIX1, LYPD1, and DAPL1 expression.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:aff5a4273772cd0ca9b1
claim_id: claim:aff5a4273772cd0ca9b1
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
A second cell population (4B) differentially expressed ID1 , MEG3 , and DAPL1 , and induced NPCs (4C) expressed CCND1 , PAX8 , and LHX1 , and contained a small subpopulation of differentiating MAFB and PODXL expressing cells likely initiating podocyte differentiation

summary:
In Homo sapiens, nephron progenitor cell subpopulation 4B differentially expressed ID1, MEG3, and DAPL1.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:a7d2cfd4cb1336f74394
claim_id: claim:a7d2cfd4cb1336f74394
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
As in the mouse, CITED1 and SIX2 were strongly expressed within mesenchymal cells capping the ureteric epithelial branch tips, the likely human NPC population

summary:
In Homo sapiens, CITED1 and SIX2 were strongly expressed within nephron progenitor cells capping the ureteric epithelial branch tips.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:7db900c63d1982926d9f
claim_id: claim:7db900c63d1982926d9f
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
summary: In Homo sapiens, interstitial progenitor cells expressed FOXD1 and MEIS1.
span_literal:
Examining FOXD1 and MEIS1 , we observed a FOXD1+/MEIS1+ population of peripheral mesenchymal cells similarly positioned to mouse IPCs, that are likely human IPC counterparts


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:148190ce58dd0984d370
claim_id: claim:148190ce58dd0984d370
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
Applying similar thresholding criteria as in earlier MARIS data, 503 genes showed enriched expression in hIPCs versus hNPC cell fractions ( Figure 6A , Supplemental Table 4 ), including genes associated with extracellular matrix or matrix interactions ( ITGA9 , ITGA1 , COL3A1 ), transcription ( GATA3 ), and cell signaling ( PDGFRB ).

summary:
In Homo sapiens, interstitial progenitor cells showed enriched expression of ITGA9, ITGA1, COL3A1, GATA3, and PDGFRB compared with nephron progenitor cells.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:1bab81cb231c03382e33
claim_id: claim:1bab81cb231c03382e33
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
These included well characterized NPC marker genes such as SIX2 , CITED1 , and EYA1 ; genes identified earlier in SIX2 MARIS comparisons such as PCDH15 , LYPD1 , and ECEL1 ; and novel gene predictions including ELAVL4 , FAT3 , and CRABP2 .

summary:
In Homo sapiens, nephron progenitor cells showed enriched expression of SIX2, CITED1, EYA1, PCDH15, LYPD1, ECEL1, ELAVL4, FAT3, and CRABP2 compared with interstitial progenitor cells.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:e84b8ae8e347dca1f3f3
claim_id: claim:e84b8ae8e347dca1f3f3
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal: Enrichment of PDGFRA, PDGFRB, and PBX1 within hIPCs was confirmed through immunolabeling studies
summary:
In Homo sapiens, enrichment of PDGFRA, PDGFRB, and PBX1 within interstitial progenitor cells was confirmed through immunolabeling studies.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:f1843e3928850b6f4bd3
claim_id: claim:f1843e3928850b6f4bd3
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
Matching the differential expression predictions, HIP1R , UNC5B , LYPD1 , DAPL1 , ECEL1 , COL9A2 , WASF3 , and TNFRSF19 were expressed at high levels in human NPCs

summary:
In Homo sapiens, HIP1R, UNC5B, LYPD1, DAPL1, ECEL1, COL9A2, WASF3, and TNFRSF19 were expressed at high levels in nephron progenitor cells.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:32806612a63c56ea022d
claim_id: claim:32806612a63c56ea022d
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
TMEM100 and ROBO2 displayed a restricted localization within NPCs, but unlike CITED1 their expression did not persist into early nephron-forming stages

summary:
In Homo sapiens, TMEM100 and ROBO2 displayed a restricted localization within nephron progenitor cells.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:28a03b7775ed8c67dc5a
claim_id: claim:28a03b7775ed8c67dc5a
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
These approaches identified the transcription factor SIX1 as a specific component of the human NPC population during periods of active nephrogenesis.

summary:
In Homo sapiens, the transcription factor SIX1 was identified as a specific component of the nephron progenitor cell population during periods of active nephrogenesis.


claim_key: hca:0280_10.1681_asn.2017080890_022062f455:claim:8b4965ec540a08fbba22
claim_id: claim:8b4965ec540a08fbba22
paper_key: hca:0280_10.1681_asn.2017080890_022062f455
span_literal:
Genes common to both mouse and human nephron progenitors included known progenitor markers such as SIX2 , CITED1 , PHF19 , OSR1 , SALL1 , and EYA1 .

summary:
In Homo sapiens, nephron progenitor cells expressed known progenitor markers SIX2, CITED1, PHF19, OSR1, SALL1, and EYA1.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:947c7d92de4fd4a65c8e
claim_id: claim:947c7d92de4fd4a65c8e
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal: MAFB+ podocyte precursors emerged first in the proximal segment of the renal vesicle (RV).
summary:
In Homo sapiens, MAFB-positive podocyte precursors emerged first in the proximal segment of the renal vesicle.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:7a64a8189a5cb18ff74f
claim_id: claim:7a64a8189a5cb18ff74f
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
We confirmed that co-expression of PDGFRB and GATA3 marked the pericytes recruited to renal corpuscles, and committed mesangial cells in late RC co-expressed GATA3 and TMEFF2

summary:
In Homo sapiens, co-expression of PDGFRB and GATA3 marks pericytes recruited to renal corpuscles, and committed mesangial cells in late renal corpuscle co-express GATA3 and TMEFF2.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:fae74c67aa53827b49fe
claim_id: claim:fae74c67aa53827b49fe
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
NPC genes such as SIX1, SIX2, EYA1 and MEOX1 were present at the start of the trajectory and downregulated along the predicted developmental progression.

summary:
In Homo sapiens, nephron progenitor cells express SIX1, SIX2, EYA1, and MEOX1, which are downregulated along podocyte developmental progression.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:1dda5dfd40ebe349e0d3
claim_id: claim:1dda5dfd40ebe349e0d3
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
A cohort of genes predicted to display a distinct transient early podocyte (EP)-restricted activity (including LHX1, PAX8, FBLN2, OLFM3, PCDH9, SLC16A1, GFRA3, and LEFTY1 ) gave way to a late podocyte (LP) gene expression signature (including PLA2R1, ARMH4, F3, SYNPO, NPHS2, MAFB, TGFBR3, COL4A3, COL4A4, TNNT2, PLCE1 and ANXA1 )

summary:
In Homo sapiens, early podocytes transiently express LHX1, PAX8, FBLN2, OLFM3, PCDH9, SLC16A1, GFRA3, and LEFTY1, which give way to a late podocyte gene expression signature.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:fa5105ac79819716641a
claim_id: claim:fa5105ac79819716641a
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
A cohort of genes predicted to display a distinct transient early podocyte (EP)-restricted activity (including LHX1, PAX8, FBLN2, OLFM3, PCDH9, SLC16A1, GFRA3, and LEFTY1 ) gave way to a late podocyte (LP) gene expression signature (including PLA2R1, ARMH4, F3, SYNPO, NPHS2, MAFB, TGFBR3, COL4A3, COL4A4, TNNT2, PLCE1 and ANXA1 )

summary:
In Homo sapiens, late podocytes express PLA2R1, ARMH4, F3, SYNPO, NPHS2, MAFB, TGFBR3, COL4A3, COL4A4, TNNT2, PLCE1, and ANXA1.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:86351a79c2d13d83a47a
claim_id: claim:86351a79c2d13d83a47a
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
RV and SSB podocyte precursors expressed EP markers ( OLFM3 , PAX8, and LHX1) but expression ceased prior to or at CLSN stages

summary:
In Homo sapiens, renal vesicle and S-shaped body podocyte precursors express early podocyte markers OLFM3, PAX8, and LHX1, but expression ceases prior to or at capillary loop stage.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:45100ea7c48e4d554919
claim_id: claim:45100ea7c48e4d554919
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
LP markers (NPHS2, SYNPO, ARMH4, ANXA1, F3, TGFBR3, PLA2R1, COL4A3, and TNNT2) were first detected in SSB or CLSNs, and the highest levels were observed in mature renal corpuscles

summary:
In Homo sapiens, late podocyte markers NPHS2, SYNPO, ARMH4, ANXA1, F3, TGFBR3, PLA2R1, COL4A3, and TNNT2 are first detected in S-shaped body or capillary loop stage nephrons and reach highest levels in mature renal corpuscle podocytes.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:6969d22e14d76fb82455
claim_id: claim:6969d22e14d76fb82455
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
summary: In Homo sapiens, organoid-derived interstitial cells express COL1A1 and ALDH1A2.
span_literal:
Organoids comprised cells with transcriptional signatures indicative of interstitial cells ( COL1A1 +, ALDH1A2 + ) , nephron progenitors ( SIX1 +, MEOX1 +), early developing nephron cells ( PAX8 +, LHX1 +), precursors of the medial/distal segment ( SOX9 +, MECOM +, EMX2 +), proximal tubule ( LRP2 +, SLC3A1 +), parietal epithelial cells ( LIX1 +, CDH6 +), and early and late podocytes ( OLFM3 +, MAFB +, NPHS2 +).


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:1c9997d8dbed9aa6dc64
claim_id: claim:1c9997d8dbed9aa6dc64
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
Of the twelve genes activated in podocytes, PAX2 and FAH were upregulated only in EPs, while PTPRO, COL4A3, COL4A4, PLCE1, CRB2, NPHS1, TCF21, and ARHGAP24 were first detected in EPs and showed increased activity in LPs

summary:
In Homo sapiens, among glomerular disease-associated genes activated in podocytes, PAX2 and FAH are upregulated only in early podocytes, while PTPRO, COL4A3, COL4A4, PLCE1, CRB2, NPHS1, TCF21, and ARHGAP24 are first detected in early podocytes and show increased activity in late podocytes.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:37614f566e3390b0d164
claim_id: claim:37614f566e3390b0d164
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
Of the twelve genes activated in podocytes, PAX2 and FAH were upregulated only in EPs, while PTPRO, COL4A3, COL4A4, PLCE1, CRB2, NPHS1, TCF21, and ARHGAP24 were first detected in EPs and showed increased activity in LPs

summary:
In Homo sapiens, PTPRO, COL4A3, COL4A4, PLCE1, CRB2, NPHS1, TCF21, and ARHGAP24 show increased activity in late podocytes.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:926e4ee9a9e1d51b58c7
claim_id: claim:926e4ee9a9e1d51b58c7
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
Forty-three genes were expressed in all three glomerular components: LMNA, COL4A1, MPV17, KANK2 and MYO1E were more highly expressed in the mesangial cells, while DGKE, KHDRBS3, SOX18, SLC7A7, KANK4 and TAL1 were enriched in the endothelial component.

summary:
In Homo sapiens, LMNA, COL4A1, MPV17, KANK2, and MYO1E are more highly expressed in mesangial cells among glomerular cell types.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:7dafc1daaad9001f229c
claim_id: claim:7dafc1daaad9001f229c
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
Forty-three genes were expressed in all three glomerular components: LMNA, COL4A1, MPV17, KANK2 and MYO1E were more highly expressed in the mesangial cells, while DGKE, KHDRBS3, SOX18, SLC7A7, KANK4 and TAL1 were enriched in the endothelial component.

summary:
In Homo sapiens, DGKE, KHDRBS3, SOX18, SLC7A7, KANK4, and TAL1 are enriched in the glomerular endothelial cell component.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:c5f66d570e66cdd2b7ab
claim_id: claim:c5f66d570e66cdd2b7ab
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
we also identified novel human LP-specific genes (including S100A6, MYL9, TPPP6, SNCA, TNNI1, TNNT2, MYL12, PDLIM2, PALLD, GSN ) that are associated with cytoskeletal proteins, suggesting species-specific functions in maintaining podocyte architecture.

summary:
In Homo sapiens, novel late podocyte-specific genes include S100A6, MYL9, TPPP6, SNCA, TNNI1, TNNT2, MYL12, PDLIM2, PALLD, and GSN, which are associated with cytoskeletal proteins.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:40382c63b398fbdc187e
claim_id: claim:40382c63b398fbdc187e
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal: SIX1, SIX2, EYA1 and MEOX1 , which are linked to the maintenance of mouse and human NPCs
summary:
In Homo sapiens, SIX1, SIX2, EYA1, and MEOX1 are linked to the maintenance of nephron progenitor cells.


claim_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef:claim:0fa0b8c1593ed209ee17
claim_id: claim:0fa0b8c1593ed209ee17
paper_key: hca:0281_10.1016_j.devcel.2019.06.001_238d93bfef
span_literal:
Transcription factors known to play essential role specifically in podocyte development (e.g. TCF21 and MAFB ) were first detected in RV-stage podocyte precursors overlapping with NPC genes ( SIX1 and TMEM100 ).

summary:
In Homo sapiens, transcription factors TCF21 and MAFB are first detected in renal vesicle-stage podocyte precursors, overlapping with nephron progenitor cell genes SIX1 and TMEM100.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:88c2e05afe774d6ae64c
claim_id: claim:88c2e05afe774d6ae64c
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
We identified 12 563 ECs within the integrated lung dataset based on the canonical endothelial markers PECAM1 (CD31), CDH5 (VE-cadherin), CLDN5 , and ERG

summary:
In Homo sapiens lung, endothelial cells are identified by the canonical markers PECAM1, CDH5, CLDN5, and ERG.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:bb8a6721d5fdeb282681
claim_id: claim:bb8a6721d5fdeb282681
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Panendothelial markers include genes coding for proteins associated with endothelial-intrinsic structures like the glycocalyx ( PODXL , ST6GALNAC3 , GALNT18 ), caveolae ( CAV1 , CAV2 , CAVIN1 , CAVIN2 ), focal adhesion structures ( ITGA5 , ITGB1 , LAMB2 , AKT3 , PXN , MYL12A , MYL12B , PRK2 ), and adherens junctions ( AFDN , TJP1 , PTPRM

summary:
In Homo sapiens lung, panendothelial marker genes of endothelial cells include PODXL, ST6GALNAC3, GALNT18, CAV1, CAV2, CAVIN1, CAVIN2, ITGA5, ITGB1, LAMB2, AKT3, PXN, MYL12A, MYL12B, PRK2, AFDN, TJP1, and PTPRM.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:91015a81d7dd96bb0b0a
claim_id: claim:91015a81d7dd96bb0b0a
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
All EC subpopulations express common transcription factors ( ERG , ETS1 , FLI1 , SOX18 ) and regulators of endothelial migration ( ANXA3 , SASH1 , LDB2 , PTK2 , MEF2C , STARD13 ).

summary:
In Homo sapiens lung, all endothelial cell subpopulations express the transcription factors ERG, ETS1, FLI1, SOX18 and the migration regulators ANXA3, SASH1, LDB2, PTK2, MEF2C, and STARD13.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:8a3ac7c5333cb6449284
claim_id: claim:8a3ac7c5333cb6449284
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Other panendothelial markers include angiopoietin receptor TIE1 , subunits of the receptors for calcitonin gene-related peptide and adrenomedullin CALCRL and RAMP2/RAMP3 , as well as general endothelial receptors ROBO4 and S1PR1

summary:
In Homo sapiens lung, panendothelial markers of endothelial cells include TIE1, CALCRL, RAMP2, RAMP3, ROBO4, and S1PR1.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:8f3bd1de54af01d9a648
claim_id: claim:8f3bd1de54af01d9a648
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Lymphatic ECs were identified on the basis of the expression of canonical lymphatic markers PROX1 , 15 LYVE1 , 15 FLT4 , 15 , 16 and PDPN 16 , 17

summary:
In Homo sapiens lung, lymphatic endothelial cells are identified by the canonical markers PROX1, LYVE1, FLT4, and PDPN.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:f59892ff03bafb978c2c
claim_id: claim:f59892ff03bafb978c2c
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
summary: In Homo sapiens lung, lymphatic endothelial cells express CCL21, SEMA3A, and SEMA3D.
span_literal:
Lymphatic ECs express secreted proteins like CCL21 16 mediating homing of T cells and semaphorins SEMA3A and SEMA3D, 18 both necessary for lymphatic vessel maturation.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:f3f444a42b09ad799c4b
claim_id: claim:f3f444a42b09ad799c4b
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Lymphatic marker genes comprise transcription factors TBX1, HOXD3, NR2F1, and NR2F2 and receptors KDR, GPR182, and TEK.

summary:
In Homo sapiens lung, lymphatic endothelial cell marker genes include the transcription factors TBX1, HOXD3, NR2F1, and NR2F2 and the receptors KDR, GPR182, and TEK.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:ccbc87f17322cebe19c8
claim_id: claim:ccbc87f17322cebe19c8
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Panvascular markers (n=142) expressed across the remaining, nonlymphatic ECs include transmembrane glycoproteins such as ENG, PCDH17, CLEC14A, CLEC1A (C-type lectin domain family 1 member A), ESAM, and ITM2A; the cell surface receptors BMPR2, FLT1, ADGRL4, VIPR1, PLXNA2, FZD4, IL4R, and IL15RA; transporter and channel proteins such as SLCO2A1, SLCO4A1, and AQP1; as well as the transcription factors EPAS1, GATA2, FOXF1, and ETS2

summary:
In Homo sapiens lung, panvascular markers of vascular endothelial cells include ENG, PCDH17, CLEC14A, CLEC1A, ESAM, ITM2A, BMPR2, FLT1, ADGRL4, VIPR1, PLXNA2, FZD4, IL4R, IL15RA, SLCO2A1, SLCO4A1, AQP1, EPAS1, GATA2, FOXF1, and ETS2.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:8237164fb247cea10bf1
claim_id: claim:8237164fb247cea10bf1
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Arterial ECs were identified by EFNB2 , 19 – 22 SOX17 , 20 , 23 BMX , 19 , 24 SEMA3G , 19 HEY1 , 20 , 21 LTBP4 , 25 FBLN5 , 25 GJA5 , 20 and GJA4 . 20

summary:
In Homo sapiens lung, arterial endothelial cells are identified by EFNB2, SOX17, BMX, SEMA3G, HEY1, LTBP4, FBLN5, GJA5, and GJA4.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:cdac4c0f821934b9568d
claim_id: claim:cdac4c0f821934b9568d
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Capillary ECs were identified by canonical markers CA4 16 , 26 and PRX , 27 as well as organism-wide capillary markers RGCC , 16 SPARC , 16 and SGK1 . 16

summary:
In Homo sapiens lung, capillary endothelial cells are identified by the canonical markers CA4 and PRX, as well as RGCC, SPARC, and SGK1.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:d0694ff8caf01ee313e5
claim_id: claim:d0694ff8caf01ee313e5
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Venous ECs were identified through the canonical transcription factor NR2F2 20 – 22 (COUP-TFII [COUP transcription factor 2]), as well as VCAM1 , 16 , 22 ACKR1 28 (Figure 2 ), and SELP 28 expression

summary:
In Homo sapiens lung, venous endothelial cells are identified by the canonical transcription factor NR2F2, as well as VCAM1, ACKR1, and SELP.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:a0884de45fb91642dd9d
claim_id: claim:a0884de45fb91642dd9d
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
arterial ECs express genes encoding for tight and gap junction proteins such as CLDN10 , GJA5 , GJA4 , and FBLIM1 ; extracellular matrix proteins that contribute to wall elasticity and strength such as FBLN5 , FBLN2 , MGP , BGN , LTBP4 , LTBP1 , and FN1 ; and the protease inhibitors SERPINE2 29 and CPAMD8

summary:
In Homo sapiens lung, arterial endothelial cells express CLDN10, GJA5, GJA4, FBLIM1, FBLN5, FBLN2, MGP, BGN, LTBP4, LTBP1, FN1, SERPINE2, and CPAMD8.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:1fc3cc6861f31d627e99
claim_id: claim:1fc3cc6861f31d627e99
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Arterial ECs are active secretory cells and express signaling molecules such as CXCL12, EFBN2, SEMA3G , 30 VEGFA, and enzymes of the nitric oxide pathway involved in modulating vascular tonus like NOS1, PDE3A, and PDE4D.

summary:
In Homo sapiens lung, arterial endothelial cells express CXCL12, EFNB2, SEMA3G, VEGFA, NOS1, PDE3A, and PDE4D.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:e531c1ee87851d57718d
claim_id: claim:e531c1ee87851d57718d
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Maintenance of their arterial identity is accomplished through the expression of Wnt signaling modulator DKK2, the Notch ligand DLL4, and the transcription factors HEY1, SOX5, SOX17, HES4, and PRDM16

summary:
In Homo sapiens lung, arterial endothelial cells express DKK2, DLL4, HEY1, SOX5, SOX17, HES4, and PRDM16 for maintenance of arterial identity.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:e37e83fb803a39356e78
claim_id: claim:e37e83fb803a39356e78
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Capillary ECs express genes coding for enzymes related to gas exchange including CA4 16 , 26 and CYB5A ; multiple receptors including ACVRL1/TMEM100 , ADGRF5 , ADGRL2 , F2RL3 , IFNGR1 , VIPR1 , and ADRB1 ; intracellular signaling molecules like ARHGAP6 , IFI27 , PREX1 , PRKCE , SGK1 , 16 SH2D3C , and SORBS1 ; structural proteins PRX, 27 SPARC, 16 EMP2, ITGA1, and SLC9A3R2; and transcription regulators AFF3 and MEIS1

summary:
In Homo sapiens lung, capillary endothelial cells express CA4, CYB5A, ACVRL1, TMEM100, ADGRF5, ADGRL2, F2RL3, IFNGR1, VIPR1, ADRB1, ARHGAP6, IFI27, PREX1, PRKCE, SGK1, SH2D3C, SORBS1, PRX, SPARC, EMP2, ITGA1, SLC9A3R2, AFF3, and MEIS1.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:a9e7fed98e85c3ac7f0d
claim_id: claim:a9e7fed98e85c3ac7f0d
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
venous ECs express genes encoding for proteins associated with diapedesis of leukocytes like VCAM1 , 16 , 22 SELP , 28 and SELE 28

summary:
In Homo sapiens lung, venous endothelial cells express VCAM1, SELP, and SELE, which are associated with diapedesis of leukocytes.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:07a2d5d9fa203b70ac15
claim_id: claim:07a2d5d9fa203b70ac15
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Venous ECs are further characterized by the major transcription factor NR2F2, 20 – 22 as well as genes coding for secreted ( ADAMTS9 , IGFBP7 ), nuclear ( HDAC9 , RORA ), and membrane proteins ( ACTN1 , LDLRAD3 , LDLRAD4 , and LRRC1

summary:
In Homo sapiens lung, venous endothelial cells are characterized by NR2F2, ADAMTS9, IGFBP7, HDAC9, RORA, ACTN1, LDLRAD3, LDLRAD4, and LRRC1.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:0ef32c6f9bd692b7374d
claim_id: claim:0ef32c6f9bd692b7374d
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Aerocytes (n=2317) can be distinguished by their expression of genes encoding for the endothelin receptor EDNRB, the transcription factors TBX2 and FOXP2, the pattern recognition receptors CLEC4E and SPON2, and signaling mediators such as PRKG, CHRM2, S100A4, and EDA

summary:
In Homo sapiens lung, aerocytes can be distinguished by expression of EDNRB, TBX2, FOXP2, CLEC4E, SPON2, PRKG, CHRM2, S100A4, and EDA.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:ce68ea038eacce375262
claim_id: claim:ce68ea038eacce375262
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
summary: In Homo sapiens lung, aerocytes are the only endothelial cell type expressing HPGD.
span_literal:
Aerocytes are the only EC type expressing prostaglandin-degrading HPGD, which is responsible for the first-pass deactivation of most prostaglandins as they pass through the vascular bed of the lung.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:edec37686665ec39b202
claim_id: claim:edec37686665ec39b202
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
summary: In Homo sapiens lung, aerocytes specifically express SOSTDC1.
span_literal:
Aerocytes specifically express SOSTDC1, antagonist to BMPR2, which itself is expressed in all ECs and its mutations are associated with pulmonary arterial hypertension.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:c973a819bc7607bf9fd8
claim_id: claim:c973a819bc7607bf9fd8
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
In contrast to all other ECs, aerocytes do not express major components of endothelial-specific Weibel-Palade bodies (vWF, SELP, EDN), storage granules essential for hemostasis and extravasation of leukocytes.

summary:
In Homo sapiens lung, aerocytes do not express VWF, SELP, or EDN, which are major components of Weibel-Palade bodies.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:0c14322dffa610929a66
claim_id: claim:0c14322dffa610929a66
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Aerocytes are characterized by the absence of expression of genes otherwise expressed in all other ECs including THBD , CD93 , PTPRB , ANO2 , CRIM1 , MECOM , LIFR , PALMD , GNA14 , CYYR1 , and LEPR .

summary:
In Homo sapiens lung, aerocytes are characterized by the absence of expression of THBD, CD93, PTPRB, ANO2, CRIM1, MECOM, LIFR, PALMD, GNA14, CYYR1, and LEPR.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:617237bd5b8466cf35c7
claim_id: claim:617237bd5b8466cf35c7
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
the general capillary EC population can be identified by the expression of genes related to transcytosis of low-density lipoprotein cholesterol and other lipids such as GPIHBP1 16 and CD36 33 ; innate immune response including FCN3 , BTNL9 , BTNL8 , and CD14 ; and cytokine receptors such as IL7R and IL18R1

summary:
In Homo sapiens lung, general capillary endothelial cells are identified by expression of GPIHBP1, CD36, FCN3, BTNL9, BTNL8, CD14, IL7R, and IL18R1.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:41a9a9a8961c1ffcc79d
claim_id: claim:41a9a9a8961c1ffcc79d
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
summary: In Homo sapiens lung, systemic–venous endothelial cells express VWA1 and PLVAP.
span_literal:
We also identified the extracellular matrix protein vWA1, as well as PLVAP , which encodes an EC-specific protein that forms the stomatal and fenestral diaphragms of blood vessels and regulates basal permeability, leukocyte migration, and angiogenesis


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:cb091eb3c399a3ddc2b5
claim_id: claim:cb091eb3c399a3ddc2b5
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
Systemic–venous ECs express genes that encode for specific sets of transcription factors, including EBF1 , EBF3 , MEOX1 , MEOX2 , and ZNF385D ; the cell surface receptors TACR1, ROBO1, and CYSLTR1; the peptidases CPXM2 and MMP16; the phosphodiesterases PDE7B and PDE2A ; as well as antagonist of fibroblast growth factor signaling SPRY1.

summary:
In Homo sapiens lung, systemic–venous endothelial cells express EBF1, EBF3, MEOX1, MEOX2, ZNF385D, TACR1, ROBO1, CYSLTR1, CPXM2, MMP16, PDE7B, PDE2A, and SPRY1.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:1e882c1cf24b297c694c
claim_id: claim:1e882c1cf24b297c694c
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
pulmonary–venous ECs—which are located downstream—express genes encoding for proteins associated with prostaglandin synthesis including PTGS1 and PTGIS , and with complement and coagulation cascades such as C7, PLAT, PROCR, THBD, C1R, and CLU

summary:
In Homo sapiens lung, pulmonary–venous endothelial cells express PTGS1, PTGIS, C7, PLAT, PROCR, THBD, C1R, and CLU.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:c92c663b3dd4e33f28c1
claim_id: claim:c92c663b3dd4e33f28c1
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
summary: In Homo sapiens lung, pulmonary–venous endothelial cells express CPE and DKK3.
span_literal:
Pulmonary–venous ECs express the most specific pulmonary–venous gene CPE as well as Wnt modulator DKK3 , which contrasts with the DKK2 expression in arterial ECs.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:aac5ab5f4131acda935b
claim_id: claim:aac5ab5f4131acda935b
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
summary: In Homo sapiens lung, pulmonary–venous endothelial cells express MMRN1 and PKHD1L1.
span_literal:
Overlapping with lymphatic ECs, but expressed at lower levels compared with them, pulmonary–venous ECs express factor V/Va binding and extracellular matrix protein MMRN1 16 and PKHD1L1


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:7cf4bbdf7cc16fa3b195
claim_id: claim:7cf4bbdf7cc16fa3b195
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
among venous EC, we identified 2 previously indistinguishable populations: pulmonary–venous ECs (COL15A1 neg ) localized to the lung parenchyma and systemic–venous ECs (COL15A1 pos ) localized to the airways and the visceral pleura

summary:
In Homo sapiens lung, pulmonary–venous endothelial cells are COL15A1 negative and systemic–venous endothelial cells are COL15A1 positive.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:e1c93874e291f8df7c39
claim_id: claim:e1c93874e291f8df7c39
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
among venous EC, we identified 2 previously indistinguishable populations: pulmonary–venous ECs (COL15A1 neg ) localized to the lung parenchyma and systemic–venous ECs (COL15A1 pos ) localized to the airways and the visceral pleura

summary:
In Homo sapiens lung, systemic–venous endothelial cells are COL15A1 positive, distinguishing them from pulmonary–venous endothelial cells.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:b991fbae3d687f396f6c
claim_id: claim:b991fbae3d687f396f6c
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
among capillary ECs, we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB , SOSTDC1 , and TBX2 and general capillary EC.

summary:
In Homo sapiens lung, aerocytes are characterized by EDNRB, SOSTDC1, and TBX2, distinguishing them from general capillary endothelial cells.


claim_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441:claim:775c49fecadc092a5ae8
claim_id: claim:775c49fecadc092a5ae8
paper_key: hca:0283_10.1161_circulationaha.120.052318_08d58c2441
span_literal:
BMPR2 , known to be associated with pulmonary arterial hypertension, was expressed in all ECs, but SOX17 only in arterial ECs

summary:
In Homo sapiens lung, BMPR2 is expressed in all endothelial cells, but SOX17 is expressed only in arterial endothelial cells.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:b442db41247e6c1eb226
claim_id: claim:b442db41247e6c1eb226
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
These annotations were confirmed using known pericentral marker genes (cytochrome P450 3A4 [ CYP3A4 ], alcohol dehydrogenase 4 [ ADH4 ], glutamate‐ammonia ligase [ GLUL ], and butyrylcholinesterase [ BCHE ]) and periportal marker genes (histidine ammonia‐lyase [ HAL ], carbamoyl‐phosphate synthase 1 [ CPS1 ], and 3‐hydroxy‐3‐methylglutaryl‐CoA synthase 1 [ HMGCS1 ])

summary:
In Homo sapiens, pericentral hepatocytes are marked by cytochrome P450 3A4 (CYP3A4), alcohol dehydrogenase 4 (ADH4), glutamate‐ammonia ligase (GLUL), and butyrylcholinesterase (BCHE).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:10294d706ba651f25c33
claim_id: claim:10294d706ba651f25c33
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
These annotations were confirmed using known pericentral marker genes (cytochrome P450 3A4 [ CYP3A4 ], alcohol dehydrogenase 4 [ ADH4 ], glutamate‐ammonia ligase [ GLUL ], and butyrylcholinesterase [ BCHE ]) and periportal marker genes (histidine ammonia‐lyase [ HAL ], carbamoyl‐phosphate synthase 1 [ CPS1 ], and 3‐hydroxy‐3‐methylglutaryl‐CoA synthase 1 [ HMGCS1 ])

summary:
In Homo sapiens, periportal hepatocytes are marked by histidine ammonia‐lyase (HAL), carbamoyl‐phosphate synthase 1 (CPS1), and 3‐hydroxy‐3‐methylglutaryl‐CoA synthase 1 (HMGCS1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:926f8a5c61588b2ef8d4
claim_id: claim:926f8a5c61588b2ef8d4
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Markers identified from these two clusters (histidine triad nucleotide binding protein 1 [ HINT1 ], cytochrome C oxidase subunit 7C [ COX7C ], apolipoprotein C1 [ APOC1 ], fatty acid binding protein 1, liver [ FABP1 ], metallothionein 2A [ MT2A ], metallothionein 1G [ MT1G ], and ubiquinone oxidoreductase subunit B1 [ NDUFB1 ]) were validated using spatial transcriptomics and immunohistochemistry

summary:
In Homo sapiens, interzonal hepatocytes are marked by histidine triad nucleotide binding protein 1 (HINT1), cytochrome C oxidase subunit 7C (COX7C), apolipoprotein C1 (APOC1), fatty acid binding protein 1 (FABP1), metallothionein 2A (MT2A), metallothionein 1G (MT1G), and ubiquinone oxidoreductase subunit B1 (NDUFB1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:e61dbd92b2637606488f
claim_id: claim:e61dbd92b2637606488f
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Our previous attempt to characterize these cells using exclusively scRNA‐seq identified only a single population encompassing 1.4% (199 of 8,444) of the cells expressing cholangiocyte markers (epithelial cell adhesion molecule [ EPCAM ], SRY (sex determining region Y)‐box 9 [ SOX9 ], and keratin 1 [ KRT1 ]).

summary:
In Homo sapiens, cholangiocytes express epithelial cell adhesion molecule (EPCAM), SRY (sex determining region Y)‐box 9 (SOX9), and keratin 1 (KRT1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:c5f12e514187ed4d160e
claim_id: claim:c5f12e514187ed4d160e
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
summary: In Homo sapiens, cholangiocytes express KRT7, SOX9, and annexin A4 (ANXA4).
span_literal:
In this study, we found that snRNA‐seq captured a higher proportion of KRT7 , SOX9 , and annexin A4 ( ANXA4 ) expressing cholangiocytes


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:2f1ff33543f4f2aa5909
claim_id: claim:2f1ff33543f4f2aa5909
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
We identified three asialoglycoprotein receptor 1–positive ( ASGR1 +) hepatocyte‐like clusters, two typical cholangiocyte‐like clusters ( KRT7 , KRT18 , and solute carrier family 4 member 2 [ SLC4A2 ] high), and a cluster of progenitors

summary:
In Homo sapiens, cholangiocyte-like cells express KRT7, KRT18, and solute carrier family 4 member 2 (SLC4A2) at high levels, while hepatocyte-like cells are asialoglycoprotein receptor 1 (ASGR1) positive.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:be8d5f08804eca06ea5c
claim_id: claim:be8d5f08804eca06ea5c
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
At the most differentiated end of the cholangiocyte branch was the Chol‐4 population, which contained mature cholangiocytes expressing differentiated cholangiocyte‐associated markers (Top DE: aquaporin 1 [ AQP1 ], KRT8 , KRT18 , KRT7 , defensin beta 1 [ DEFB1 ], CD24 , polymeric immunoglobulin receptor [ PIGR ], and ANXA4 )

summary:
In Homo sapiens, mature cholangiocytes (Chol-4) express aquaporin 1 (AQP1), KRT8, KRT18, KRT7, defensin beta 1 (DEFB1), CD24, polymeric immunoglobulin receptor (PIGR), and ANXA4.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:2035be6e73feb77e5c95
claim_id: claim:2035be6e73feb77e5c95
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Cholangiocyte identity was confirmed by the expression of key transcription factors (hepatocyte nuclear factor‐1‐beta [ HNF1B ], one cut homeobox 1 [ ONECUT1 ], and SOX9) and the enrichment of WNT signaling, ABC, and ion transporters

summary:
In Homo sapiens, cholangiocyte identity of the less-differentiated cholangiocyte population (Chol-5) is confirmed by expression of hepatocyte nuclear factor‐1‐beta (HNF1B), one cut homeobox 1 (ONECUT1), and SOX9.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:5247020af515b2f480db
claim_id: claim:5247020af515b2f480db
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
We determined this cluster contained specifically small cholangiocytes on the basis of B‐cell leukemia/lymphoma 2 ( BCL2 ) expression

summary:
In Homo sapiens, small cholangiocytes are identified by expression of B‐cell leukemia/lymphoma 2 (BCL2).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:b704d8c9475ae31ec3c2
claim_id: claim:b704d8c9475ae31ec3c2
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Markers of this cluster were identified using snRNA‐seq ( CYP3A5 , PPARG coactivator 1 alpha [ PPARGC1A ], fragile histidine triad diadenosine triphosphatase [ FHIT ], flavin containing dimethylaniline monooxygenase 5 [ FMO5 ], tryptophan 2,3‐dioxygenase [ TDO2 ], and SOX6 )

summary:
In Homo sapiens, small cholangiocytes (Chol-5) are marked by CYP3A5, PPARG coactivator 1 alpha (PPARGC1A), fragile histidine triad diadenosine triphosphatase (FHIT), flavin containing dimethylaniline monooxygenase 5 (FMO5), tryptophan 2,3‐dioxygenase (TDO2), and SOX6.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:3eb3116e21ae1d9b3424
claim_id: claim:3eb3116e21ae1d9b3424
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
At the far end of the opposite branch was Chol‐3, a population of central venous hepatocyte‐like cells, expressing high levels of CYP3A4 , glypican 6 ( GPC6 ), and aldehyde oxidase 1 ( AOX1 )

summary:
In Homo sapiens, central venous hepatocyte-like cells (Chol-3) express high levels of CYP3A4, glypican 6 (GPC6), and aldehyde oxidase 1 (AOX1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:4dadca2fad7d8eff9a59
claim_id: claim:4dadca2fad7d8eff9a59
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Two additional hepatocyte‐biased clusters, Chol‐2 and Chol‐6, expressed some typical cholangiocyte markers ( KRT7 , SOX9 , and CD24 ) but also expressed early hepatocyte lineage‐defining transcription factors ( HNF4a , forkhead box A2 [ FOXA2 ], prospero homeobox 1 [ PROX1 ], ONECUT1 , and ONECUT2 ), suggesting an intermediate or progenitor phenotype

summary:
In Homo sapiens, hepatocyte-biased progenitor cells (Chol-2 and Chol-6) express cholangiocyte markers KRT7, SOX9, and CD24, as well as hepatocyte lineage-defining transcription factors hepatocyte nuclear factor 4 alpha (HNF4a), forkhead box A2 (FOXA2), prospero homeobox 1 (PROX1), ONECUT1, and ONECUT2.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:430617d569f831bac394
claim_id: claim:430617d569f831bac394
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
The highly expressed genes of both Chol‐6 and Chol‐2 related to progenitor‐associated markers, such as FOXA2 , fibroblast growth factor receptor 3 ( FGFR3 ), hairy and enhancer of split‐1 [ HES1 ], and jagged canonical notch ligand 1 ( JAG1 )

summary:
In Homo sapiens, hepatic progenitor cells (Chol-6 and Chol-2) express progenitor-associated markers forkhead box A2 (FOXA2), fibroblast growth factor receptor 3 (FGFR3), hairy and enhancer of split‐1 (HES1), and jagged canonical notch ligand 1 (JAG1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:1df0d2bd0eaa5a7acd4f
claim_id: claim:1df0d2bd0eaa5a7acd4f
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
This cluster did not express mature cholangiocyte markers, but rather a collection of many stem‐like and progenitor markers, including pou class 5 homeobox 1 ( POU5F1 ), FOXO2 , runt‐related transcription factor 2 ( RUNX2 ), SOX6 , CD133 , alanyl aminopeptidase, membrane ( ANPEP ), and SOX9

summary:
In Homo sapiens, bipotent progenitor cells (Chol-1) express stem-like and progenitor markers including pou class 5 homeobox 1 (POU5F1), FOXO2, runt‐related transcription factor 2 (RUNX2), SOX6, CD133, alanyl aminopeptidase membrane (ANPEP), and SOX9.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:b50ce969a6a6857cf01b
claim_id: claim:b50ce969a6a6857cf01b
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Marker genes of Chol‐1 (i.e., FOXO3 , GATA binding protein 6 [ GATA6 ], FGFR3 , and ANPEP ) were localized to bile ducts in both our spatial transcriptomics data and publicly available immunohistochemistry data

summary:
In Homo sapiens, bipotent progenitor cells (Chol-1) are marked by FOXO3, GATA binding protein 6 (GATA6), fibroblast growth factor receptor 3 (FGFR3), and alanyl aminopeptidase membrane (ANPEP).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:5b6eaa7010a87c09ec33
claim_id: claim:5b6eaa7010a87c09ec33
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Seventy percent of mesenchymal nuclei consisted of quiescent HSCs (Mes‐1 and Mes‐5) specializing in vitamin A storage and metabolism, with high expression of RBP1 , lecithin retinol acyltransferase ( LRAT ), and phosphodiesterase 3B ( PDE3B )

summary:
In Homo sapiens, quiescent hepatic stellate cells (Mes-1 and Mes-5) express high levels of RBP1, lecithin retinol acyltransferase (LRAT), and phosphodiesterase 3B (PDE3B).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:cf000c56ed670e52cd17
claim_id: claim:cf000c56ed670e52cd17
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Mes1 specifically expressed hepatocyte growth factor ( HGF ), which is a key growth factor in liver regeneration and hepatocyte differentiation and growth

summary:
In Homo sapiens, hepatic stellate cell cluster Mes1 specifically expresses hepatocyte growth factor (HGF).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:4b9b0eda7674da22bc6b
claim_id: claim:4b9b0eda7674da22bc6b
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Both Mes4 and Mes6 expressed several activation‐associated genes [ ACTA2 , secreted protein acidic and cysteine rich ( SPARC ), transgelin ( TAGLN ), collagen type 1 alpha 1 chain ( COL1A1 ), and TIMP metallopeptidase inhibitor 1 ( TIMP1 )]

summary:
In Homo sapiens, mesenchymal cell clusters Mes4 and Mes6 express activation-associated genes ACTA2, secreted protein acidic and cysteine rich (SPARC), transgelin (TAGLN), collagen type 1 alpha 1 chain (COL1A1), and TIMP metallopeptidase inhibitor 1 (TIMP1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:d58b6681cd1c646e1fbf
claim_id: claim:d58b6681cd1c646e1fbf
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Both Mes4 and Mes6 expressed several activation‐associated genes [ ACTA2 , secreted protein acidic and cysteine rich ( SPARC ), transgelin ( TAGLN ), collagen type 1 alpha 1 chain ( COL1A1 ), and TIMP metallopeptidase inhibitor 1 ( TIMP1 )]

summary:
In Homo sapiens, mesenchymal cell cluster Mes6 expresses activation-associated genes ACTA2, secreted protein acidic and cysteine rich (SPARC), transgelin (TAGLN), collagen type 1 alpha 1 chain (COL1A1), and TIMP metallopeptidase inhibitor 1 (TIMP1).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:e7e3387eb526b6bef93a
claim_id: claim:e7e3387eb526b6bef93a
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Mes6 expressed VSMC markers like calponin 2 ( CNN2 ), myosin light chain 9 ( MYL9 ), TAGLN and ACTA2 , high levels of fibrogenic growth factors, and was enriched in the contractile phenotype, suggesting a fibrogenic state of VSMCs

summary:
In Homo sapiens, vascular smooth muscle cells (Mes6) express calponin 2 (CNN2), myosin light chain 9 (MYL9), transgelin (TAGLN), and ACTA2.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:3a7e9e3bb23b70ff68aa
claim_id: claim:3a7e9e3bb23b70ff68aa
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
Mes3 nuclei also express ACTA2 , MYL9 and TAGLN , but not collagen or matrix remodelers or quiescent HSC genes.

summary:
In Homo sapiens, vascular smooth muscle cell cluster Mes3 expresses ACTA2, MYL9, and transgelin (TAGLN), but does not express collagen or quiescent hepatic stellate cell genes.


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:f8abd4582b09a13cd8d1
claim_id: claim:f8abd4582b09a13cd8d1
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
several marker genes for these populations are present in both snRNA‐seq and scRNA‐seq maps ( CD68 , protein tyrosine phosphatase receptor type C [ PTPRC ], and macrophage receptor with collagenous structure [ MARCO ]).

summary:
In Homo sapiens, non-inflammatory macrophages are marked by CD68, protein tyrosine phosphatase receptor type C (PTPRC), and macrophage receptor with collagenous structure (MARCO).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:248d4906adf3c98106c8
claim_id: claim:248d4906adf3c98106c8
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
summary: In Homo sapiens, inflammatory macrophages are marked by lysozyme (LYZ), S100A8, and S100A9.
span_literal:
Meanwhile, the markers used to describe inflammatory macrophages (lysozyme [ LYZ ], S100A8 , and S100A9 ) were better represented by scRNA‐seq


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:57a99c2397cdf961d1c2
claim_id: claim:57a99c2397cdf961d1c2
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal: Mes7 is the smallest cluster of cells that express RBP1 , HGF , LRAT and Decorin ( DCN )
summary:
In Homo sapiens, mesenchymal cell cluster Mes7 expresses RBP1, hepatocyte growth factor (HGF), lecithin retinol acyltransferase (LRAT), and Decorin (DCN).


claim_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e:claim:23397df7f0b2a770cf19
claim_id: claim:23397df7f0b2a770cf19
paper_key: hca:0284_10.1002_hep4.1854_fe09f5fe1e
span_literal:
portal markers: von Willebrand factor ( VWF ), C‐type lectin domain containing 14A ( CLEC14A) , inhibitor of DNA binding 1 ( ID1 ), SPARC like 1 ( SPARCL1 ), and connective tissue growth factor ( CTGF )

summary:
In Homo sapiens, portal endothelial cells are marked by von Willebrand factor (VWF), C‐type lectin domain containing 14A (CLEC14A), inhibitor of DNA binding 1 (ID1), SPARC like 1 (SPARCL1), and connective tissue growth factor (CTGF).


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:f5e223db81f6f185a577
claim_id: claim:f5e223db81f6f185a577
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
We found six distinct hepatocyte populations, comprising Clusters 1, 3, 5, 6, 14, and 15 (Figs. 2f , 4ci ), that were generally less proliferative cells (Figs. 2e , 4a ), and showed enriched ALB (Albumin) expression, a hallmark of hepatocytes.

summary:
In Homo sapiens, hepatocytes show enriched ALB (Albumin) expression, which is a hallmark of hepatocytes in the liver.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:06eba8bbcc524f3202db
claim_id: claim:06eba8bbcc524f3202db
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
The most abundant endothelial cell cluster (Cluster 11) displayed enriched expression of F8, PECAM1 , with little expression of CD32B, LYVE-1, STAB2 , and CD14 (Fig. 5c , Supplementary Fig. 11 ).

summary:
In Homo sapiens liver, periportal liver sinusoidal endothelial cells (Cluster 11) display enriched expression of F8 and PECAM1, with little expression of CD32B, LYVE1, STAB2, and CD14.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:11aea14df75afbda058f
claim_id: claim:11aea14df75afbda058f
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
The second most abundant endothelial cell population (Cluster 12) was characterized by the enriched expression of CD32B, LYVE1, STAB2 , with little expression of VWF (Top DE genes: CCL14, CLEC1B, FCN2, S100A13, FCN3, CRHBP, STAB1, GNG11, IFI27, CLEC4G, CLDN5, CCL23, OIT3, RAMP3, SGK1, DNASE1L3, LIFR, SPARC, ADGRL4, EGFL7, PCAT19, CDKN1C )

summary:
In Homo sapiens liver, central venous liver sinusoidal endothelial cells (Cluster 12) are characterized by enriched expression of CD32B, LYVE1, and STAB2, with little expression of VWF.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:99e038725cc92610277c
claim_id: claim:99e038725cc92610277c
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
The least abundant hepatic endothelial cell population (Cluster 13) was characterized by low or no expression of LSEC markers ( LYVE1, STAB2, CD32B ).

summary:
In Homo sapiens liver, non-liver sinusoidal endothelial cells (Cluster 13) are characterized by low or no expression of LYVE1, STAB2, and CD32B.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:42774a263b524fca94db
claim_id: claim:42774a263b524fca94db
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
summary: In Homo sapiens liver, non-liver sinusoidal endothelial cells express ENG and PECAM1.
span_literal:
These cells are likely non-LSEC endothelial cells including central vein and portal arterial and venous endothelial cells based on the expression of ENG (protein alias CD105) and PECAM1 (protein alias CD31) as has been described in the human liver via immunohistochemistry 32 .


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:06d7073702a093b8fa28
claim_id: claim:06d7073702a093b8fa28
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
summary: In Homo sapiens liver, cholangiocytes express SOX9, EPCAM, and KRT19.
span_literal:
Differentially expressed genes in this cluster (Cluster 17) included SOX9 , EPCAM , and KRT19 (Fig. 6a, b, f ), in accordance with genes that were previously described as enriched in primary human cholangiocytes 45 .


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:9178c62c8bbea32e7326
claim_id: claim:9178c62c8bbea32e7326
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
Cluster 20 was identified as HSCs based on the expression of ACTA2, COL1A1, TAGLN, COL1A2, COL3A1, SPARC , and the expression of retinol binding protein 1 ( RBP1 ), a vitamin A-associated transcript (Figs. 2f , 7 ).

summary:
In Homo sapiens liver, hepatic stellate cells are identified based on the expression of ACTA2, COL1A1, TAGLN, COL1A2, COL3A1, SPARC, and RBP1.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:d7d19f39168c7b51f0ab
claim_id: claim:d7d19f39168c7b51f0ab
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
CD68 + macrophage population 1 (Cluster 4; Fig. 2f ), was characterized by enriched expression of LYZ , CSTA , CD74 54 , suggesting that this cluster represents inflammatory macrophages (Top DE genes: S100A8, LYZ, S100A9, HLA-DPB1, S100A12, RP11-1143G9.4, EVI2A, HLA-DPA1, VCAN, S100A6, CXCL8, HLA-DRA, MNDA, TYROBP, HLA-DRB1, FCN1, HLA-DQA1, IL18, C1QC, CD74, HLA-DRB5 ).

summary:
In Homo sapiens liver, inflammatory macrophages (CD68-positive macrophage population 1) are characterized by enriched expression of LYZ, CSTA, and CD74.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:928e0f227caaab00419c
claim_id: claim:928e0f227caaab00419c
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
CD68 + macrophage population 2 (Cluster 10; Fig. 2f ) was characterized by enriched expression of CD5L, MARCO, VSIG4, CPVL, CD163, CCDC88A, C5AR1, LIPA, LILRB5, MAF, CTSB, MS4A7, VMO1, RAB31, SLC31A2, TTYH3, VCAM1, KLF4, HMOX1, AIF1l, TMIGD3 (top DE genes).

summary:
In Homo sapiens liver, non-inflammatory macrophages (CD68-positive macrophage population 2) are characterized by enriched expression of CD5L, MARCO, VSIG4, CPVL, CD163, CCDC88A, C5AR1, LIPA, LILRB5, MAF, CTSB, MS4A7, VMO1, RAB31, SLC31A2, TTYH3, VCAM1, KLF4, HMOX1, AIF1L, and TMIGD3.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:e13ec5cc76b63b7683ed
claim_id: claim:e13ec5cc76b63b7683ed
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal: MARCO (MAcrophage Receptor with COllagenous structure) is only expressed in non-inflammatory KCs
summary:
In Homo sapiens liver, MARCO (macrophage receptor with collagenous structure) is only expressed in non-inflammatory Kupffer cells.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:9e70b0d16073880dd1c9
claim_id: claim:9e70b0d16073880dd1c9
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
CD68 + MARCO − macrophages have a similar transcriptional profile to inflammatory, recently recruited macrophages including decreased expression of CD163 58 and increased expression of PLBD1 57 .

summary:
In Homo sapiens liver, CD68-positive MARCO-negative inflammatory macrophages show decreased expression of CD163 and increased expression of PLBD1.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:3b5370a356c73e0d59f4
claim_id: claim:3b5370a356c73e0d59f4
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
The most abundant population of T cells (Cluster 2) was characterized by the expression of CD2, CD3D, TRAC, GZMK, CCL5, CCL4L2, PYHIN1, TRBC1, TRBC2, GZMA, CD3E, JUNB, CD69, IL7R, DUSP2, IFNG, LTB, IL32, CD52 (Top DE genes)

summary:
In Homo sapiens liver, αβ T cells (Cluster 2) are characterized by the expression of CD2, CD3D, TRAC, GZMK, CCL5, CCL4L2, PYHIN1, TRBC1, TRBC2, GZMA, CD3E, JUNB, CD69, IL7R, DUSP2, IFNG, LTB, IL32, and CD52.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:f4dd11ab8f4c6987e61e
claim_id: claim:f4dd11ab8f4c6987e61e
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
The second cluster of CD3 + cells (Cluster 9), was a population of CD3D expressing cells with enriched expression of TBX21 (aka T-bet), KLRB1 (protein alias CD161), FCGR3A ( CD16 ), NKG7 , and GNLY ( NKG5 ) with enriched expression of the TCR delta chain TRDC and the TCR gamma chain TRGC1 .

summary:
In Homo sapiens liver, γδ T cells (Cluster 9) express CD3D with enriched expression of TBX21, KLRB1, FCGR3A, NKG7, GNLY, TRDC, and TRGC1.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:904be7563666f2019204
claim_id: claim:904be7563666f2019204
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
We found a population of NK-like cells (Cluster 8) characterized by enriched expression of CD7 , C–type lectin receptor KLRD1 ( CD94 ) , GZMK ( Granzyme K), NCR1 (NKp46), and NCAM1 (CD56), without upregulated expression of FCGR3A (CD16) or ITGA1 (CD49a)

summary:
In Homo sapiens liver, natural killer-like cells (Cluster 8) are characterized by enriched expression of CD7, KLRD1, GZMK, NCR1, and NCAM1, without upregulated expression of FCGR3A or ITGA1.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:2ceabd6493a4fa16139d
claim_id: claim:2ceabd6493a4fa16139d
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
This population also showed enriched expression of EOMES , suggesting that the predominant population in this cluster may correlate with the long-lived NK cell population previously described in human liver biopsies by flow cytometry 72 .

summary:
In Homo sapiens liver, natural killer-like cells show enriched expression of EOMES, correlating with the long-lived natural killer cell population.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:398d7f3dc17d0a332459
claim_id: claim:398d7f3dc17d0a332459
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
Cluster 16 identified a subset of cells that were enriched for the expression of IGHD, CD19, MS4A1 (protein alias CD20) , CD22, CD52 without expression of either CD27 or CD138 which suggest that this cluster is comprised of mature antigen inexperienced B cells 77 , 78

summary:
In Homo sapiens liver, mature antigen inexperienced B cells (Cluster 16) are enriched for the expression of IGHD, CD19, MS4A1, CD22, and CD52, without expression of CD27 or CD138.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:0822d4fcca9f4a7b3544
claim_id: claim:0822d4fcca9f4a7b3544
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
The cells of Cluster 7 were enriched for the expression of immunoglobulin heavy and light chains, CD27, CD38 78 , and had reduced expression of MS4A1 (CD20) 80 , suggesting that this cluster is comprised of plasma cells

summary:
In Homo sapiens liver, plasma cells (Cluster 7) are enriched for the expression of CD27 and CD38, with reduced expression of MS4A1.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:22641e7230102a171dc0
claim_id: claim:22641e7230102a171dc0
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
CD69 is a marker for recently activated T cells, and is enriched in tissue resident memory T cells when compared to circulating memory T cells 67 , 68 .

summary:
In Homo sapiens, CD69 is a marker enriched in tissue resident memory T cells when compared to circulating memory T cells.


claim_key: hca:0286_10.1038_s41467-018-06318-7_d818827349:claim:788b95fd36887c281a56
claim_id: claim:788b95fd36887c281a56
paper_key: hca:0286_10.1038_s41467-018-06318-7_d818827349
span_literal:
We found that MARCO-positive macrophages secreted less TNF-α in response to LPS/ IFN-γ stimulation than MARCO-negative CD68 + macrophages, suggesting that CD68 + MARCO - cells are more pro-inflammatory (Fig. 8d , Supplementary Fig. 15 ).

summary:
In Homo sapiens liver, MARCO-positive macrophages secrete less TNF-α than MARCO-negative CD68-positive macrophages, suggesting CD68-positive MARCO-negative macrophages are more pro-inflammatory.


claim_key: hca:0289_10.1172_jci.insight.93009_72829a2871:claim:cb45712d46036cef06e3
claim_id: claim:cb45712d46036cef06e3
paper_key: hca:0289_10.1172_jci.insight.93009_72829a2871
summary: In Homo sapiens, keratinocytes are identified by expression of KRT1 and KRT10 in skin.
span_literal:
the presence of skin keratins KRT1 and KRT10 in cluster 5 identifies this cell type as keratinocytes


claim_key: hca:0289_10.1172_jci.insight.93009_72829a2871:claim:03416c3e3e17db3fa6b6
claim_id: claim:03416c3e3e17db3fa6b6
paper_key: hca:0289_10.1172_jci.insight.93009_72829a2871
summary: In Homo sapiens, fibroblasts are identified by expression of COL1A2, FBN, and DCN.
span_literal:
Fibroblasts were identified by expression of the type I collagen gene COL1A2 , as well as other extracellular matrix proteins such as FBN and DCN


claim_key: hca:0289_10.1172_jci.insight.93009_72829a2871:claim:47492734addc3f75c41e
claim_id: claim:47492734addc3f75c41e
paper_key: hca:0289_10.1172_jci.insight.93009_72829a2871
span_literal:
T cells and myeloid cells were assigned by expression of the T cell receptor protein CD3G and the antibacterial enzyme LYZ , respectively

summary:
In Homo sapiens, T cells are marked by expression of CD3G, and myeloid cells are marked by expression of LYZ.


claim_key: hca:0289_10.1172_jci.insight.93009_72829a2871:claim:e6e99afcc7620d05c723
claim_id: claim:e6e99afcc7620d05c723
paper_key: hca:0289_10.1172_jci.insight.93009_72829a2871
span_literal: loop of Henle cells expressed UMOD and SLC12A1 known to be restricted to the thick ascending limb
summary:
In Homo sapiens, loop of Henle cells express UMOD and SLC12A1, which are known to be restricted to the thick ascending limb.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:bc9e292458747257d44f
claim_id: claim:bc9e292458747257d44f
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
Less identifiable and potentially off-target populations included a small neural population marked by ELAVL3 and ELAVL4 , and a more substantial population expressing glial markers including FABP7 .

summary:
In Homo sapiens kidney organoids, a neural population is marked by ELAVL3 and ELAVL4, and a glial population is marked by FABP7.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:ecea02851200f7b203ae
claim_id: claim:ecea02851200f7b203ae
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary: In Homo sapiens kidney organoids, muscle progenitor cells express MYOD1, MYOG, and PITX2.
span_literal:
An additional off-target population of muscle progenitors expressing MYOD1 , MYOG and PITX2 was detected for the first time (Fig. 1 a).


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:759bd7fb0b18c66d6d81
claim_id: claim:759bd7fb0b18c66d6d81
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
This re-clustering produced five organoid nephron (ON) clusters with similarity to nephron progenitor cells (ON2 marked by DAPL1 , LYPD1 , SIX1 , CRABP2 ), podocyte precursors as seen in the proximal early nephron (ON1 CTGF , OLFM3 , MAFB , NPHS1 , low levels of LHX1 and PAX8 ), podocytes (ON0 marked by TCF21 , PODXL , VEGFA , WT1 ), proximal tubule precursors (ON3 IGFBP7 , FXYD2 , CDH6 , HNF1B ), and cluster expressing markers common to the ureteric epithelium and distal nephron ( EPCAM , EMX2 , SPP1 , MAL and PAX2 (ON4)) (Fig. 1 b, Additional file 3 ).

summary:
In Homo sapiens kidney organoids, nephron progenitor cells are marked by DAPL1, LYPD1, SIX1, and CRABP2.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:8c48732485dbd94f8327
claim_id: claim:8c48732485dbd94f8327
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
This re-clustering produced five organoid nephron (ON) clusters with similarity to nephron progenitor cells (ON2 marked by DAPL1 , LYPD1 , SIX1 , CRABP2 ), podocyte precursors as seen in the proximal early nephron (ON1 CTGF , OLFM3 , MAFB , NPHS1 , low levels of LHX1 and PAX8 ), podocytes (ON0 marked by TCF21 , PODXL , VEGFA , WT1 ), proximal tubule precursors (ON3 IGFBP7 , FXYD2 , CDH6 , HNF1B ), and cluster expressing markers common to the ureteric epithelium and distal nephron ( EPCAM , EMX2 , SPP1 , MAL and PAX2 (ON4)) (Fig. 1 b, Additional file 3 ).

summary:
In Homo sapiens kidney organoids, podocyte precursor cells express CTGF, OLFM3, MAFB, NPHS1, LHX1, and PAX8.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:65a019109eb12cd7d7d8
claim_id: claim:65a019109eb12cd7d7d8
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary:
In Homo sapiens kidney organoids, proximal tubule precursor cells express IGFBP7, FXYD2, CDH6, and HNF1B.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:1143af3281720c459c06
claim_id: claim:1143af3281720c459c06
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary:
In Homo sapiens kidney organoids, a cluster expressing markers common to the ureteric epithelium and distal nephron expresses EPCAM, EMX2, SPP1, MAL, and PAX2.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:2002b42e0c6cbf922547
claim_id: claim:2002b42e0c6cbf922547
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary: In Homo sapiens kidney organoids, the distal tubule cell cluster also expresses DEFB1 and TMEM52B.
span_literal:
The EPCAM + PAX2 + cluster ON4 also expressed markers enriched in the distal tubule such as DEFB1 and TMEM52B .


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:c83c0bd63b67dd6a9060
claim_id: claim:c83c0bd63b67dd6a9060
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary: In Homo sapiens, the glial cell cluster is marked by TTYH1, FABP7, and SOX2.
span_literal:
Organoid-enriched clusters include a glial cluster C11 (marked by TTYH1 , FABP7 , SOX2 ), which included less than ten hFK cells, and C14 (marked by SOX11 , ELAVL3 , ELAVL4 ) that mostly contained organoid cells.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:1feef3e7075026600982
claim_id: claim:1feef3e7075026600982
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary: In Homo sapiens, the immune cell cluster is marked by PTPRC, TYROBP, and FCER1G.
span_literal:
An immune cell cluster (C12, marked by PTPRC , TYROBP , FCER1G ) was mostly derived from hFK cells but surprisingly, 20 organoid cells contributed to this cluster and shared expression of immune response genes.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:18400ce360a7c1263fe9
claim_id: claim:18400ce360a7c1263fe9
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary: In Homo sapiens fetal kidney, blood cells are marked by HBG1, HBB, and HBA2.
span_literal:
Top markers of cluster C13 included genes highly expressed in blood ( HBG1 , HBB , HBA2 ), a signature primarily driven by the hFK-derived cells within the cluster as organoid-derived cells within this cluster did not share expression of these cell type-specific markers.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:119943dbcccc9d3fa79c
claim_id: claim:119943dbcccc9d3fa79c
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
The endothelial cluster C4 featured extensive conservation of established markers such as CLDN5 , CDH5 , CD34 , KDR , TIE1 , SOX17 , SOX7 and FLT1 .

summary:
In Homo sapiens, endothelial cells show conserved expression of established markers CLDN5, CDH5, CD34, KDR, TIE1, SOX17, SOX7, and FLT1.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:1768decdd8b6348acc40
claim_id: claim:1768decdd8b6348acc40
paper_key: hca:0290_10.1101_235499_566cff6e3c
summary: In Homo sapiens, podocyte precursor cells are marked by MAFB, CTGF, and OLFM3.
span_literal:
CN3 featured conserved expression of recently defined human podocyte precursor markers MAFB , CTGF and OLFM3


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:62ca6f89c3b590ad5d63
claim_id: claim:62ca6f89c3b590ad5d63
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
hFK and organoid cells in CN0 expressed podocyte markers TCF21 , POXDL , ROBO2 and NPHS2 but hFK cells within this cluster maintained expression of human nephron progenitor markers LGALS1 and LYPD1

summary:
In Homo sapiens, podocytes express TCF21, PODXL, ROBO2, and NPHS2, while human fetal kidney nephron progenitor cells maintain expression of LGALS1 and LYPD1.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:8ce757f647b357dde93a
claim_id: claim:8ce757f647b357dde93a
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
the combined cluster C0 correlating to the L10–12 clusters (conserved markers include TCF21 , ALDH1A2 , ANGPT1 and TAGLN )

summary:
In Homo sapiens, stromal cell cluster C0 is marked by conserved expression of TCF21, ALDH1A2, ANGPT1, and TAGLN.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:a4bbb9a30b67992a06b1
claim_id: claim:a4bbb9a30b67992a06b1
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
Stromal clusters C3 (marked by MAB21L2 , CXCL14 , PRRX1 ) and C9 ( COL2A1 , COL9A3 , CNMD) had smaller contributions of hFK cells (less than 5% of total cells)

summary:
In Homo sapiens, stromal cell cluster C3 is marked by MAB21L2, CXCL14, and PRRX1, while stromal cell cluster C9 is marked by COL2A1, COL9A3, and CNMD.


claim_key: hca:0290_10.1101_235499_566cff6e3c:claim:591d1d03b855e5ddf033
claim_id: claim:591d1d03b855e5ddf033
paper_key: hca:0290_10.1101_235499_566cff6e3c
span_literal:
the conserved signature also features several smooth muscle-associated genes such as GATA3 , MEF2C , ACTA2 , HOPX , ANGPT2 and PDGFRB

summary:
In Homo sapiens, the vascular smooth muscle and mesangial stromal cell cluster C3 has a conserved signature featuring GATA3, MEF2C, ACTA2, HOPX, ANGPT2, and PDGFRB.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:6d135a945d55b1608d16
claim_id: claim:6d135a945d55b1608d16
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
These included astrocytic markers in meta-module #3 ( S100B, GFAP, SLC1A3, GLAST and MLC1 ), oligodendroglial lineage markers in meta-module #4 ( OLIG1, OMG, PLP1, PLLP, TNR and ALCAM ), stem/progenitor cell signatures in meta-modules# 5–6, including NPC markers ( SOX4, SOX11 and DCX )

summary:
In Homo sapiens glioblastoma, the astrocyte-like state is marked by S100B, GFAP, SLC1A3, GLAST, and MLC1.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:de7398e18a4bed4e5b3a
claim_id: claim:de7398e18a4bed4e5b3a
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
These included astrocytic markers in meta-module #3 ( S100B, GFAP, SLC1A3, GLAST and MLC1 ), oligodendroglial lineage markers in meta-module #4 ( OLIG1, OMG, PLP1, PLLP, TNR and ALCAM ), stem/progenitor cell signatures in meta-modules# 5–6, including NPC markers ( SOX4, SOX11 and DCX )

summary:
In Homo sapiens glioblastoma, the oligodendrocyte-progenitor-like state is marked by OLIG1, OMG, PLP1, PLLP, TNR, and ALCAM.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:b326475593c66f314262
claim_id: claim:b326475593c66f314262
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
summary: In Homo sapiens, the astrocyte-like glioblastoma state contains radial glia markers such as HOPX.
span_literal:
the AC-like meta-module was most highly expressed by astrocytes, it was also expressed in radial glia (RG) and contained RG markers such as HOPX


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:cf445b8b7e3fa6cc1df4
claim_id: claim:cf445b8b7e3fa6cc1df4
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
In situ RNA hybridization of glioblastoma for NPC-like (CD24), MES-like (CD44) and proliferation (Ki67) markers.

summary:
In Homo sapiens glioblastoma, CD24 is a marker of the neural progenitor-like state and CD44 is a marker of the mesenchymal-like state.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:23f90e4bfb9ecec5a028
claim_id: claim:23f90e4bfb9ecec5a028
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
In situ RNA hybridization of glioblastoma for NPC-like ( CD24 ), OPC-like ( PDGFRA ), AC-like (S100B) and proliferation ( Ki67 ) markers.

summary:
In Homo sapiens glioblastoma, CD24 marks the neural progenitor-like state, PDGFRA marks the oligodendrocyte-progenitor-like state, and S100B marks the astrocyte-like state.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:d0f8344eb882ae28a5df
claim_id: claim:d0f8344eb882ae28a5df
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
One of these meta-modules was strongly associated with hypoxia-response genes (e.g. HILPDA ), stress (e.g. DDIT3 ) and glycolytic (e.g. ENO2 , LDHA ) genes, suggesting that in some tumors the mesenchymal state is linked to hypoxia and increased glycolysis.

summary:
In Homo sapiens glioblastoma, the mesenchymal-like hypoxia-dependent state is associated with expression of HILPDA, DDIT3, ENO2, and LDHA.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:26e245a260e65a9b795f
claim_id: claim:26e245a260e65a9b795f
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
summary: In Homo sapiens glioblastoma, the mesenchymal-like state is associated with high expression of VIM.
span_literal:
two meta-modules that were associated with high expression of mesenchymal-related genes (e.g. VIM ) and gene-sets (P<10 −9 , hypergeometric test).


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:a69826c24b7e712b3eae
claim_id: claim:a69826c24b7e712b3eae
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
NPC-like was further subdivided into two subprograms (NPC1 and NPC2, STAR Methods , Table S2 ) that were distinguished by inclusion of OPC-related genes in NPC1 (e. g ., OLIG1 and TNR) vs . neuronal lineage genes in NPC2 (e.g. STMN1/2/4 and DLX5/6-AS1 )

summary:
In Homo sapiens glioblastoma, the neural progenitor-like cell state 1 includes OLIG1 and TNR, while the neural progenitor-like cell state 2 includes STMN1, STMN2, STMN4, and DLX5/6-AS1.


claim_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2:claim:ee55e9cf9c2a51c53942
claim_id: claim:ee55e9cf9c2a51c53942
paper_key: hca:0291_10.1016_j.cell.2019.06.024_7d6cf2f1e2
span_literal:
NPC-like was further subdivided into two subprograms (NPC1 and NPC2, STAR Methods , Table S2 ) that were distinguished by inclusion of OPC-related genes in NPC1 (e. g ., OLIG1 and TNR) vs . neuronal lineage genes in NPC2 (e.g. STMN1/2/4 and DLX5/6-AS1 )

summary:
In Homo sapiens glioblastoma, the neural progenitor-like cell state 2 is distinguished by neuronal lineage genes including STMN1, STMN2, STMN4, and DLX5/6-AS1.


claim_key: hca:0292_10.1371_journal.pone.0225466_ac5a0b0b14:claim:4803e9f737d98d17d1b6
claim_id: claim:4803e9f737d98d17d1b6
paper_key: hca:0292_10.1371_journal.pone.0225466_ac5a0b0b14
span_literal:
While in cluster 5, the top 10 expressed genes were mainly interferon induced protein related (Interferon Induced Protein with Tetratricopeptide Repeats 1, 2, 3 ( IFIT1 , 2 , 3 ), Interferon-Stimulated Protein ( ISG15 ), Interferon Stimulated Exonuclease Gene 20 ( ISG20 ))

summary:
In Homo sapiens HeLa-CCL2 cells, cluster 5 is marked by high expression of interferon induced genes including IFIT1, IFIT2, IFIT3, ISG15, and ISG20.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:394ef97f2065c3aa9c89
claim_id: claim:394ef97f2065c3aa9c89
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
summary: In Homo sapiens, endothelial cells are marked by CLDN5, VWF, and CD34.
span_literal:
In addition to ECs ( CLDN5 , VWF , CD34 ) and due to the lack of CD45 – selection, other clusters including macrophage ( APOC1 , CD163 , F13A1 ), microglia ( CX3CR1 , P2RY12 , P2RY13 ), neutrophils ( IL1R2 , CXCR2 , FPR2 ), T cells ( CD3D , CD3E , GZMK ), B cells ( IGHG1 , IGHG3 , CD79A ), DCs ( HLA-DQA1 , HLA-DPB1 ), glia/neuronal cells ( FABP7 , PTPRZ1 ), and vascular mural cells ( RGS5 , PDGFRB , NOTCH3 ) were also identified in this data set


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:9955e988978eb672b449
claim_id: claim:9955e988978eb672b449
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal:
Cluster 1 ECs (referred to as peripheral EC type I [Pe1] because it originates mainly from the brain tissue surrounding the tumor mass) displayed a quiescent endothelial marker profile, as expected of normal brain ECs, and were characterized by a high expression level of genes implicated in vascular integrity ( KLF2 , TIMP3 ) and BBB function ( SLC2A1 , SLCO1A2 )

summary:
In Homo sapiens, peripheral endothelial cell type I (Pe1) in brain is characterized by high expression of KLF2, TIMP3, SLC2A1, and SLCO1A2.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:75d84673db5bc0865675
claim_id: claim:75d84673db5bc0865675
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal:
Cluster 2 ECs (tumor core EC type I: Co1) resembled endothelial angiogenic phenotypes as they have been mapped in both developmental and tumor angiogenesis, and included for example a gene signature associated with vascular basement membrane remodeling ( COL4A1 , COL4A2 , LAMB1 , LAMA4 , HSPG2 , PXDN , PLOD1 , NID1 , NID2 ), cytoskeletal rearrangements ( CD93 , MYO1B , SPARC , INSR ), angiogenic sprouting ( KDR , PGF , ANGPT2 , NOX4 , PTP4A3 , FLT4 ), and endothelial tip cell formation ( APLN , SOX4 , ITGA5 , PGF , NOTCH4 )

summary:
In Homo sapiens, tumor core endothelial cell type I (Co1) is characterized by expression of COL4A1, COL4A2, LAMB1, LAMA4, HSPG2, PXDN, PLOD1, NID1, NID2, CD93, MYO1B, SPARC, INSR, KDR, PGF, ANGPT2, NOX4, PTP4A3, FLT4, APLN, SOX4, ITGA5, and NOTCH4.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:9a1a5e98eb1d7b96fd88
claim_id: claim:9a1a5e98eb1d7b96fd88
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal:
cluster 4 (peripheral EC type II: Pe2), expressing inflammatory cytokines ( CCL4 , CCL3 ) and genes involved in MHC-II-Mediated antigen presentation ( HLA-DRB1 , HLA-DRA , HLA-DPA1 , HLA-DPB1 , HAL-DQB1 )

summary:
In Homo sapiens, peripheral endothelial cell type II (Pe2) expresses inflammatory cytokines CCL4 and CCL3, and MHC class II antigen presentation genes HLA-DRB1, HLA-DRA, HLA-DPA1, HLA-DPB1, and HLA-DQB1.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:c24652b0434c671fb9cf
claim_id: claim:c24652b0434c671fb9cf
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal:
Cluster 5 (tumor core EC type III: Co3), were mainly derived from tumor core and were characterized by upregulation of immune-activated genes including IL1B , ACKR1 , SELE , and VACM1 , which are associated with inflammation and immune cell recruitment

summary:
In Homo sapiens, tumor core endothelial cell type III (Co3) is characterized by upregulation of IL1B, ACKR1, SELE, and VCAM1.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:509cd1740103ed115bf1
claim_id: claim:509cd1740103ed115bf1
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal:
ECs in tumor peripheral tissue have a quiescence phenotype (cluster 1, Pe1), characterized by high expression of BBB enriched genes including SLC2A1 and KLF2 .

summary:
In Homo sapiens, peripheral endothelial cell type I (Pe1) in brain is characterized by high expression of SLC2A1 and KLF2.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:2885b1d4c4fb86544c1a
claim_id: claim:2885b1d4c4fb86544c1a
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal: ECs in GBM express a high level of PLVAP , which is a vascular marker of BBB disruption.
summary:
In Homo sapiens, endothelial cells in glioblastoma express a high level of PLVAP, a vascular marker of blood-brain barrier disruption.


claim_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad:claim:fd82f84a0064389ad89a
claim_id: claim:fd82f84a0064389ad89a
paper_key: hca:0293_10.1172_jci.insight.150861_5764a5bfad
span_literal:
Several key BBB transporters, including SLC2A1 , ABCG2 , ABCB1 , SLCO1A2 , and ATP10A , were highly expressed in the ECs of the brain tissue surrounding the GBM core.

summary:
In Homo sapiens, endothelial cells of the brain tissue surrounding the glioblastoma core highly express the blood-brain barrier transporters SLC2A1, ABCG2, ABCB1, SLCO1A2, and ATP10A.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:6f776a80cc77a98b0fb4
claim_id: claim:6f776a80cc77a98b0fb4
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens tonsil, GATA3 is a marker of type 2 innate lymphoid cells.
span_literal:
Next we explored the four clusters of cells and confirmed their cellular identity by their elevated expression of known cell population–specific transcripts (e.g., GATA3 in ILC2 cells, RORC in ILC3 cells, GZMA in NK cells, and CXCR3 in ILC1 cells)


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:c92030e3a3f873b8a4b1
claim_id: claim:c92030e3a3f873b8a4b1
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
Among transcripts shared by all CD127 + ILCs were RARG , which encodes a receptor (RARγ) for retinoic acid (RA), and RORA , which encodes the 'orphan' receptor RORα

summary:
In Homo sapiens, RARG is commonly expressed by all CD127-positive innate lymphoid cells. In Homo sapiens, RORA is commonly expressed by all CD127-positive innate lymphoid cells.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:6b5d5f7a958e027a7562
claim_id: claim:6b5d5f7a958e027a7562
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens, CXCR3 and IFNG are signature transcripts for type 1 innate lymphoid cells.
span_literal:
ILC1 cells showed significantly elevated expression of 79 genes, including CXCR3 and IFNG , which are signature transcripts for human ILC1 cells 5


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:3b37aea456209b88e018
claim_id: claim:3b37aea456209b88e018
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
Notably, ILC1 cells had significantly higher expression of IKZF3 , which encodes the transcription factor Aiolos that has been suggested to function as a negative regulator of mouse NK cell function 30 and might serve as a functional target and useful marker for ILC1 cells.

summary:
In Homo sapiens, IKZF3, which encodes the transcription factor Aiolos, has significantly higher expression in type 1 innate lymphoid cells and might serve as a useful marker for type 1 innate lymphoid cells.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:7a68acb5e37140d67b29
claim_id: claim:7a68acb5e37140d67b29
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens, type 1 innate lymphoid cells express IFNG-AS1 and IL18BP.
span_literal:
Furthermore, ILC1 cells expressed IFNG-AS1 and IL18BP ( Fig. 5 ); these encode IFN-γ antisense RNA and IL-18-binding protein, respectively, which might restrict ILC1 function in homeostatic conditions.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:e80503afce3613327ac9
claim_id: claim:e80503afce3613327ac9
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
ILC1 cells also expressed IL6R and IL6ST , which encode the two functional subunits of the IL-6 receptor (the α-subunit (CD126) and β-subunit (CD130), respectively).

summary:
In Homo sapiens, type 1 innate lymphoid cells express IL6R and IL6ST, which encode the two functional subunits of the interleukin-6 receptor.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:2376b25634706498615d
claim_id: claim:2376b25634706498615d
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
They also expressed SOCS3 , which encodes a signaling molecule downstream of IL-6, known to inhibit signaling via the kinase JAK and STAT transcription factors.

summary:
In Homo sapiens, type 1 innate lymphoid cells express SOCS3, which encodes a signaling molecule downstream of interleukin-6.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:90f196fb7ef2b242a3f0
claim_id: claim:90f196fb7ef2b242a3f0
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
Among other differentially expressed transcripts with higher expression in ILC1 cells were those from other genes typically expressed by T cells, including CD4 , CD5 , CD6 , CD28 , CD27 and CCR7

summary:
In Homo sapiens, type 1 innate lymphoid cells show higher expression of CD4, CD5, CD6, CD28, CD27, and CCR7.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:e3085f010623a9f5580b
claim_id: claim:e3085f010623a9f5580b
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens, type 1 innate lymphoid cells express TNFRSF1B, TNFRSF10A, and TNFSF8.
span_literal:
Furthermore, ILC1 cells expressed several transcripts encoding members of the tumor-necrosis factor (TNF) receptor and TNF superfamilies, including TNFRSF1B (which encodes TNF receptor 2), TNFRSF10A (which encodes the receptor for the apoptosis-inducing cytokine TRAIL) and TNFSF8 (which encodes the cytokine CD30L)


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:81a8b0a877dd394fe4b4
claim_id: claim:81a8b0a877dd394fe4b4
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
Similar analyses of ILC2 cells identified 58 genes with significantly elevated expression, including genes encoding several previously reported ILC2 markers, such as PTGDR2 (which encodes the prostaglandin D 2 receptor CRTH2), IL1RL1 (which encodes the IL-33 receptor), IL17RB (which encodes the IL-25 receptor), KLRG1 (which encodes the activation marker KLRG1) and GATA3 (which encodes the transcription factor GATA-3)

summary:
In Homo sapiens, type 2 innate lymphoid cells show significantly elevated expression of PTGDR2, IL1RL1, IL17RB, KLRG1, and GATA3, which are previously reported markers of type 2 innate lymphoid cells.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:0f67f0e0022a0b4883d6
claim_id: claim:0f67f0e0022a0b4883d6
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
In addition to identifying GATA3 , we identified a set of transcription factor–encoding genes whose expression was significantly elevated in ILC2 cells, including the gene encoding MAF, which is involved in IL-4 production, and the gene encoding KLF7, which is involved in hematopoiesis.

summary:
In Homo sapiens, type 2 innate lymphoid cells show significantly elevated expression of MAF and KLF7.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:75a4307919a0b68fc7f9
claim_id: claim:75a4307919a0b68fc7f9
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
These included transcripts encoding hematopoietic prostaglandin D synthase ( HPGDS ), hydroxyprostaglandin dehydrogenase 15-(NAD) ( HPGD ), the transcription factor PPARγ ( PPARG ) and the prostaglandin E 2 receptor EP2 ( PTGER2 )

summary:
In Homo sapiens, type 2 innate lymphoid cells show differential expression of HPGDS, HPGD, PPARG, and PTGER2.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:aac67ccde06956a9c53b
claim_id: claim:aac67ccde06956a9c53b
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
We found TCF7 expression in fewer human ILC2 cells (72 of 143 ILC2 cells) than cells in the other ILC populations (426 of a total of 505 ILC1, ILC3 and NK cells)

summary:
In Homo sapiens, TCF7 expression is found in fewer type 2 innate lymphoid cells compared to other innate lymphoid cell populations.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:ba4f6a6816e115777312
claim_id: claim:ba4f6a6816e115777312
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
ILC2 cells also expressed TLE4 ( Fig. 6a ), which encodes a member of the Groucho family of co-repressors that is part of the Notch signaling pathway 36 and has been shown to repress IFN-γ expression through epigenetic changes of IFNG regulatory elements 37 .

summary:
In Homo sapiens, type 2 innate lymphoid cells express TLE4, which encodes a member of the Groucho family of co-repressors.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:8eb6d86dd624520ff1d4
claim_id: claim:8eb6d86dd624520ff1d4
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
In addition, ILC2 cells showed upregulation of the expression of various transcripts encoding molecules involved in environmental sensing, such as CD150 ( SLAMF1 ), the purinergic receptor P2Y ( P2RY1 ), CD137 ( TNFRSF9 ), CD11b ( ITGAM ) and CD95L ( FASLG )

summary:
In Homo sapiens, type 2 innate lymphoid cells show upregulation of SLAMF1, P2RY1, TNFRSF9, ITGAM, and FASLG.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:4d887a453ac5a8ee3409
claim_id: claim:4d887a453ac5a8ee3409
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
Among such transcripts were ID2 , RORC , AHR , TOX , TOX2 and IKZF2, and IL2RB , LTBR , IL1R1 and IL23R 3 , 6 , 38

summary:
In Homo sapiens, type 3 innate lymphoid cells show upregulated expression of ID2, RORC, AHR, TOX, TOX2, IKZF2, IL2RB, LTBR, IL1R1, and IL23R.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:0e2b6d1d2b107ef6c6d7
claim_id: claim:0e2b6d1d2b107ef6c6d7
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens, type 3 innate lymphoid cells express KIT, PTPN6, FES, and LYN.
span_literal:
In addition to expressing KIT (which encodes c-Kit), ILC3 cells expressed several genes encoding products associated with c-Kit signaling, including PTPN6 , FES and LYN .


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:b5f974ff20fde1730c3c
claim_id: claim:b5f974ff20fde1730c3c
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens, type 3 innate lymphoid cells show upregulation of DLL1, JAG2, ADAM10, and RBPJ.
span_literal:
Furthermore, ILC3 cells showed upregulation of many genes encoding molecules of the Notch pathway, including the ligands DLL1 and JAG2, the proteinase ADAM10, the intracellular signaling molecule RBPJ and the transcription factor TCF-1


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:5893b29c540631382cbc
claim_id: claim:5893b29c540631382cbc
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
ILC3 cells showed differential expression (higher than that of the other ILCs, according to SCDE analysis) of NCR2 (which encodes NKp44) and a set of transcripts encoding products associated with signaling via NKp44 and immunoreceptor tyrosine-based activation motifs, which has shown to induce an inflammatory program in ILC3 cells 12

summary:
In Homo sapiens, type 3 innate lymphoid cells show differential expression of NCR2, which encodes NKp44, higher than that of the other innate lymphoid cells.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:6b773b52f19e75ba1022
claim_id: claim:6b773b52f19e75ba1022
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
Differentially upregulated transcripts encoding products in the NKp44 signaling motif included TYROBP (which encodes DAP12), FGR and LYN (which encode kinases of the Src family) and SYK , PLCG2 , VAV3 , LAT2 and CLNK (which encode signaling molecules downstream of NKp44)

summary:
In Homo sapiens, type 3 innate lymphoid cells show upregulated expression of TYROBP, FGR, LYN, SYK, PLCG2, VAV3, LAT2, and CLNK.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:52ab689121239ecef95c
claim_id: claim:52ab689121239ecef95c
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
summary: In Homo sapiens, type 3 innate lymphoid cells express NRP1, PECAM1, AMICA1, EREG, and KLRF2.
span_literal:
Furthermore, ILC3 cells expressed NRP1 (which encodes neuropilin-1), PECAM1 (which encodes the immunoreceptor tyrosine-based inhibitory motif–containing molecule CD31), AMICA1 (which encodes a γδ T cell–associated molecule), EREG (which encodes a growth factor) and KLRF2 (which encodes the C-type lectin–like receptor NKp65)


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:8abb4bf1d404f5d2f878
claim_id: claim:8abb4bf1d404f5d2f878
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
One cluster (cluster A) showed enrichment for cells expressing the gene encoding NKp44 ( NCR2 ) and the gene encoding its downstream signaling molecule DAP12 ( TYROBP )

summary:
In Homo sapiens, the NKp44-positive type 3 innate lymphoid cell subpopulation (cluster A) shows enrichment for NCR2 and TYROBP expression.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:6a0f9e068a8d6d27b17a
claim_id: claim:6a0f9e068a8d6d27b17a
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal: This cluster showed enrichment for cells expressing SELL (which encodes L-selectin (CD62L))
summary:
In Homo sapiens, the CD62L-positive type 3 innate lymphoid cell subpopulation (cluster B) shows enrichment for SELL expression.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:06481a5dcf89ffa25f63
claim_id: claim:06481a5dcf89ffa25f63
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
A third cluster (cluster C) showed enrichment for cells expressing HLA-encoding transcripts, including HLA-DRA , HLA-DRB1 , HLA-DRB5 , HLA-DPA1 and HLA-DPB1

summary:
In Homo sapiens, the HLA-DR-positive type 3 innate lymphoid cell subpopulation (cluster C) shows enrichment for HLA-DRA, HLA-DRB1, HLA-DRB5, HLA-DPA1, and HLA-DPB1 expression.


claim_key: hca:0294_10.1038_ni.3368_b6f196ee59:claim:1083b210d3c1b4aaf375
claim_id: claim:1083b210d3c1b4aaf375
paper_key: hca:0294_10.1038_ni.3368_b6f196ee59
span_literal:
This cluster also showed expression of transcripts encoding the IL-1β receptor ( IL1R1 ), the apoptosis-inducing cytokine TRAIL ( TNFSF10 ) and the intracellular signaling molecule PRAM1 (the retinoic acid–induced gene PRAM1 )

summary:
In Homo sapiens, the HLA-DR-positive type 3 innate lymphoid cell subpopulation (cluster C) shows expression of IL1R1, TNFSF10, and PRAM1.


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:624931bdb9278f30d3c7
claim_id: claim:624931bdb9278f30d3c7
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, lipofibroblasts are marked by LIMCH1 and MACF1 expression.
span_literal:
Novel marker genes and transcription factors for this population included many genes identified in murine lipofibroblasts, like LIMCH1 and MACF1


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:45060d792fdfb5925287
claim_id: claim:45060d792fdfb5925287
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens lung, lipofibroblasts are marked by A2M, LIMCH1, GPC3, SCN7A, and RGCC expression.
span_literal:
UMAP visualization of averaged expression of novel human lipofibroblast signature genes ( A2M, LIMCH1, GPC3, SCN7A, RGCC) in P1, M21 and integrated healthy/IPF lungs.


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:abb31a2706e3177a233b
claim_id: claim:abb31a2706e3177a233b
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, smooth muscle cells are marked by high expression of CNN1, SYNPO2, and ACTG2.
span_literal:
High expression of SMC-related marker genes, represented by CNN1, SYNP O 2, ACTG2, was used to differentiate these related, and closely associated, populations in the integrated adult data set


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:1f4c765adcefe34fb5f1
claim_id: claim:1f4c765adcefe34fb5f1
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens lung, smooth muscle cells are marked by ACTG2, SYNPO2, and CNN1 expression.
span_literal:
UMAP visualization of averaged expression of human SMC ( ACTG2 , SYNP O 2 , CNN1 ) and myofibroblast (Myo1: ADIRF , CRIP1 , MCAM , FAM129A ; Myo2: CLU , ASPN , WIF1 , ITGBL1 ) signature genes in P1, M21 and integrated healthy/IPF lungs.


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:220e409b005ac0b4c7fa
claim_id: claim:220e409b005ac0b4c7fa
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
span_literal:
UMAP visualization of averaged expression of human SMC ( ACTG2 , SYNP O 2 , CNN1 ) and myofibroblast (Myo1: ADIRF , CRIP1 , MCAM , FAM129A ; Myo2: CLU , ASPN , WIF1 , ITGBL1 ) signature genes in P1, M21 and integrated healthy/IPF lungs.

summary:
In Homo sapiens lung, myofibroblast subtype 1 is marked by ADIRF, CRIP1, MCAM, and FAM129A expression.


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:57e2d44443f91948dff4
claim_id: claim:57e2d44443f91948dff4
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, airway smooth muscle cells express the marker HHIP.
span_literal:
In addition to commonly used SMC markers, the P1 dataset expressed the reported human airway SMC marker HHIP


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:4f6f8ee7a3718b8ab7a3
claim_id: claim:4f6f8ee7a3718b8ab7a3
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, vascular smooth muscle cells are marked by MEF2C and NTRK3 expression.
span_literal:
SMC markers, including recently reported vascular smooth muscle specific genes MEF2C and NTRK3, were clearly discriminative


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:b6009b6d398b092f32ea
claim_id: claim:b6009b6d398b092f32ea
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, myofibroblasts are negative for THY1 expression.
span_literal:
Myofibroblasts were Thy1/THY1 - , as reported in the literature but other suggested myofibroblast delineating markers, like S100A4 ( Rock, et al., 2011 ; Sanders, et al., 2007 ; Niessen, et al., 2004 ), were not discriminative.


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:29f03551b9444bdffe97
claim_id: claim:29f03551b9444bdffe97
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, pericytes are marked by HIGD1B, NDUFA4L2, COX4I2, and FAM162B expression.
span_literal:
Conserved expression of more novel pericyte marker genes, represented by HIGD1B , NDUFA4L2 , COX4I2 and FAM162B among others, were identified


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:868253fc768b0867d359
claim_id: claim:868253fc768b0867d359
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
span_literal:
UMAP visualization of averaged expression of human EBF1 + ( CCDC80 , SERPINF1 , CFD , SCARA5 ) and pericyte ( COX4I2 , HIGD1B , NDUFA4L2 , FAM162B ) signature genes in P1, M21, and integrated healthy/IPF lungs.

summary:
In Homo sapiens lung, EBF1-positive fibroblasts are marked by CCDC80, SERPINF1, CFD, and SCARA5 expression.


claim_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd:claim:86fc5576f04b0166816e
claim_id: claim:86fc5576f04b0166816e
paper_key: hca:0295_10.1016_j.isci.2021.102551_1c1e582cdd
summary: In Homo sapiens, smooth muscle cells are marked by ACTG2 and MEF2C expression.
span_literal:
We identified a number of SMC-associated genes that displayed discrete expression in the SMC clusters, like Actg2/ATCG2 in both species, Actc1 in mice, or MEF2C in humans


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:1eb6752fc5d3191a0155
claim_id: claim:1eb6752fc5d3191a0155
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
summary: In Homo sapiens, induced pluripotent stem cells are marked by NANOG and OCT3/4 (POU5F1).
span_literal:
The expression of markers for iPSCs ( NANOG, OCT3/4 ), presomitic mesoderm ( TBX6 , HES7 ), somites ( PAX3 , MEOX1 ), sclerotome ( PAX1 , UNCX ), and syndetome ( SCX , COL1A2 )


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:693087d4af9c18693969
claim_id: claim:693087d4af9c18693969
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
summary: In Homo sapiens, induced pluripotent stem cells are marked by OCT3/4 (POU5F1).
span_literal:
We thus identified several specific markers at appropriate time points, such as OCT3/4 ( POU5F1 ) in iPSCs, DLL3 in PSM, PAX3 in somites, CRABP1 39 in sclerotome, and SCX , COL9A3 , COL3A1 , COL12A1 , and POSTN in syndetome


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:8842098b30d6dcd7e6d8
claim_id: claim:8842098b30d6dcd7e6d8
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
summary: In Homo sapiens, tenocytes universally express the markers SCX, COL1A2, COL3A1, and DCN.
span_literal:
The whole syndetome clusters [0–4, 7] revealed universal expression of representative tenocyte markers such as SCX , COL1A2 , COL3A1 , and DCN


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:54c49a0fc09f6239542c
claim_id: claim:54c49a0fc09f6239542c
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
span_literal:
Cell cycle-related genes, including CENPF , TOP2A , and MKI67 , accounted for most of the top 20 genes

summary:
In Homo sapiens, the proliferating syndetome cell cluster is distinguished from the G1-phase syndetome cell cluster by cell cycle-related genes including CENPF, TOP2A, and MKI67.


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:b0653f033d423479334a
claim_id: claim:b0653f033d423479334a
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
span_literal:
gene expression of syndetome- and tenocyte-specific transcription factors and extracellular matrix proteins, including SCX , MKX , TNMD , COL1A1 , COL1A2 , and FMOD , was time-dependently upregulated

summary:
In Homo sapiens, syndetome and tenocyte-specific markers include SCX, MKX, TNMD, COL1A1, COL1A2, and FMOD.


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:e8ca4184584f303fe138
claim_id: claim:e8ca4184584f303fe138
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
summary: In Homo sapiens, sclerotome cells express PAX1.
span_literal:
we used a medium containing smoothened agonist (SAG) and the BMP inhibitor LDN193189 (LDN) 36 to differentiate the somites into sclerotomes expressing PAX1


claim_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21:claim:0bbd0e4e6c97d1e39548
claim_id: claim:0bbd0e4e6c97d1e39548
paper_key: hca:0296_10.1038_s41467-021-25328-6_8814b43a21
span_literal:
The expression of markers for sclerotome ( PAX1 ) and syndetome ( SCX , MKX , TNMD , COL1A1 , COL1A2 , FMOD ) was assessed by RT-qPCR.

summary:
In Homo sapiens, sclerotome cells are marked by PAX1, and syndetome cells are marked by SCX, MKX, TNMD, COL1A1, COL1A2, and FMOD.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:8fd9230091d3a7a1f1a7
claim_id: claim:8fd9230091d3a7a1f1a7
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
summary: In Homo sapiens nail unit, KRT1 and KRT5 are canonical markers for keratinocytes.
span_literal:
Canonical markers clearly demarcated each cell cluster (Fig. 1d ): KRT 1 or KRT5 for keratinocytes; COL1A1 for fibroblasts; RSG5 for myofibroblast-like cells; VWF for endothelial cells; LYVE-1 for lymphatic endothelial cells; PTPRC for lymphocytes; AIF1 for macrophage/dendritic cells; TPSB2 for mast cells; SCGB1B2P for eccrine gland cells; DEFB1 for eccrine duct cells; COL9A2 for chondrocytes; NRXN1 for neural cells, and PMEL for melanocytes


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:96a20c77abd359f40378
claim_id: claim:96a20c77abd359f40378
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
summary: In Homo sapiens nail unit, onychofibroblasts are defined by high MME expression level.
span_literal:
Violin and feature plot demonstrated a distinct cluster of fibroblasts (Fibroblast 4 cluster) demonstrating a high MME expression level. Hence, we defined this cluster as onychofibroblasts.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:1cf5aeadd3f728493dda
claim_id: claim:1cf5aeadd3f728493dda
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
summary: In Homo sapiens nail unit, the onychofibroblast cluster demonstrates high expression of RSPO4.
span_literal:
We observed that the onychofibroblast cluster also demonstrated a high expression of RSPO4 (Fig. 2b ).


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:777492f97bf89d273047
claim_id: claim:777492f97bf89d273047
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal:
We also found additional genes that were strongly and specifically expressed in the onychofibroblast cluster including MSX1 , TWIST1 , CRABP1 , WIF1 , and BMP5 (Fig. 2c ).

summary:
In Homo sapiens nail unit, MSX1, TWIST1, CRABP1, WIF1, and BMP5 are strongly and specifically expressed in the onychofibroblast cluster.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:81d26b738be2fd3830d6
claim_id: claim:81d26b738be2fd3830d6
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
summary: In Homo sapiens nail unit, basal keratinocytes are defined by expression of KRT5 and KRT14.
span_literal:
Basal keratinocytes were defined by the expression of KRT5 and KRT14 , suprabasal keratinocytes by KRT1 and KRT10 expression, proliferating keratinocytes by MKI67 expression, and cornified cells by SPRR1B expression


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:e440193b89fbe6f0c2ac
claim_id: claim:e440193b89fbe6f0c2ac
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal:
SPINK6 + keratinocytes mainly expressed KRT16 suggesting that they might be derived primarily from nail bed

summary:
In Homo sapiens nail unit, SPINK6-positive keratinocytes mainly express KRT16, suggesting derivation from nail bed.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:e494834e4596ad34f0d5
claim_id: claim:e494834e4596ad34f0d5
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal: SPINK6 expression distinguished the nail-specific keratinocytes from epidermal keratinocytes.
summary:
In Homo sapiens, SPINK6 expression distinguishes nail-specific keratinocytes from epidermal keratinocytes.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:ac6f9d918b3c3b39f876
claim_id: claim:ac6f9d918b3c3b39f876
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal:
By comparing LGR6 and WNT6 expressions amongst the two nail-specific keratinocyte subpopulations, we found that they were limited to the Keratinocyte-1 cluster, implying that it was mainly isolated from nail matrix (Fig. 3d ).

summary:
In Homo sapiens nail unit, LGR6 and WNT6 expression is limited to the nail keratinocyte-1 cluster, implying isolation from nail matrix.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:a6994ca15f69256b2155
claim_id: claim:a6994ca15f69256b2155
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal:
Also, ISH studies showed LGR6 was mainly expressed in the basal layer of nail matrix just above the RSPO4 expressing mesenchyme (Fig. 3e–g ).

summary:
In Homo sapiens nail unit, LGR6 is mainly expressed in the basal layer of nail matrix keratinocytes.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:8b3841761a8f28fc4bf6
claim_id: claim:8b3841761a8f28fc4bf6
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal:
Nail-specific mesenchymal cell population (onychofibroblast cluster) which were characterized by MME (CD10) expression demonstrated high expression of RSPO4 .

summary:
In Homo sapiens, the nail-specific onychofibroblast cluster, characterized by MME (CD10) expression, demonstrates high expression of RSPO4.


claim_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae:claim:2594ea4e1b51dd677c81
claim_id: claim:2594ea4e1b51dd677c81
paper_key: hca:0297_10.1038_s42003-021-02223-w_f1c781baae
span_literal: Two nail-specific epithelial cell populations demonstrated high expression of SPINK6 and WNT6 .
summary:
In Homo sapiens nail unit, two nail-specific epithelial cell populations demonstrate high expression of SPINK6 and WNT6.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:8fa25c19a68a7aa748b6
claim_id: claim:8fa25c19a68a7aa748b6
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
Tissue-resident macrophage subpopulations (MΦ1-LYVE1, MΦ2-peritoneal and MΦ3-APOE) were distinguished by the expression of FOLR2— a gene associated with embryonic-derived tissue-resident macrophages

summary:
In Homo sapiens, tissue-resident macrophage subpopulations (MΦ1-LYVE1, MΦ2-peritoneal, and MΦ3-APOE) are distinguished by the expression of FOLR2.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:069dacc60b77e2b0a5ab
claim_id: claim:069dacc60b77e2b0a5ab
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
Tissue-resident macrophage subpopulations (MΦ1-LYVE1, MΦ2-peritoneal and MΦ3-APOE) were distinguished by the expression of FOLR2— a gene associated with embryonic-derived tissue-resident macrophages

summary:
In Homo sapiens, MΦ2-peritoneal tissue-resident macrophage is distinguished by the expression of FOLR2.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:44df495f580e60dfd5fb
claim_id: claim:44df495f580e60dfd5fb
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
MΦ2-peritoneal cells were exclusive to peritoneal tissue and expressed ICAM2 , a known marker for peritoneal macrophages

summary:
In Homo sapiens, MΦ2-peritoneal macrophage expresses ICAM2, a known marker for peritoneal macrophages.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:0999ecad08169c166790
claim_id: claim:0999ecad08169c166790
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
MΦ4-infiltrated cells were present in all tissues, expressed CLEC5A , CCR2 and VEGFA , all markers for blood-infiltrated macrophages

summary:
In Homo sapiens, MΦ4-infiltrated macrophage expresses CLEC5A, CCR2, and VEGFA, which are markers for blood-infiltrated macrophages.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:62d5e0619ef69d2b5169
claim_id: claim:62d5e0619ef69d2b5169
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
summary: In Homo sapiens, perivascular CCL19 (Prv-CCL19) cells express both STEAP4 and MYH11.
span_literal:
we observed an unreported perivascular CCL19 (Prv-CCL19) subpopulation expressing both STEAP4 and MYH11


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:2b63cdab0bd45840c7eb
claim_id: claim:2b63cdab0bd45840c7eb
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
Notably, SUSD2 , a marker for endometrial mesenchymal stem cells identified in endometriosis 12 , was specifically co-expressed in EcP and EcPA CCL19 + perivascular cells

summary:
In Homo sapiens, SUSD2 is a marker for endometrial mesenchymal stem cells and is co-expressed in CCL19-positive perivascular cells in ectopic peritoneal lesions.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:f11b8c31797324b09dfa
claim_id: claim:f11b8c31797324b09dfa
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal: CD1C expression was prevalent in three DC subpopulations: pre-cDC2, cDC2 and DC3.
summary:
In Homo sapiens, CD1C expression is prevalent in three dendritic cell subpopulations: pre-conventional dendritic cell type 2, conventional dendritic cell type 2, and DC3.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:74265003ddb9402e32f6
claim_id: claim:74265003ddb9402e32f6
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
A cDC2 subset in eutopic endometrium and peritoneal lesions, but not EcO, specifically expressed CD207 , a gene expressed by Langerhans cells and immature DCs

summary:
In Homo sapiens, a conventional dendritic cell type 2 subset specifically expresses CD207, a gene expressed by Langerhans cells and immature dendritic cells.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:0a1d8b7f9ce87dcc39d4
claim_id: claim:0a1d8b7f9ce87dcc39d4
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
CD207 + cDC2 cells expressing genes related to immunogenic DC maturation ( IL18 , GNLY , RUNX3 and LTB

summary:
In Homo sapiens, CD207-positive conventional dendritic cell type 2 cells express IL18, GNLY, RUNX3, and LTB, genes related to immunogenic dendritic cell maturation.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:1a27b30ad0ededdf2cab
claim_id: claim:1a27b30ad0ededdf2cab
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal: whereas MSR1 + cDC2s expressed immunomodulatory genes ( MRC1 , VSIG4 , SGK1 and PECAM1 )
summary:
In Homo sapiens, MSR1-positive conventional dendritic cell type 2 cells express immunomodulatory genes MRC1, VSIG4, SGK1, and PECAM1.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:911e413016bfff7792b4
claim_id: claim:911e413016bfff7792b4
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal: FPR2 was specifically expressed by myeloid cells, particularly monocytes and MΦ4-infiltrated cells
summary:
In Homo sapiens, FPR2 is specifically expressed by myeloid cells, particularly monocytes and MΦ4-infiltrated macrophages.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:d90e45877a4f9465c40f
claim_id: claim:d90e45877a4f9465c40f
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
The MUC5B + population was present in both eutopic (4–10% of epithelial cells) and ectopic tissues (<1%) and specifically expressed RUNX3 , TFF3 and SAA1

summary:
In Homo sapiens, the MUC5B-positive epithelial cell population specifically expresses RUNX3, TFF3, and SAA1.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:64fe1ccd735ac5221f95
claim_id: claim:64fe1ccd735ac5221f95
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
Additionally, we noted the co-expression of PROM1 and SIX1 , which are progenitor cell markers 57 , 58 , in in vivo MUC5B + cells

summary:
In Homo sapiens, MUC5B-positive epithelial cells co-express PROM1 and SIX1, which are progenitor cell markers.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:745b74ca0825189e606d
claim_id: claim:745b74ca0825189e606d
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
interactions between CD86 (expressed in MΦ1-LYVE1) and CTLA4 (expressed in regulatory T (T Reg ) cells) was upregulated in endometriosis

summary:
In Homo sapiens, CD86 is expressed in MΦ1-LYVE1 macrophages and CTLA4 is expressed in regulatory T cells.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:07358416af48ca03a5b5
claim_id: claim:07358416af48ca03a5b5
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
interactions between CD86 (expressed in MΦ1-LYVE1) and CTLA4 (expressed in regulatory T (T Reg ) cells) was upregulated in endometriosis

summary:
In Homo sapiens, CTLA4 is expressed in regulatory T cells, and CD86 is expressed in MΦ1-LYVE1 macrophages.


claim_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c:claim:f56f8c40814a938d6076
claim_id: claim:f56f8c40814a938d6076
paper_key: hca:0298_10.1101_2021.07.28.453839_0003c16e5c
span_literal:
we found that endometriosis MΦ1-LYVE1 upregulated tolerogenic genes ( VSIG4 , RGS1 , IL10 , EGFL7 and LYVE1 ) and angiogenesis-related genes ( THBS1 , HBEGF , PDGFB , PDGFC and IGF1 )

summary:
In Homo sapiens, MΦ1-LYVE1 macrophages upregulate tolerogenic genes VSIG4, RGS1, IL10, EGFL7, and LYVE1, and angiogenesis-related genes THBS1, HBEGF, PDGFB, PDGFC, and IGF1 in endometriosis.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:aa0da48f0c2c99089cc1
claim_id: claim:aa0da48f0c2c99089cc1
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
summary: In Homo sapiens, EpCAM-positive adult biliary epithelial cells express KRT19, SOX9, and ALB.
span_literal:
EpCAM + adult cells express progenitor/BEC markers KRT19 and SOX9 , but interestingly most are highly ALB + as well


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:9f576523cbf670fd3b98
claim_id: claim:9f576523cbf670fd3b98
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
we identified a foetal hepatocyte population expressing hepatoblast markers AFP and DLK1 , but negative for traditional biliary markers

summary:
In Homo sapiens, foetal hepatocytes express the hepatoblast markers AFP and DLK1 and are negative for traditional biliary markers.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:bfdd2e5e507d3b026a2e
claim_id: claim:bfdd2e5e507d3b026a2e
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Foetal HHyP cells expressed hepatic genes ALB, APOE , TF and HNF4A , but were also positive for BEC markers KRT19 , SOX9 and CD24

summary:
In Homo sapiens, foetal hepatobiliary hybrid progenitor cells express hepatic genes ALB, APOE, TF, and HNF4A, and are also positive for biliary epithelial cell markers KRT19, SOX9, and CD24.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:ff66eee570a81c97348f
claim_id: claim:ff66eee570a81c97348f
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
foetal hepatocytes express none of the traditional progenitor/BEC markers enriched in HHyPs, including KRT7 , SPP1 , STAT1 , SOX9 and HNF1B

summary:
In Homo sapiens, foetal hepatocytes do not express KRT7, SPP1, STAT1, SOX9, or HNF1B, which are enriched in hepatobiliary hybrid progenitor cells.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:5c69f5dc8aa54e5669fb
claim_id: claim:5c69f5dc8aa54e5669fb
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Genes, including TACSTD2 (TROP-2) , CLDN4 , CLDN10 and KRT7 are enriched in adult HHyPs compared to the foetal HHyP population

summary:
In Homo sapiens, TACSTD2 (TROP-2), CLDN4, CLDN10, and KRT7 are enriched in adult hepatobiliary hybrid progenitor cells compared to foetal hepatobiliary hybrid progenitor cells.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:2f16af4061e994b5402a
claim_id: claim:2f16af4061e994b5402a
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal: expression of CLDN6 and the transcription factor STAT4 are exclusively detected in foetal HHyPs
summary:
In Homo sapiens, CLDN6 and STAT4 are exclusively expressed in foetal hepatobiliary hybrid progenitor cells.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:ad3225821515651e068c
claim_id: claim:ad3225821515651e068c
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal: MCAM , CDH6 and STAT1 are also enriched in foetal HHyPs over adult
summary:
In Homo sapiens, MCAM, CDH6, and STAT1 are enriched in foetal hepatobiliary hybrid progenitor cells compared to adult hepatobiliary hybrid progenitor cells.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:4460bcca06b77f91590b
claim_id: claim:4460bcca06b77f91590b
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Mature BECs uniquely express the genes CLDN10 , CLDN4 , CXCL2 , LGALS2 , MMP7 , MUC1 , MUC5B , TROP-2 , TFF1 , TFF2 , TFF3 and TSPAN8 as determined by our study and MacParland et al.

summary:
In Homo sapiens, mature biliary epithelial cells uniquely express CLDN10, CLDN4, CXCL2, LGALS2, MMP7, MUC1, MUC5B, TACSTD2 (TROP-2), TFF1, TFF2, TFF3, and TSPAN8.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:2ba2678c39ed32947470
claim_id: claim:2ba2678c39ed32947470
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Genes, including CAV1 , CLDN6 , GPRC5B , MCAM , NCAM and STAT4 are restricted to expression in HHyPs

summary:
In Homo sapiens, CAV1, CLDN6, GPRC5B, MCAM, NCAM, and STAT4 are restricted to expression in hepatobiliary hybrid progenitor cells.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:dee2e26dfd0008506418
claim_id: claim:dee2e26dfd0008506418
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
These cells transcriptionally resemble the periportal hybrid progenitors previously identified in mice, being positive for SOX9 , HNF1B and KRT19 , but also ALB , APOE and TF

summary:
In Homo sapiens, hepatobiliary hybrid progenitor cells are positive for SOX9, HNF1B, KRT19, ALB, APOE, and TF.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:11c7a70a5030ebe33478
claim_id: claim:11c7a70a5030ebe33478
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal: They also express BEC/progenitor markers CD24 , CD133 , CLDN3 , FGFR2 , KRT7 and SPP1
summary:
In Homo sapiens, hepatobiliary hybrid progenitor cells also express biliary epithelial cell/progenitor markers CD24, CD133, CLDN3, FGFR2, KRT7, and SPP1.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:76222adb766bea6ff190
claim_id: claim:76222adb766bea6ff190
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal: We found that HHyPs were distinct from foetal hepatoblasts which are AFP + / DLK +
summary:
In Homo sapiens, foetal hepatoblasts are positive for AFP and DLK, and are distinct from hepatobiliary hybrid progenitor cells.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:471395d388081c1216bd
claim_id: claim:471395d388081c1216bd
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
these cells were negative for mature BEC markers identified in the recent MacParland et al. 23 scRNA-seq study of human liver, including Trefoil factors (TFF)1–3 and mucins MUC1 , MUC3A and MUC5B

summary:
In Homo sapiens, adult hepatobiliary hybrid progenitor cells are negative for mature biliary epithelial cell markers TFF1, TFF2, TFF3, MUC1, MUC3A, and MUC5B.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:c20dd2317cf94f3c00d0
claim_id: claim:c20dd2317cf94f3c00d0
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Pseudo state 3 revealed an enrichment of ductal marker genes KRT7 , KRT23 and TROP -2, while hepatic transcription factors ATF5 , MLXIPL and CREB3L3 were enriched in pseudo state 4

summary:
In Homo sapiens, adult hepatobiliary hybrid progenitor cells in pseudo state 3 are enriched for ductal markers KRT7, KRT23, and TACSTD2 (TROP-2), while those in pseudo state 4 are enriched for hepatic transcription factors ATF5, MLXIPL, and CREB3L3.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:9f25b758922a7033aa33
claim_id: claim:9f25b758922a7033aa33
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Pseudo state 3 revealed an enrichment of ductal marker genes KRT7 , KRT23 and TROP -2, while hepatic transcription factors ATF5 , MLXIPL and CREB3L3 were enriched in pseudo state 4

summary:
In Homo sapiens, adult hepatobiliary hybrid progenitor cells in pseudo state 4 are enriched for hepatic transcription factors ATF5, MLXIPL, and CREB3L3.


claim_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52:claim:0467b5013dd940c6015a
claim_id: claim:0467b5013dd940c6015a
paper_key: hca:0299_10.1038_s41467-019-11266-x_d55119ff52
span_literal:
Pseudo state 1 contained all foetal HHyPs, and a sub-population of adult HHyPs (blue), enriched markers DCDC2, CDH6 , STAT1 and ANXA13

summary:
In Homo sapiens, pseudo state 1 hepatobiliary hybrid progenitor cells are enriched for DCDC2, CDH6, STAT1, and ANXA13.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:bf3a48cb6d282702b581
claim_id: claim:bf3a48cb6d282702b581
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
A total of 7 major cell types were identified including fibroblasts (FB; Dcn + Ddr2 +), endothelial cell (EC; Cdh5 + Kdr +), T cells and natural killer cell ( Cd3g + Nkg7 +), macrophage/monocyte/dendritic cell (MF/Mo/DC; Adgre1 + Csf1r +), B cell (BC; Cd79a + Cd19 +), smooth muscle cell (SMC; Acta2 + Tagln +) and Schwann cell ( Plp1 + Nrn1 +), based on their respective molecular signatures

summary:
In Homo sapiens, fibroblasts are identified by expression of DCN and DDR2 in the mouse heart, but similar cell types are also found in human heart failure data.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:f371d5f9c579ea188444
claim_id: claim:f371d5f9c579ea188444
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
Since cluster 4 enriched the expression of genes (VWF, PECAM1) related to EC function, we defined it as a subcluster undergoing endothelial to mesenchymal transition (EndoMT).

summary:
In Homo sapiens, a fibroblast subcluster undergoing endothelial to mesenchymal transition is marked by expression of VWF and PECAM1 in the human heart.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:da4799f9b0dd0ef17959
claim_id: claim:da4799f9b0dd0ef17959
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
Consistent with our mouse data, cluster 6 (subtypes with high expression of extracellular matrix protein including POSTN, THBS4) at heart failure which showed elevated capacity of ECM organization, extracellular structure organization

summary:
In Homo sapiens, fibroblast cluster 6 in the heart during heart failure is marked by high expression of POSTN and THBS4.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:6f052ca2834b7750753c
claim_id: claim:6f052ca2834b7750753c
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
In addition, GO analysis demonstrated that cluster 7 showed elevated capacity of lymphocyte activation and regulation of immune response, and it also with the high expression of genes (S100A8, CD74, CD69).

summary:
In Homo sapiens, fibroblast cluster 7 in the human heart shows high expression of S100A8, CD74, and CD69.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:37b47b4b0af70de2d2df
claim_id: claim:37b47b4b0af70de2d2df
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
in addition, this cluster also showed elevated expression of PI16 (progenitor cell markers) and CD248

summary:
In Homo sapiens, CD34-high fibroblasts (cluster 3) in the human heart show elevated expression of PI16, a progenitor cell marker, and CD248.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:3dc449eb99a19985a73f
claim_id: claim:3dc449eb99a19985a73f
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
Consistent with above data, cluster 1 (subtypes with high expression of extracellular matrix protein including DDR2, THBS4, FN1, POSTN) at heart failure which involved in ECM organization, extracellular structure organization

summary:
In Homo sapiens, CD34 lineage fibroblast cluster 1 in the human heart during heart failure is marked by high expression of DDR2, THBS4, FN1, and POSTN.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:3572b6bfc653e5413b54
claim_id: claim:3572b6bfc653e5413b54
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
In addition, cluster 8 (with the high expression of COL3A1, FN1 and CD68) was associated with inflammatory response by GO analysis.

summary:
In Homo sapiens, CD34 lineage fibroblast cluster 8 in the human heart shows high expression of COL3A1, FN1, and CD68.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:a840bc54dd65b00c7fa7
claim_id: claim:a840bc54dd65b00c7fa7
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
we also found this new subpopulation (cluster 2 with high expression of VEGFD and CD248) in human CD34 lineage fibroblasts, and GO analysis demonstrated that cluster 2 is involved in extracellular matrix formation and vascular development

summary:
In Homo sapiens, CD34 lineage fibroblast cluster 2 in the human heart shows high expression of VEGFD and CD248.


claim_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed:claim:14f3b5eb87180364c44f
claim_id: claim:14f3b5eb87180364c44f
paper_key: hca:0300_10.1186_s13287-023-03256-0_d71fd1c1ed
span_literal:
we observed the proportion of markers associated with fibroblasts (VIM, POSTN, DDR2, THBS4, COL1A1, COL1A2, FN1) were significantly higher in heart failure than the control group in the human data

summary:
In Homo sapiens, fibroblasts in the heart are associated with markers VIM, POSTN, DDR2, THBS4, COL1A1, COL1A2, and FN1, which are increased in heart failure.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:e40886282cc76a5578c8
claim_id: claim:e40886282cc76a5578c8
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
span_literal: GRIK1 and GRM6 were used as OFF and ON markers, respectively.
summary:
In Homo sapiens retina, GRIK1 is a marker of OFF bipolar cells and GRM6 is a marker of ON bipolar cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:7bab5ec0b83c6fd93ba9
claim_id: claim:7bab5ec0b83c6fd93ba9
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
span_literal: Among them, AGBL1 and SORCS3 showed high specificity for the GB and BB cells, respectively
summary:
In Homo sapiens retina, AGBL1 shows high specificity for giant bipolar cells and SORCS3 shows high specificity for blue bipolar cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:99887295c359dabd2a8f
claim_id: claim:99887295c359dabd2a8f
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
span_literal:
two clusters (HAC10, HAC26) were annotated as Starburst AC (SAC) by CHAT and ON-SAC/OFF-SAC by MEGF10 and TENM3, respectively.

summary:
In Homo sapiens retina, CHAT is a marker of Starburst amacrine cells, and MEGF10 and TENM3 distinguish ON-Starburst amacrine cell and OFF-Starburst amacrine cell, respectively.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:49e141deb483a8bb958a
claim_id: claim:49e141deb483a8bb958a
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
summary: In Homo sapiens retina, TBR1 is a marker of OFF midget retinal ganglion cell.
span_literal:
OFF midget RGC (MG_OFF) by TBR1 (HRGC1), ON midget RGC (MG_ON) by TPBG (HRGC2), OFF parasol RGC (PG_OFF) by FABP4 (HRGC6), ON parasol RGC (PG_ON) by CHRNA2 (HRGC7), and an intrinsically photosensitive RGC (ipRGC) by OPN4 (HRGC10).


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:f9ecc1983fbf8c9ddfd6
claim_id: claim:f9ecc1983fbf8c9ddfd6
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
span_literal:
A significant portion of the identified TFs have been implicated in specification of individual retinal cell classes, such as OTX2 and CRX for photoreceptor cells, NR2E3 for rods, RAX2 for cones, NEUROD4 for BCs, ONECUT1 and ONECUT2 for HCs, TFAP2A for ACs, and NFIB and LHX2 for MGs

summary:
In Homo sapiens retina, OTX2 and CRX are transcription factors implicated in specification of photoreceptor cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:ab8b1bdb78b95f6ef14c
claim_id: claim:ab8b1bdb78b95f6ef14c
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
span_literal:
A significant portion of the identified TFs have been implicated in specification of individual retinal cell classes, such as OTX2 and CRX for photoreceptor cells, NR2E3 for rods, RAX2 for cones, NEUROD4 for BCs, ONECUT1 and ONECUT2 for HCs, TFAP2A for ACs, and NFIB and LHX2 for MGs

summary:
In Homo sapiens retina, NR2E3 is a transcription factor implicated in specification of rod photoreceptor cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:dc0e9b092e3077e28dde
claim_id: claim:dc0e9b092e3077e28dde
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
span_literal:
A significant portion of the identified TFs have been implicated in specification of individual retinal cell classes, such as OTX2 and CRX for photoreceptor cells, NR2E3 for rods, RAX2 for cones, NEUROD4 for BCs, ONECUT1 and ONECUT2 for HCs, TFAP2A for ACs, and NFIB and LHX2 for MGs

summary:
In Homo sapiens retina, RAX2 is a transcription factor implicated in specification of cone photoreceptor cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:b50d2b185c903debf2e1
claim_id: claim:b50d2b185c903debf2e1
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
summary:
In Homo sapiens retina, NEUROD4 is a transcription factor implicated in specification of bipolar cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:4965bad37f9d3e2cd83d
claim_id: claim:4965bad37f9d3e2cd83d
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
summary:
In Homo sapiens retina, ONECUT1 and ONECUT2 are transcription factors implicated in specification of horizontal cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:ead6c201d17a86fcf6a7
claim_id: claim:ead6c201d17a86fcf6a7
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
summary:
In Homo sapiens retina, TFAP2A is a transcription factor implicated in specification of amacrine cells.


claim_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad:claim:cf064be3fbd08f198a8a
claim_id: claim:cf064be3fbd08f198a8a
paper_key: hca:0301_10.1101_2023.11.07.566105_6b05614dad
summary:
In Homo sapiens retina, NFIB and LHX2 are transcription factors implicated in specification of Müller glia cells.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:6bc5586704aee6ebd2cd
claim_id: claim:6bc5586704aee6ebd2cd
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Stem cells ( PTPRC -/ PECAM1- / CD34+ / PDGFRA+ / PDGFRB+ ) accounted for 7% of total WAT ( Figure 1 B).

summary:
In Homo sapiens white adipose tissue, stem cells are negative for PTPRC and PECAM1 and positive for CD34, PDGFRA, and PDGFRB.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:7cc4ef9f23c0c4d53527
claim_id: claim:7cc4ef9f23c0c4d53527
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Pre-adipocytes were defined by their increased ATXN1 , ZNF423 , and CD38 expression and decreased expression of stem cell markers ( PDGFRA/PDGFRB/DCN) and comprised three distinct clusters accounting for 37% of total WAT ( Figure 1 B).

summary:
In Homo sapiens white adipose tissue, pre-adipocytes are defined by increased ATXN1, ZNF423, and CD38 expression and decreased expression of PDGFRA, PDGFRB, and DCN.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:39bfa949eee302e54cf4
claim_id: claim:39bfa949eee302e54cf4
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
summary: In Homo sapiens white adipose tissue, endothelial cells are enriched with PECAM1, CDH5, and VWF.
span_literal:
Endothelial cells were enriched with PECAM1 , CDH5 , and VWF and accounted for 11% of total WAT ( Figure 1 B).


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:7412a279fafd1194dac8
claim_id: claim:7412a279fafd1194dac8
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
The immune cluster (3%) was enriched specifically with macrophage transcripts ( FCGR1A/HLA-DRB1/HLA-DPA1/ITGAX/TREM2 ; Figure 1 B).

summary:
In Homo sapiens white adipose tissue, the macrophage cluster is enriched with FCGR1A, HLA-DRB1, HLA-DPA1, ITGAX, and TREM2.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:ff0b35c0e683bf71770f
claim_id: claim:ff0b35c0e683bf71770f
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Adipocytes were initially identified with known marker genes ( DGAT2/PLIN1/LEP/ADIPOQ/PPARG/LIPE/FABP4/SAA1 ) and had downregulation of pre-adipocyte ( ATXN1/CD38) and stem cell markers ( PDGFRA/PDGRFB/DCN) and accounted for 43% of whole WAT and comprised 3 clusters.

summary:
In Homo sapiens white adipose tissue, adipocytes are identified by marker genes DGAT2, PLIN1, LEP, ADIPOQ, PPARG, LIPE, FABP4, and SAA1 and have downregulation of ATXN1, CD38, PDGFRA, PDGFRB, and DCN.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:8f545f0b788ba5ec47bc
claim_id: claim:8f545f0b788ba5ec47bc
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
This cluster also had the highest expressions of mature adipocyte markers LEP , ADIPOQ , PPARG , and SAA1 ( Figure 1 B) and likely represents fully developed adipocytes.

summary:
In Homo sapiens white adipose tissue, adipocyte 2 has the highest expression of mature adipocyte markers LEP, ADIPOQ, PPARG, and SAA1 and likely represents fully developed adipocytes.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:60e49eaea266af39b991
claim_id: claim:60e49eaea266af39b991
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
In addition to upregulation of glucose homeostasis genes ( MLXIPL/PIK3CA/HK2 ), Adipocyte 3 also had upregulation of insulin signaling genes ( IRS1/IRS2/PIK3CA ; Figure 1 B; Table S1 ), indicative of a glycolytic phenotype.

summary:
In Homo sapiens white adipose tissue, adipocyte 3 has upregulation of glucose homeostasis genes MLXIPL, PIK3CA, and HK2 and insulin signaling genes IRS1 and IRS2, indicative of a glycolytic phenotype.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:87be46f700dec0b3c56c
claim_id: claim:87be46f700dec0b3c56c
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Adipocyte 1 had an upregulation of genes related to early stages of adipogenesis ( CEBPA / STAT5A ; Figure 1 B; Table S1 ) and lipid droplet formation ( SYNGR2/PLIN4/CES1 ; Table S1 ) but did not have the highest expression of the quintessential adipocyte lipid droplet marker PLIN1 .

summary:
In Homo sapiens white adipose tissue, adipocyte 1 has upregulation of early adipogenesis genes CEBPA and STAT5A and lipid droplet formation genes SYNGR2, PLIN4, and CES1.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:353f3afc1bce777f95f3
claim_id: claim:353f3afc1bce777f95f3
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal: Stem cells ( PTPRC -/ PECAM1- / CD34+ / PDGFRA+ / PDGFRB+ ) accounted for 28% of the total SVF.
summary:
In Homo sapiens stromal vascular fraction, stem cells are negative for PTPRC and PECAM1 and positive for CD34, PDGFRA, and PDGFRB.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:b4651123a88f4cc4e853
claim_id: claim:b4651123a88f4cc4e853
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Stem cell 2 was subcategorized as hematopoietic-derived stem cells owing to higher expressions of CD34 , CD59 , and THY1 and a lower expression of PDGFRA ( Gao et al., 2017 ) compared to stem cell 1.

summary:
In Homo sapiens stromal vascular fraction, hematopoietic-derived stem cell (stem cell 2) has higher expression of CD34, CD59, and THY1 and lower expression of PDGFRA compared to stem cell 1.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:3befe1911f5e229fb35e
claim_id: claim:3befe1911f5e229fb35e
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Stem cell 3 had upregulation of transcripts related to very early signs of adipogenesis ( WISP2/SFRP2 ; Table S5 ) and a lower expression of CD34 ( Figure 3 B).

summary:
In Homo sapiens stromal vascular fraction, stem cell 3 has upregulation of WISP2 and SFRP2 related to early adipogenesis and lower expression of CD34.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:88da8e340662d84d9241
claim_id: claim:88da8e340662d84d9241
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Committed pre-adipocytes (9%) were identified by ATXN1 , ZNF423 , and CD38 and downregulation of stem cell markers (PDGFRA/PDGFRB/DCN) ( Figure 3 B).

summary:
In Homo sapiens stromal vascular fraction, committed pre-adipocytes are identified by ATXN1, ZNF423, and CD38 and downregulation of PDGFRA, PDGFRB, and DCN.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:0f578e806ddba006153f
claim_id: claim:0f578e806ddba006153f
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Differential expressions of DLK1 , DGAT2 , and CIDEC between the subclusters Pre-Ad 1 and Pre-Ad 2 suggested differing degrees of commitment along the adipogenic lineage.

summary:
In Homo sapiens stromal vascular fraction, differential expression of DLK1, DGAT2, and CIDEC between pre-adipocyte 1 and pre-adipocyte 2 suggests differing degrees of commitment along the adipogenic lineage.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:11f397b9f5626d558b54
claim_id: claim:11f397b9f5626d558b54
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Endothelial cells were identified with expressions of VWF , PECAM1 , and CDH5 and accounted for 16% of total cells ( Figure 3 A).

summary:
In Homo sapiens stromal vascular fraction, endothelial cells are identified by expression of VWF, PECAM1, and CDH5.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:d899e96988f9c1c50386
claim_id: claim:d899e96988f9c1c50386
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
In agreement with previous work ( Vijay et al., 2020 ), we subclassified endothelial cluster 2 as fatty acid (FA) handling endothelial cells due to high expressions of FA handling transcripts ( FAPB4/CD36/RGS5 ; Figure 3 B), frequently associated with the microvasculature of WAT ( Briot et al., 2018 ).

summary:
In Homo sapiens white adipose tissue, fatty acid handling endothelial cells (endothelial cluster 2) have high expression of FABP4, CD36, and RGS5.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:267975d4534aa8b6c525
claim_id: claim:267975d4534aa8b6c525
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Endothelial cluster 3 also showed high expressions of stem cell markers ( PDGFRA/PDGRB ) commonly observed with pericytes ( Smyth et al., 2018 ).

summary:
In Homo sapiens stromal vascular fraction, endothelial cluster 3 (pericytes) shows high expression of PDGFRA and PDGFRB.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:8bc10950b94541d780b4
claim_id: claim:8bc10950b94541d780b4
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Immune cells ( PTPRC+ ) comprised the majority of the remaining cell populations (38%) and were further subclassified as mast cells (Immune 1: KIT/TPSAB1/CMA1/CTSG ), NK/T cells (Immune 2: NKG7/GNLY/CD8A/CD8B/CD3E ), resident macrophages (Immune 4 and 5: CD14/LGMN/HLA-DP1/CD8/ , CD163) and pro-inflammatory macrophages (Immune 6: ITGAX/HLA-DP1/CD86 ; Immune 7: FCGR1A/ITGAX/TREM2 ).

summary:
In Homo sapiens stromal vascular fraction, immune cells are positive for PTPRC, and are subclassified as mast cells marked by KIT, TPSAB1, CMA1, and CTSG.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:8cd98e59fd591f91076c
claim_id: claim:8cd98e59fd591f91076c
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Immune cells ( PTPRC+ ) comprised the majority of the remaining cell populations (38%) and were further subclassified as mast cells (Immune 1: KIT/TPSAB1/CMA1/CTSG ), NK/T cells (Immune 2: NKG7/GNLY/CD8A/CD8B/CD3E ), resident macrophages (Immune 4 and 5: CD14/LGMN/HLA-DP1/CD8/ , CD163) and pro-inflammatory macrophages (Immune 6: ITGAX/HLA-DP1/CD86 ; Immune 7: FCGR1A/ITGAX/TREM2 ).

summary:
In Homo sapiens stromal vascular fraction, natural killer/T cells are marked by NKG7, GNLY, CD8A, CD8B, and CD3E.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:d84e1b8223ab5c7cacd4
claim_id: claim:d84e1b8223ab5c7cacd4
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Immune cells ( PTPRC+ ) comprised the majority of the remaining cell populations (38%) and were further subclassified as mast cells (Immune 1: KIT/TPSAB1/CMA1/CTSG ), NK/T cells (Immune 2: NKG7/GNLY/CD8A/CD8B/CD3E ), resident macrophages (Immune 4 and 5: CD14/LGMN/HLA-DP1/CD8/ , CD163) and pro-inflammatory macrophages (Immune 6: ITGAX/HLA-DP1/CD86 ; Immune 7: FCGR1A/ITGAX/TREM2 ).

summary:
In Homo sapiens stromal vascular fraction, resident macrophages are marked by CD14, LGMN, HLA-DP1, and CD163.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:311987b2653257cd989c
claim_id: claim:311987b2653257cd989c
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
summary:
In Homo sapiens stromal vascular fraction, pro-inflammatory macrophages (Immune 6) are marked by ITGAX, HLA-DP1, and CD86.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:fed081dc4a4773d6d3a3
claim_id: claim:fed081dc4a4773d6d3a3
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
summary:
In Homo sapiens stromal vascular fraction, pro-inflammatory macrophages (Immune 7) are marked by FCGR1A, ITGAX, and TREM2.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:e5a73cd7319851b7c092
claim_id: claim:e5a73cd7319851b7c092
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Immune cell 3 had upregulated expressions of macrophages markers ( LYVE1/CCL8/CCL4L4/CCL2) , in addition to fibroblast markers ( PDGFRA/PDGFRB) suggesting that these cells may be transitioning from hematopoietic-derived stem cells.

summary:
In Homo sapiens stromal vascular fraction, immune cell 3 has upregulated expression of macrophage markers LYVE1, CCL8, CCL4L4, and CCL2 and fibroblast markers PDGFRA and PDGFRB.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:246b7f9c0d8a5e191ade
claim_id: claim:246b7f9c0d8a5e191ade
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Cluster 4 had upregulated expressions of adipocyte-specific markers such as PLIN1 and vasculature markers such as VEGFB .

summary:
In Homo sapiens stromal vascular fraction, cluster 4 has upregulated expression of adipocyte-specific marker PLIN1 and vasculature marker VEGFB.


claim_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0:claim:35bc8d5199bbb2483bf2
claim_id: claim:35bc8d5199bbb2483bf2
paper_key: hca:0302_10.1016_j.isci.2022.104772_3e028c0be0
span_literal:
Due to Pre-Adipocyte 2 having higher expressions of committed pre-adipocyte markers ( DLK1/DGAT2/CIDEC ), we hypothesized that the pre-adipocyte clusters differ by their degree of commitment to the adipogenic lineage.

summary:
In Homo sapiens stromal vascular fraction, pre-adipocyte 2 has higher expression of committed pre-adipocyte markers DLK1, DGAT2, and CIDEC.


claim_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444:claim:600f82f9d8126e1fb625
claim_id: claim:600f82f9d8126e1fb625
paper_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444
span_literal: Human cDC1s are characterized by surface expression of CD141, CADM1, CLEC9A and XCR1
summary:
In Homo sapiens, conventional type 1 dendritic cells are characterized by surface expression of CD141, CADM1, CLEC9A, and XCR1.


claim_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444:claim:c354ab8867b3f6ae728f
claim_id: claim:c354ab8867b3f6ae728f
paper_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444
summary: In Homo sapiens, human embryonic fibroblasts are positive for ACTA2.
span_literal:
t-Distributed stochastic neighbor embedding (t-SNE) visualization highlighted four clusters: HEFs ( ACTA2 + ), cDC1s ( CLEC9A + ), cDC2s ( CD1C + ) and pDCs ( IL3RA + )


claim_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444:claim:4fb3278b920682440045
claim_id: claim:4fb3278b920682440045
paper_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444
span_literal:
DC1-affiliated cells express higher levels of the cDC1-specific genes CADM1 and WDFY4 when compared to their unaffiliated counterparts

summary:
In Homo sapiens, DC1-affiliated cells express higher levels of the conventional type 1 dendritic cell-specific genes CADM1 and WDFY4.


claim_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444:claim:59f380aeb13ab83bb2b9
claim_id: claim:59f380aeb13ab83bb2b9
paper_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444
span_literal: cDC1-specific genes C1orf54, ANPEP, TACSTD2 and SLAMF8
summary:
In Homo sapiens, conventional type 1 dendritic cells specifically express C1orf54, ANPEP, TACSTD2, and SLAMF8.


claim_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444:claim:c2382be333d2212d9a6d
claim_id: claim:c2382be333d2212d9a6d
paper_key: hca:0304_10.1126_sciimmunol.abg5539_d30f748444
span_literal:
Extraction of genes encoding surface molecules and transcriptional regulators from these modules highlighted fibroblast genes enriched in unsuccessful reprogramming ( CD248 and PRRX1 ) and DC genes upregulated in successful reprogrammed cells, including the cDC1 marker CD226

summary:
In Homo sapiens, CD226 is a marker of conventional type 1 dendritic cells, while CD248 and PRRX1 are enriched in fibroblasts.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:2237873c677587106114
claim_id: claim:2237873c677587106114
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal: there was a subpopulation of proximal tubule that had increased expression of VCAM1 (PT_VCAM1).
summary:
In Homo sapiens adult kidney, a subpopulation of proximal tubule cells (PT_VCAM1) is marked by increased expression of VCAM1.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:ef170a589fe9f1e64a0b
claim_id: claim:ef170a589fe9f1e64a0b
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
This subpopulation also expressed HAVCR1 (kidney injury molecule-1), which is a gene upregulated in the proximal tubule after acute injury and a predictor of long-term renal outcomes

summary:
In Homo sapiens adult kidney, the PT_VCAM1 subpopulation of proximal tubule cells expresses HAVCR1 (kidney injury molecule-1).


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:f80e7264c5e92a351025
claim_id: claim:f80e7264c5e92a351025
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
summary: In Homo sapiens kidney, a small subset of proximal tubule cells express vimentin, CD24, and CD133.
span_literal:
a small subset of cells within the proximal tubule and Bowman’s capsule express vimentin, CD24, and CD133


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:6cbbc79df40f27d91574
claim_id: claim:6cbbc79df40f27d91574
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
PCT showed greater chromatin accessibility in SLC5A2 , which encodes sodium glucose cotransporter 2 (SGLT2); whereas PST showed greater accessibility in SLC5A1

summary:
In Homo sapiens kidney, proximal convoluted tubule cells show greater chromatin accessibility in SLC5A2 (encoding sodium glucose cotransporter 2), whereas proximal straight tubule cells show greater accessibility in SLC5A1.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:2ddf214a766f3bcdac06
claim_id: claim:2ddf214a766f3bcdac06
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
PCT showed greater chromatin accessibility in SLC5A2 , which encodes sodium glucose cotransporter 2 (SGLT2); whereas PST showed greater accessibility in SLC5A1

summary:
In Homo sapiens kidney, proximal straight tubule cells show greater chromatin accessibility in SLC5A1, compared to proximal convoluted tubule cells.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:cf0491998e49c2503564
claim_id: claim:cf0491998e49c2503564
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
summary: In Homo sapiens kidney, LRP2 is a lineage-specific gene expressed in the proximal tubule cell.
span_literal:
LRP2 is a lineage-specific gene expressed in the proximal tubule and a coverage plot in this region shows an increase in number and amplitude of ATAC peaks within its promoter and gene body


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:c9e168185ff5f5351bdf
claim_id: claim:c9e168185ff5f5351bdf
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal: HNF4A encodes a key transcription factor that drives proximal tubule differentiation
summary:
In Homo sapiens kidney, HNF4A encodes a key transcription factor that drives proximal tubule cell differentiation.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:4c6e38bb3c1ef5a22b56
claim_id: claim:4c6e38bb3c1ef5a22b56
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal: chromVAR detected an enrichment of HNF4A binding motifs within DAR in the proximal tubule
summary:
In Homo sapiens kidney, HNF4A binding motifs are enriched within differentially accessible chromatin regions in the proximal tubule cell.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:fd17aa95247d350eef39
claim_id: claim:fd17aa95247d350eef39
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
There was increased TFAP2B transcription factor “activity” in the thick ascending limb and distal convoluted tubule

summary:
In Homo sapiens kidney, TFAP2B transcription factor activity is increased in the thick ascending limb cell.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:12ad8b056eed62c90f66
claim_id: claim:12ad8b056eed62c90f66
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
There was increased TFAP2B transcription factor “activity” in the thick ascending limb and distal convoluted tubule

summary:
In Homo sapiens kidney, TFAP2B transcription factor activity is increased in the distal convoluted tubule cell.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:d95938e88ccfe8346103
claim_id: claim:d95938e88ccfe8346103
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
There was a group of cells ( SLC12A1 + UMOD +) that expressed thick ascending limb markers ( CLDN16 , KCNJ10, and PTH1R ): TAL1 and a second group that expressed another set of TAL specific markers such as CLDN10 : TAL2

summary:
In Homo sapiens kidney, thick ascending limb subpopulation 1 (TAL1) cells express SLC12A1, UMOD, CLDN16, KCNJ10, and PTH1R, whereas thick ascending limb subpopulation 2 (TAL2) cells express CLDN10.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:0f44d47335360f8d2241
claim_id: claim:0f44d47335360f8d2241
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
There was a group of cells ( SLC12A1 + UMOD +) that expressed thick ascending limb markers ( CLDN16 , KCNJ10, and PTH1R ): TAL1 and a second group that expressed another set of TAL specific markers such as CLDN10 : TAL2

summary:
In Homo sapiens kidney, thick ascending limb subpopulation 2 (TAL2) cells express CLDN10 as a marker distinguishing them from thick ascending limb subpopulation 1 (TAL1).


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:7332a478daefc26c9560
claim_id: claim:7332a478daefc26c9560
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
HNF1B was the most enriched motif in open chromatin regions in TAL1 whereas ESRRB was enriched in open regions in TAL2

summary:
In Homo sapiens kidney, HNF1B motif is the most enriched in open chromatin regions in thick ascending limb subpopulation 1 (TAL1), whereas ESRRB is enriched in thick ascending limb subpopulation 2 (TAL2).


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:0e3319fc01fb61664c14
claim_id: claim:0e3319fc01fb61664c14
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
HNF1B was the most enriched motif in open chromatin regions in TAL1 whereas ESRRB was enriched in open regions in TAL2

summary:
In Homo sapiens kidney, ESRRB motif is enriched in open chromatin regions in thick ascending limb subpopulation 2 (TAL2), compared to thick ascending limb subpopulation 1 (TAL1).


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:4c7fa9d3d40dd2763c20
claim_id: claim:4c7fa9d3d40dd2763c20
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
PT_VCAM1 also expressed VIM (vimentin), CD24 , and CD133 (Supplementary Fig. 14 ), which is consistent with a previously described population of cells with progenitor-like features in the proximal tubule

summary:
In Homo sapiens kidney, the VCAM1-positive proximal tubule cell subpopulation (PT_VCAM1) expresses VIM (vimentin), CD24, and CD133.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:70a45a3f13a1a1de255e
claim_id: claim:70a45a3f13a1a1de255e
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
We identified VCAM1 and TPM1 as genes that show increased expression in PT_VCAM1 cells and SLC5A12 and SLC4A4 as genes that show decreased expression

summary:
In Homo sapiens kidney, VCAM1 and TPM1 show increased expression in VCAM1-positive proximal tubule cells (PT_VCAM1), while SLC5A12 and SLC4A4 show decreased expression.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:2b14e8e8f5914c36e6c8
claim_id: claim:2b14e8e8f5914c36e6c8
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
the proximal tubule showed robust activity of HNF4A, which was decreased in the PT_VCAM1 cluster and coincided with increased activity of REL and RELA

summary:
In Homo sapiens kidney, the proximal tubule cell shows robust HNF4A activity, which is decreased in the VCAM1-positive proximal tubule cell (PT_VCAM1) cluster, where REL and RELA activity is increased.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:88b9f566394ff3b5479b
claim_id: claim:88b9f566394ff3b5479b
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
We used snRNA-seq and snATAC-seq to identify a subpopulation of proximal tubule (PT_VCAM1) that expressed VCAM1, HAVCR1 (KIM-1), VIM (vimentin), CD133 , and CD24

summary:
In Homo sapiens kidney, the VCAM1-positive proximal tubule cell subpopulation (PT_VCAM1) expresses VCAM1, HAVCR1 (kidney injury molecule-1), VIM (vimentin), CD133, and CD24.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:9b07af4a8c2afc227d61
claim_id: claim:9b07af4a8c2afc227d61
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
We observed two distinct subpopulations of UMOD + cells in the thick ascending limb ( CLDN10 + CLDN16− and CLDN10−CLDN16 +) with enrichment of KCNJ10 and PTH1R in CLDN10-CLDN16 + cells

summary:
In Homo sapiens kidney, two distinct subpopulations of UMOD-positive thick ascending limb cells are defined by CLDN10 and CLDN16 expression, with KCNJ10 and PTH1R enriched in CLDN10-negative CLDN16-positive cells.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:1f22165c6d85c2ab03ee
claim_id: claim:1f22165c6d85c2ab03ee
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
Claudin-10 (CLDN10) expression is enriched in the medullary thick ascending limb, whereas claudin-16 (CLDN16) is expressed predominantly in the cortical thick ascending limb

summary:
In Homo sapiens kidney, CLDN10 expression is enriched in the medullary thick ascending limb cell, whereas CLDN16 is expressed predominantly in the cortical thick ascending limb cell.


claim_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05:claim:cd2638dc88561d4968ba
claim_id: claim:cd2638dc88561d4968ba
paper_key: hca:0306_10.1038_s41467-021-22368-w_5524560e05
span_literal:
Claudin-10 (CLDN10) expression is enriched in the medullary thick ascending limb, whereas claudin-16 (CLDN16) is expressed predominantly in the cortical thick ascending limb

summary:
In Homo sapiens kidney, CLDN16 is expressed predominantly in the cortical thick ascending limb cell.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:a648a0ba4ba9bd9cabf2
claim_id: claim:a648a0ba4ba9bd9cabf2
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal: endothelial (End/Endo), majorly expressing CDH5, PECAM1, CD34
summary:
In Homo sapiens full-thickness skin, endothelial cells are marked by expression of CDH5, PECAM1, and CD34.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:c4a53380fae50cb8cc49
claim_id: claim:c4a53380fae50cb8cc49
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal: epidermis (EpD), majorly expressing KRT10, KRT14, KRT1
summary:
In Homo sapiens full-thickness skin, epidermis cells are marked by expression of KRT10, KRT14, and KRT1.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:19b608e77236f87e1e59
claim_id: claim:19b608e77236f87e1e59
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal: immune (IM), majorly expressing PTPRC (CD45), ITGAM, CD3E
summary:
In Homo sapiens full-thickness skin, immune cells are marked by expression of PTPRC (CD45), ITGAM, and CD3E.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:a78e3a45d0f31f8b0d9e
claim_id: claim:a78e3a45d0f31f8b0d9e
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal: mesenchymal (Mes), majorly expressing PDGFRB, LUM, COL1A1
summary:
In Homo sapiens full-thickness skin, mesenchymal cells are marked by expression of PDGFRB, LUM, and COL1A1.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:f3c403881ab25454dd58
claim_id: claim:f3c403881ab25454dd58
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal: neural crest-like (Schwann/Melanocyte-like, SchM), majorly expressing SOX10, MLANA, S100B
summary:
In Homo sapiens full-thickness skin, neural crest-like cells (Schwann/melanocyte-like) are marked by expression of SOX10, MLANA, and S100B.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:2a784cad457b2e06cf9e
claim_id: claim:2a784cad457b2e06cf9e
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal:
three basal cell types (EpD_Basal1–3) majorly expressing basal epithelium markers KRT5, KRT14, ITGA6, and ITGB1

summary:
In Homo sapiens skin, epidermal basal cells are marked by expression of KRT5, KRT14, ITGA6, and ITGB1.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:61f27a82ab5bc6785d48
claim_id: claim:61f27a82ab5bc6785d48
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal:
four epithelial differentiated cell types (EpD_Spinous, EpD_Granualr/spinous, EpD_Granular, EpD_Corneum) majorly recognized by epithelial differentiation marker KRT10, KRT1, and GRHL1

summary:
In Homo sapiens skin, epithelial differentiated cells (spinous, granular/spinous, granular, corneum) are marked by expression of KRT10, KRT1, and GRHL1.


claim_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da:claim:32cdf6040eef5950cc90
claim_id: claim:32cdf6040eef5950cc90
paper_key: hca:0307_10.1038_s41419-021-03724-6_32b837a8da
span_literal:
End/Endo constituted 15.69% (3802 cells) of the full-thickness skin cells, was identified by its archetypal marker PECAM1

summary:
In Homo sapiens full-thickness skin, endothelial cells are identified by the archetypal marker PECAM1.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:6755906e583fe4bd8c46
claim_id: claim:6755906e583fe4bd8c46
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
summary: In Homo sapiens, SOX2 is a marker of neural progenitors in the developing spinal cord.
span_literal:
Feature plots of markers of neural progenitors ( SOX2 ), neurons ( ELAVL3 ) and neural crest progenitors ( SOX10 ) and neurons ( SIX1 ).


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:18ebdd6ebbf35536cfb5
claim_id: claim:18ebdd6ebbf35536cfb5
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
summary: In Homo sapiens, expression of the SRY gene indicates male sex in embryonic samples.
span_literal:
Expression of the male-specific SRY gene ( Berta et al., 1990 ; Gubbay et al., 1990 ; Sinclair et al., 1990 ) was detected in CS12 and CS17 embryos, indicating these samples were male, whereas the lack of SRY expression in the CS14 and CS19 samples indicated that these were female ( Fig. S1F ).


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:b7ff03c5a0de4040a739
claim_id: claim:b7ff03c5a0de4040a739
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
PAX7 expression was observed in dorsal progenitors of both mouse and human, but in addition PAX7 expression was observed in floor plate (FP) cells of CS12, CS14 and CS17 human embryos.

summary:
In Homo sapiens, PAX7 is expressed in dorsal progenitors and floor plate cells of the developing spinal cord.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:7dd3b0ad3e7d27c47973
claim_id: claim:7dd3b0ad3e7d27c47973
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
Inspection of genes correlating with PAX7 in human FP cells highlighted several, including CDH7 , TXLNB , CDHR3 , PIFO and RRAD , that were expressed in human FP cells but not in mouse FP cells ( Fig. 3 A-C).

summary:
In Homo sapiens, CDH7, TXLNB, CDHR3, PIFO and RRAD are expressed in floor plate cells but not in mouse floor plate cells.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:ace26c559d97dd9684b8
claim_id: claim:ace26c559d97dd9684b8
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal: NKX6-2 expression in human was detected in p1, p2, pMN, p3 and FP progenitors ( Fig. 2 A).
summary:
In Homo sapiens, NKX6-2 is expressed in p1, p2, pMN, p3 and floor plate progenitors of the developing spinal cord.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:4bcaffad8a8627ca60bb
claim_id: claim:4bcaffad8a8627ca60bb
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
Other notable differences between human and mouse included the apparent scarce expression of TBX20 in human visceral MNs.

summary:
In Homo sapiens, TBX20 shows scarce expression in visceral motor neurons of the developing spinal cord.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:3db34674852cc4d6942b
claim_id: claim:3db34674852cc4d6942b
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
Analysis of PHOX2B -expressing neurons in the human dataset revealed that although these cells expressed TBX2 and TBX3 there was little or no expression of TBX20 ( Fig. 3 E, Fig. S3D ).

summary:
In Homo sapiens, PHOX2B-expressing neurons express TBX2 and TBX3 but show little or no expression of TBX20.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:ec66d00fe31243d8d462
claim_id: claim:ec66d00fe31243d8d462
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
We established a classification scheme to subdivide cells into the three cell types characteristic of the embryonic day (E) 11.5 mouse trunk dorsal root ganglia ( Soldatov et al., 2019 ): (1) progenitors, marked by the expression of SOX10 alone or in combination with SOX2 ; (2) sensory neuron precursors, marked by the expression of NEUROG1 , NEUROG2 and NEUROD1 ; and (3) postmitotic sensory neurons expressing ELAVL3 ( Fig. 5 A), as the expression of the broad mouse somatosensory neuron marker advillin (AVIL) was limited to a small subset of cells in the human dataset ( Fig. 5 A).

summary:
In Homo sapiens, peripheral nervous system progenitors are marked by SOX10 alone or in combination with SOX2, sensory neuron precursors are marked by NEUROG1, NEUROG2 and NEUROD1, and postmitotic sensory neurons express ELAVL3, while advillin (AVIL) expression is limited to a small subset of cells.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:f65badcaf4d391009c0b
claim_id: claim:f65badcaf4d391009c0b
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
We established a classification scheme to subdivide cells into the three cell types characteristic of the embryonic day (E) 11.5 mouse trunk dorsal root ganglia ( Soldatov et al., 2019 ): (1) progenitors, marked by the expression of SOX10 alone or in combination with SOX2 ; (2) sensory neuron precursors, marked by the expression of NEUROG1 , NEUROG2 and NEUROD1 ; and (3) postmitotic sensory neurons expressing ELAVL3 ( Fig. 5 A), as the expression of the broad mouse somatosensory neuron marker advillin (AVIL) was limited to a small subset of cells in the human dataset ( Fig. 5 A).

summary:
In Homo sapiens, sensory neuron precursors are marked by the expression of NEUROG1, NEUROG2 and NEUROD1.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:cfc10d0f2f268a7d9ef0
claim_id: claim:cfc10d0f2f268a7d9ef0
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
In addition, we identified a small number of cells ( n =77), present from CS12 onwards, expressing SOX10 , SOX9 , PDGFRA and S100B , characteristic of oligodendrocytes ( Fig. 6 E).

summary:
In Homo sapiens, oligodendrocytes are characterized by expression of SOX10, SOX9, PDGFRA and S100B in the developing spinal cord.


claim_key: hca:0308_10.1242_dev.199711_724ab19d33:claim:2a498b0e0e435aa58b4f
claim_id: claim:2a498b0e0e435aa58b4f
paper_key: hca:0308_10.1242_dev.199711_724ab19d33
span_literal:
Consistent with this, human OLIG2 + /NKX2-2 + cells expressed FABP7 , OLIG1 and OLIG2 , characteristic of gliogenic progenitors, like mouse Olig2 + /Nkx2-2 + cells from older embryos ( Fig. 8 H,I).

summary:
In Homo sapiens, OLIG2+/NKX2-2+ cells express FABP7, OLIG1 and OLIG2, characteristic of gliogenic progenitors.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:b9664bd106458ff7cc04
claim_id: claim:b9664bd106458ff7cc04
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
based on typical lineage markers (assessed by protein and/or mRNA), were annotated as T-cells (CD3), plasma cells (PCs) (CD19 and SDC1 (CD138)), myeloid cells (CD14, CD11c and HLA-DR), mast cells (MC) (KIT) and B cells (MS4A1 (CD20))

summary:
In Homo sapiens small intestine, T cells are marked by CD3, plasma cells by CD19 and SDC1, myeloid cells by CD14, CD11c (ITGAX), and HLA-DR, mast cells by KIT, and B cells by MS4A1.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:5e861c52ebe06669726c
claim_id: claim:5e861c52ebe06669726c
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
We identified 181 genes differentially expressed in the T-cell compartment with IL7R, GZMA, RORA amongst the top genes.

summary:
In Homo sapiens small intestine, the T cell compartment is marked by IL7R, GZMA, and RORA among the top differentially expressed genes.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:784023ee3f3719802f35
claim_id: claim:784023ee3f3719802f35
paper_key: hca:0309_10.1101_721258_f9cb0ad906
summary: In Homo sapiens small intestine, plasma cells are marked by IGLC2, IGLC3, and IGHA1.
span_literal:
For PCs, 104 genes largely consisting of immunoglobulin related genes such as IGLC2, IGLC3, and IGHA1.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:b113bf6a18aec542ac4b
claim_id: claim:b113bf6a18aec542ac4b
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
We found 245 marker genes distinguishing myeloid cells with SELENOP, SLC40A1, HLA-DRA and CD74 among the top genes.

summary:
In Homo sapiens small intestine, myeloid cells are marked by SELENOP, SLC40A1, HLA-DRA, and CD74 among the top differentially expressed genes.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:c3686bb75a60aa95094c
claim_id: claim:c3686bb75a60aa95094c
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal: MC analysis yielded 229 genes with the top ranked genes being HPGD, LAPTM4A, VIM and LMO4.
summary:
In Homo sapiens small intestine, mast cells are marked by HPGD, LAPTM4A, VIM, and LMO4 as top ranked marker genes.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:16c8b56bc77e57f2a57a
claim_id: claim:16c8b56bc77e57f2a57a
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
We could identify in total 98 genes as B cell markers with CR2, RALGPS2 and FCRL2 as top ranked genes

summary:
In Homo sapiens small intestine, B cells are marked by CR2, RALGPS2, and FCRL2 as top ranked marker genes.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:b1d8f91936fb1d95caad
claim_id: claim:b1d8f91936fb1d95caad
paper_key: hca:0309_10.1101_721258_f9cb0ad906
summary: In Homo sapiens small intestine, natural killer cells are identified by expression of GNLY.
span_literal:
Expression of the canonical GNLY [18](https://doi.org/10.1016/j.immuni.2018.09.009) amongst 29 other known and novel genes, identified cluster C8 as natural killer (NK) cells


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:9cb7771fce671f4e5fd4
claim_id: claim:9cb7771fce671f4e5fd4
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
Cells of cluster C9 were less present in CeD and identified as innate lymphoid cells class 3 (ILC3) based on their expression of PCDH9, KIT, ALDOC, AHR and RUNX2 genes as previously reported

summary:
In Homo sapiens small intestine, innate lymphoid cell class 3 is identified by expression of PCDH9, KIT, ALDOC, AHR, and RUNX2.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:b4d886e47a1d4139214d
claim_id: claim:b4d886e47a1d4139214d
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
We classify cluster C5 cells as ‘NK-T’ as they express classical NK as well as T cell genes such as TRDC, GZMA, FCER1G, CDH17, CD69, TYROBP and ID2

summary:
In Homo sapiens small intestine, NK-T cells express TRDC, GZMA, FCER1G, CDH17, CD69, TYROBP, and ID2.


claim_key: hca:0309_10.1101_721258_f9cb0ad906:claim:4b26c0405613d5cddaf5
claim_id: claim:4b26c0405613d5cddaf5
paper_key: hca:0309_10.1101_721258_f9cb0ad906
span_literal:
C1 cells differentially express KLRC2 and KLRD1 both NK markers known to be involved in the cytotoxic activity of CD8 IELs in CeD

summary:
In Homo sapiens small intestine, CD8 intraepithelial lymphocytes in celiac disease differentially express KLRC2 and KLRD1, both natural killer cell markers.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:31ef46d11fcabe3f1458
claim_id: claim:31ef46d11fcabe3f1458
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
The top differentially expressed genes in cluster 19 included known markers from principal ( FXYD4 ) and intercalated (ICA [ SLC26A7 ] and ICB [ SLC4A9 ]) collecting duct cells ( Figure 5A ).

summary:
In Homo sapiens, FXYD4 is a marker of principal cells of the collecting duct, SLC26A7 is a marker of intercalated cell type A, and SLC4A9 is a marker of intercalated cell type B.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:88b3135e43743d8e2eae
claim_id: claim:88b3135e43743d8e2eae
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
The cell type markers of cluster 30 included CTGF , CRB2 , VCAM1 , SLC4A11 , and CLDN1 ( Supplemental Table 1 ).

summary:
In Homo sapiens, the cell type markers of cluster 30 (containing parietal epithelial cells and loop of Henle cells) included CTGF, CRB2, VCAM1, SLC4A11, and CLDN1.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:d408474f7fc47900c990
claim_id: claim:d408474f7fc47900c990
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
The expression of WT1 , CLDN1 , and CRB2 in subcluster 0 suggests that this subcluster was enriched for PEC, while the expression of TACSTD2 and SPP1 in subcluster 1 indicates enrichment for LOH-derived cells.

summary:
In Homo sapiens, WT1, CLDN1, and CRB2 are markers of parietal epithelial cells, while TACSTD2 and SPP1 are markers of loop of Henle-derived cells.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:ec9278015d0ffcd7c53a
claim_id: claim:ec9278015d0ffcd7c53a
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
summary: In Homo sapiens, NPHS1, NPHS2, and PODXL are podocyte-specific markers.
span_literal:
Cluster 2 is composed of 170 cells identified as podocytes based on expression of known, podocyte-specific markers NPHS1 , NPHS2 , and PODXL .


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:fc3c65440a40099e6244
claim_id: claim:fc3c65440a40099e6244
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal: CRB2 was significantly overexpressed in podocytes compared with all other cell types.
summary:
In Homo sapiens, CRB2 is significantly overexpressed in podocytes compared with all other cell types.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:15c544fc895896c7c000
claim_id: claim:15c544fc895896c7c000
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
summary: In Homo sapiens, ACTA2 and TAGLN are markers of vascular smooth muscle cells and mesangial cells.
span_literal:
Cluster 9 contained cells with known markers of smooth muscle cells, ACTA2 , and TAGLN , consistent with vascular smooth muscle cells and mesangial cells (VSMC/MC).


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:62a4af3571cb198a6eaf
claim_id: claim:62a4af3571cb198a6eaf
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
Cluster 1 — the smallest cluster, comprising only 58 cells — was identified as a fibroblast cluster based on its top markers, including decorin ( DCN ), collagen type 1 α 2 ( COL1A2 ), and lumican ( LMN ).

summary:
In Homo sapiens, decorin (DCN), collagen type 1 alpha 2 (COL1A2), and lumican (LMN) are markers of fibroblasts in the kidney.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:15fd03d88f2fdc61ab24
claim_id: claim:15fd03d88f2fdc61ab24
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
Based on the known endothelial marker CD34 , three endothelial clusters were identified (clusters 6, 7, and 8); specific markers for these 3 clusters include SERPINE2 (cluster 6), PLVAP (cluster 7), and EHD3 (cluster 8) ( Figure 3B ).

summary:
In Homo sapiens, CD34 is a known endothelial cell marker, and SERPINE2, PLVAP, and EHD3 are specific markers for three distinct endothelial cell clusters in the kidney.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:523fe470fe5ff7b0ebd9
claim_id: claim:523fe470fe5ff7b0ebd9
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
Based on the known endothelial marker CD34 , three endothelial clusters were identified (clusters 6, 7, and 8); specific markers for these 3 clusters include SERPINE2 (cluster 6), PLVAP (cluster 7), and EHD3 (cluster 8) ( Figure 3B ).

summary:
In Homo sapiens, SERPINE2 is a specific marker for arteriolar endothelial cells (cluster 6) in the kidney.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:44321c99445d6c4b5170
claim_id: claim:44321c99445d6c4b5170
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
Based on the known endothelial marker CD34 , three endothelial clusters were identified (clusters 6, 7, and 8); specific markers for these 3 clusters include SERPINE2 (cluster 6), PLVAP (cluster 7), and EHD3 (cluster 8) ( Figure 3B ).

summary:
In Homo sapiens, PLVAP is a specific marker for peritubular capillary endothelial cells (cluster 7) in the kidney.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:00e34a7c2de822c38f28
claim_id: claim:00e34a7c2de822c38f28
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
summary:
In Homo sapiens, EHD3 is a specific marker for glomerular endothelial cells (cluster 8) in the kidney.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:17078421afd03b0c5bea
claim_id: claim:17078421afd03b0c5bea
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
As predicted from the scRNAseq analysis, the ISH signal for SOST was found to be specific to glomerular endothelial cells (GECs) (cluster 6); PLVAP probes hybridized to peritubular capillary endothelial cells (cluster 7) and SERPINE2 were specifically expressed in arteriolar endothelial cells (cluster 8).

summary:
In Homo sapiens, SOST is specifically expressed in glomerular endothelial cells, PLVAP in peritubular capillary endothelial cells, and SERPINE2 in arteriolar endothelial cells, as validated by in situ hybridization.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:a08e3d909dbe437adbd7
claim_id: claim:a08e3d909dbe437adbd7
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
As predicted from the scRNAseq analysis, the ISH signal for SOST was found to be specific to glomerular endothelial cells (GECs) (cluster 6); PLVAP probes hybridized to peritubular capillary endothelial cells (cluster 7) and SERPINE2 were specifically expressed in arteriolar endothelial cells (cluster 8).

summary:
In Homo sapiens, PLVAP is specifically expressed in peritubular capillary endothelial cells, as validated by in situ hybridization.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:cab5a35415483f21a7e9
claim_id: claim:cab5a35415483f21a7e9
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
As predicted from the scRNAseq analysis, the ISH signal for SOST was found to be specific to glomerular endothelial cells (GECs) (cluster 6); PLVAP probes hybridized to peritubular capillary endothelial cells (cluster 7) and SERPINE2 were specifically expressed in arteriolar endothelial cells (cluster 8).

summary:
In Homo sapiens, SERPINE2 is specifically expressed in arteriolar endothelial cells, as validated by in situ hybridization.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:e11566d76fd502cac857
claim_id: claim:e11566d76fd502cac857
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
Cluster 28, which we annotated to contain CNT-PC (cortical CNT IC) expressed known markers of both PCs ( FXYD4 , STC1 ) and CNT cells ( SLC8A1 ) ( Supplemental Figure 1C ), consistent with transitional states between CNT to cortical collecting duct cells.

summary:
In Homo sapiens, FXYD4 and STC1 are known markers of principal cells, and SLC8A1 is a known marker of connecting tubule cells.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:99849e1cf8ea5bf7b843
claim_id: claim:99849e1cf8ea5bf7b843
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
The specific antibody staining of ITGA8 and SYNPO2 in the HPA authenticated the presence of MCs in this cluster ( Supplemental Figure 2 ).

summary:
In Homo sapiens, ITGA8 and SYNPO2 are markers of mesangial cells, as validated by antibody staining in the Human Protein Atlas.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:5a501a636adac41c9d85
claim_id: claim:5a501a636adac41c9d85
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
In scRNAseq A2M expression was found in the 3 endothelial cell subtypes and VSMC/MCs in adult human kidney ( Figure 10C ).

summary:
In Homo sapiens, alpha-2-macroglobulin (A2M) is expressed in the three endothelial cell subtypes and vascular smooth muscle cells/mesangial cells in the adult kidney.


claim_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c:claim:83dc1af02eb0653e699b
claim_id: claim:83dc1af02eb0653e699b
paper_key: hca:0310_10.1172_jci.insight.133267_ab6c49313c
span_literal:
In scRNAseq A2M expression was found in the 3 endothelial cell subtypes and VSMC/MCs in adult human kidney ( Figure 10C ).

summary:
In Homo sapiens, alpha-2-macroglobulin (A2M) is expressed in vascular smooth muscle cells/mesangial cells in the adult kidney.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:3e28afef317a6491e1eb
claim_id: claim:3e28afef317a6491e1eb
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
Basal SC communities BAS-I – BAS-IV represented ~4%, ~9%, ~7% and ~3% of the entire population pool, respectively, and were enriched for known basal keratinocyte marker genes including KRT14 , KRT5 , and CDH3

summary:
In Homo sapiens, basal stem cell communities are enriched for the known basal keratinocyte marker genes KRT14, KRT5, and CDH3.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:d9c28d93657a1475f238
claim_id: claim:d9c28d93657a1475f238
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
The spinous community SPN, representing ~54% of the entire population pool, showed heightened expression of KRT1 , KRT10 , DSG1 , and CDH1 that continued to be expressed in granular keratinocytes

summary:
In Homo sapiens, the spinous keratinocyte community shows heightened expression of KRT1, KRT10, DSG1, and CDH1.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:53b4209e4738e58565ff
claim_id: claim:53b4209e4738e58565ff
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
granular keratinocytes (GRN, ~16% of total cells) expressed the differentiation gene markers DSC1 , KRT2 , IVL , and TGM3

summary:
In Homo sapiens, differentiated granular keratinocytes express the differentiation gene markers DSC1, KRT2, IVL, and TGM3.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:00e25fe026fe1aca4b35
claim_id: claim:00e25fe026fe1aca4b35
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
Basal cluster BAS-III is defined by expression of ASS1 , COL17A1 , and POSTN , where ASS1 and COL17A1 immunofluorescence staining of neonatal human epidermis shows enrichment between rete ridges, suggesting a specific zone of basal SCs surrounding the papillary dermis

summary:
In Homo sapiens, the basal stem cell cluster BAS-III is defined by expression of ASS1, COL17A1, and POSTN in the epidermis.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:61928ea92580b3fa78ce
claim_id: claim:61928ea92580b3fa78ce
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal: BAS-IV basal cluster is defined by expression of GJB2 , KRT6A , and KRT16
summary:
In Homo sapiens, the basal stem cell cluster BAS-IV is defined by expression of GJB2, KRT6A, and KRT16.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:0f0ee2bbd71fcdd9bb16
claim_id: claim:0f0ee2bbd71fcdd9bb16
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
BAS-I is defined by expression of PTTG1 and CDC20 , whereas BAS-II is defined by RRM2 , HELLS, UHRF1 , and PCLAF expression

summary:
In Homo sapiens, basal stem cell cluster BAS-I is defined by expression of PTTG1 and CDC20, whereas basal stem cell cluster BAS-II is defined by RRM2, HELLS, UHRF1, and PCLAF expression.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:38d4127087e34fd64c7d
claim_id: claim:38d4127087e34fd64c7d
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
BAS-I is defined by expression of PTTG1 and CDC20 , whereas BAS-II is defined by RRM2 , HELLS, UHRF1 , and PCLAF expression

summary:
In Homo sapiens, basal stem cell cluster BAS-II is defined by expression of RRM2, HELLS, UHRF1, and PCLAF.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:9d423fd0394e6eced9e6
claim_id: claim:9d423fd0394e6eced9e6
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal:
We are also able to identify specific granular keratinocyte genes such as ZNF750 , SPINK5 , and CALML5 , with the latter two showing robust protein enrichment in the granular layer of human neonatal epidermis

summary:
In Homo sapiens, granular keratinocytes are marked by expression of ZNF750, SPINK5, and CALML5 in the epidermis.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:852197c3c869ec7fad32
claim_id: claim:852197c3c869ec7fad32
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal: kBAS-I can be spatially defined by expression of PTTG1
summary:
In Homo sapiens, the basal stem cell subpopulation kBAS-I can be spatially defined by expression of PTTG1.


claim_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b:claim:6568e87ce0cd4e9d8713
claim_id: claim:6568e87ce0cd4e9d8713
paper_key: hca:0311_10.1038_s41467-020-18075-7_c64a47b29b
span_literal: kBAS-II can be spatially defined by expression of RRM2
summary:
In Homo sapiens, the basal stem cell subpopulation kBAS-II can be spatially defined by expression of RRM2.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:49c0565efde46e433a5f
claim_id: claim:49c0565efde46e433a5f
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
summary: In Homo sapiens pituitary, FSHB, LHB, and GNRHR are markers of gonadotropes.
span_literal:
Key cell type markers included FSHB, LHB , and GNRHR for gonadotropes; GH1 for somatotropes; POMC for corticotropes; DIO2 for thyrotropes ( Cheung et al., 2018 ; Zhang et al., 2020 ); PRL for lactotropes; and SOX9 ( Rizzoti et al., 2013 ), LGR4 ( Russell et al., 2021 ), and RBPMS ( Cheung et al., 2018 ) for PSCs.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:e3a96dcdd37a3b4cfe2c
claim_id: claim:e3a96dcdd37a3b4cfe2c
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
A list of established markers used for the assignment of each cell type as well as markers identified in our datasets ( IQCJ-SCHIP1, NTNG1, EBF1, BNC2, ADGRA3 for PSCs) are listed in Table S2 .

summary:
In Homo sapiens pituitary, IQCJ-SCHIP1, NTNG1, EBF1, BNC2, and ADGRA3 are markers of pituitary stem cells.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:c44bab071e3c9ac990f2
claim_id: claim:c44bab071e3c9ac990f2
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
Cluster 6 corresponded to lineage-committed progenitor stem cells distinguished by GATA3 expression ( Figure 3B , see discussion ).

summary:
In Homo sapiens pituitary, lineage-committed progenitor stem cells are distinguished by GATA3 expression.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:16585ac0860bc9c930d5
claim_id: claim:16585ac0860bc9c930d5
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
The remaining large group of seven clusters expressed SOX2, SOX9 , and the Hippo pathway effectors WWTR1 (also known as TAZ ) and YAP1 ( Lodge et al. [2019] and reviewed in Cox et al. [2017] ; Figures 3B and S3A ), which are indicative of uncommitted PSCs.

summary:
In Homo sapiens pituitary, SOX2, SOX9, WWTR1, and YAP1 are expressed in uncommitted pituitary stem cells.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:c17cf20c6c93786488aa
claim_id: claim:c17cf20c6c93786488aa
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
summary: In Homo sapiens pituitary, GATA3 is expressed in gonadotropes.
span_literal:
GATA3 was expressed in gonadotropes and thyrotropes in addition to the committing stem cell lineage.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:376970c7e08f9c88ca41
claim_id: claim:376970c7e08f9c88ca41
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
summary: In Homo sapiens pituitary, SOX2 is expressed in stem cells and committing stem cells.
span_literal:
SOX2 is expressed in stem cells and committing stem cells, which both showed the highest promoter accessibility.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:64d94a0b98854bb1b931
claim_id: claim:64d94a0b98854bb1b931
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
However, NR5A1 has been classified as a gonadotrope-specific marker in tumors ( Asa et al., 1996 ; Llyod et al., 2017 ; Trouillas et al., 2020 ), and in our work, NR5A1 is restricted to gonadotropes both at the RNA and chromatin accessibility levels.

summary:
In Homo sapiens pituitary, NR5A1 is a gonadotrope-specific marker at both the RNA and chromatin accessibility levels.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:0556cc7f17668a4cbb87
claim_id: claim:0556cc7f17668a4cbb87
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
Furthermore, our data reveal that NESTIN is not expressed robustly in the human pituitary and hence is not a suitable PSC marker.

summary:
In Homo sapiens pituitary, NESTIN is not robustly expressed and is not a suitable pituitary stem cell marker.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:545cf00432de38d11a2f
claim_id: claim:545cf00432de38d11a2f
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
The GATA3 -expressing cluster presumably comprises cells that are committing to the gonadotrope or thyrotrope lineages ( Charles et al., 2006 ), although low NR5A1 expression precludes ultimate cell type lineage assignment ( Figure S3 ).

summary:
In Homo sapiens pituitary, the GATA3-expressing cluster of committing pituitary stem cells shows low NR5A1 expression and is presumed to commit to the gonadotrope or thyrotrope lineages.


claim_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7:claim:4056508072ada72ebaa4
claim_id: claim:4056508072ada72ebaa4
paper_key: hca:0313_10.1016_j.celrep.2022.110467_a2771a8ae7
span_literal:
POMC -expressing cells are likely precursors of the corticotrope/melanotrope lineages ( Budry et al., 2011 ), whereas POU1F1 -expressing cells represent PSCs with the potential to commit to the somatotrope, lactotrope, and thyrotrope lineages ( Li et al., 1990 ).

summary:
In Homo sapiens pituitary, POMC-expressing pituitary stem cells are likely precursors of the corticotrope/melanotrope lineages, whereas POU1F1-expressing pituitary stem cells have the potential to commit to the somatotrope, lactotrope, and thyrotrope lineages.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:83380b355fda62d0de92
claim_id: claim:83380b355fda62d0de92
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
The fraction of cells expressing known markers of organismal aging, such as CDKN2A (p16 INK4A ), were associated with age

summary:
In Homo sapiens, CDKN2A (also known as p16 INK4A) is a known marker of organismal aging, with the fraction of pancreatic cells expressing it increasing with age.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:72dcd6e27dabb49ba5db
claim_id: claim:72dcd6e27dabb49ba5db
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
A subset of α-cells and β-cells simultaneously expressed both Insulin ( INS ) and Glucagon ( GCG ) mRNA—a result that is consistent with prior studies

summary:
In Homo sapiens, a subset of alpha cells simultaneously expressed both insulin (INS) and glucagon (GCG) mRNA in the pancreas.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:4892188b1be3b7cd5be3
claim_id: claim:4892188b1be3b7cd5be3
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
A subset of α-cells and β-cells simultaneously expressed both Insulin ( INS ) and Glucagon ( GCG ) mRNA—a result that is consistent with prior studies

summary:
In Homo sapiens, a subset of beta cells simultaneously expressed both insulin (INS) and glucagon (GCG) mRNA in the pancreas.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:58b15a43210f13374a2b
claim_id: claim:58b15a43210f13374a2b
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
summary: In Homo sapiens, INS is the cell-typical marker for beta cells in the pancreas.
span_literal:
Expression of cell-typical ( INS for β-cells, GCG for α-cells) and non-typical hormone in cells, ranked by transcriptional noise.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:9622823fd450f71cc56b
claim_id: claim:9622823fd450f71cc56b
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
stress response genes such as FOSB, HSPA1A , and JUND were most highly associated with increasing transcriptional noise

summary:
In Homo sapiens, stress response genes such as FOSB, HSPA1A, and JUND are most highly associated with increasing transcriptional noise in pancreatic endocrine cells.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:85af17ce6587475e3e0f
claim_id: claim:85af17ce6587475e3e0f
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
Pancreatic islet cells are sensitive to reactive oxygen species due to low expression of antioxidant enzymes such as SOD1

summary:
In Homo sapiens, pancreatic islet cells have low expression of the antioxidant enzyme SOD1, making them sensitive to reactive oxygen species.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:0a79c2a236f4a1ea73ee
claim_id: claim:0a79c2a236f4a1ea73ee
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
The genes most highly associated with high S1 load were involved in transcription ( TCEB2 ), protein synthesis ( RPL36 ), and modulation of ROS ( ROMO1 )

summary:
In Homo sapiens, TCEB2, RPL36, and ROMO1 are the genes most highly associated with high mutational signature S1 load in endocrine pancreas cells.


claim_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227:claim:f8fe7f573e614b427416
claim_id: claim:f8fe7f573e614b427416
paper_key: hca:0314_10.1016_j.cell.2017.09.004_62170aa227
span_literal:
PON2 (a membrane protein with a putative antioxidant activity) and EGR1 displayed the highest upregulation associated with mutational load of the age-dependent S2

summary:
In Homo sapiens, PON2 and EGR1 displayed the highest upregulation associated with mutational load of the age-dependent signature S2 in endocrine pancreas cells.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:718f97846fd9de86432b
claim_id: claim:718f97846fd9de86432b
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
six T-cell clusters, mapping to effector and naïve CD8 T cells ( CD8A , GZMH, GZMM , and NKG7 ; LT1–2)

summary:
In Homo sapiens gastric cancer, effector and naïve CD8 T cells are marked by positive expression of CD8A, GZMH, GZMM, and NKG7.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:ba0c4b2997005fb96642
claim_id: claim:ba0c4b2997005fb96642
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal: naïve and helper CD4 T cells ( CCR7 and STAT4; LT3–4)
summary:
In Homo sapiens gastric cancer, naïve and helper CD4 T cells are marked by positive expression of CCR7 and STAT4.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:c275bf6c51c6ecfc678d
claim_id: claim:c275bf6c51c6ecfc678d
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal: regulatory T cells (Treg; IL2RA and STAT3 ; LT5)
summary:
In Homo sapiens gastric cancer, regulatory T cells are marked by positive expression of IL2RA and STAT3.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:c3cdf50f2041fb324f0d
claim_id: claim:c3cdf50f2041fb324f0d
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
summary: In Homo sapiens gastric cancer, plasma cells are marked by positive expression of TNFRSF17.
span_literal:
five mature B cells/plasma cell clusters ( TNFRSF17 positive; PL1–5; Supplementary Fig. S1; Supplementary Table S2)


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:a6a8376de3429abbf973
claim_id: claim:a6a8376de3429abbf973
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal: mucous pit cells ( MUC5AC and TFF1
summary:
In Homo sapiens gastric cancer, mucous pit cells are marked by positive expression of MUC5AC and TFF1.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:f432357e9ef08f6af20e
claim_id: claim:f432357e9ef08f6af20e
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal: REG4 and TFF3
summary:
In Homo sapiens gastric cancer, intestinal-type epithelial cells are marked by positive expression of REG4 and TFF3.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:890b85175b627dc86ca5
claim_id: claim:890b85175b627dc86ca5
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal: pericytes (STF2; defined by RGS5 and NOTCH3
summary:
In Homo sapiens gastric cancer, the stromal metacluster is marked by positive expression of FN1; pericytes are defined by RGS5 and NOTCH3; fibroblasts are defined by LUM and DCN; and endothelial cells are marked by PLVAP.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:cb2b2030e31c315785a9
claim_id: claim:cb2b2030e31c315785a9
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
The latter could be further partitioned into ACKR1 -positive venular endothelial cells (STE1) or nonvenular endothelial cells (STE2; ref. 20 ; Supplementary Fig. S1).

summary:
In Homo sapiens gastric cancer, venular endothelial cells are marked by positive expression of ACKR1.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:a531ab81049f7d486c87
claim_id: claim:a531ab81049f7d486c87
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
summary: In Homo sapiens gastric cancer, plasmablasts are marked by high XBP1 and low SDC1.
span_literal:
These included plasmablasts (high XBP1 and low SDC1 ), short-lived plasma cells (high SDC1 ), and long-lived plasma cells (high SDC1 , STAT3 , and IKZF3 ; refs. 22–25 ).


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:1634135cc94a1c48d80b
claim_id: claim:1634135cc94a1c48d80b
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
single-cell trajectory analysis of macrophages revealed two distinct cell states: proinflammatory “M1-like” (high CD163 and S100A12 ) and “M2-like” tumor-associated macrophages (high CD163 and FOLR2 ; refs. 27 and 28 ; Supplementary Fig. S2I).

summary:
In Homo sapiens gastric cancer, M1-like proinflammatory macrophages are marked by high CD163 and S100A12.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:a8f76a9825d3d9083689
claim_id: claim:a8f76a9825d3d9083689
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
single-cell trajectory analysis of macrophages revealed two distinct cell states: proinflammatory “M1-like” (high CD163 and S100A12 ) and “M2-like” tumor-associated macrophages (high CD163 and FOLR2 ; refs. 27 and 28 ; Supplementary Fig. S2I).

summary:
In Homo sapiens gastric cancer, M2-like tumor-associated macrophages are marked by high CD163 and FOLR2.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:364af89d822af54a58dc
claim_id: claim:364af89d822af54a58dc
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
characterization of a novel and rare cell type (STF4) within the stromal metacluster (0.4% of all cells; n = 821), expressing markers associated with both endothelial ( PLVAP ) and fibroblast ( RGS5 ) lineages

summary:
In Homo sapiens gastric cancer, the rare stromal cell type STF4 expresses markers of both endothelial (PLVAP) and fibroblast (RGS5) lineages.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:0ee66a56ff8cfe34116a
claim_id: claim:0ee66a56ff8cfe34116a
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
two fibroblast sublineages comprising LUM -associated fibroblasts (STF1 and STF3) exhibited upregulation of CAF genes such as FAP , COL8A1 , THBS2 , and CTHRC1 , whereas a third sublineage comprising proangiogenic pericytes (STF2) displayed upregulation of another set of CAF marker genes such as CSPG4 , PDGFA, ASPN , and S100A4

summary:
In Homo sapiens gastric cancer, LUM-associated cancer-associated fibroblasts (STF1 and STF3) exhibit upregulation of FAP, COL8A1, THBS2, and CTHRC1.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:ef42faa7405ffb278b08
claim_id: claim:ef42faa7405ffb278b08
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
two fibroblast sublineages comprising LUM -associated fibroblasts (STF1 and STF3) exhibited upregulation of CAF genes such as FAP , COL8A1 , THBS2 , and CTHRC1 , whereas a third sublineage comprising proangiogenic pericytes (STF2) displayed upregulation of another set of CAF marker genes such as CSPG4 , PDGFA, ASPN , and S100A4

summary:
In Homo sapiens gastric cancer, proangiogenic pericytes (STF2) exhibit upregulation of cancer-associated fibroblast marker genes CSPG4, PDGFA, ASPN, and S100A4.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:4cccd456ecea928b0fd1
claim_id: claim:4cccd456ecea928b0fd1
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
summary: In Homo sapiens gastric cancer, plasma cells are marked by positive expression of IRF4.
span_literal:
We confirmed an increased level of plasma cells in diffuse versus intestinal tumors using IRF4 (a plasma cell marker) IHC on a subset of tumors ( n = 17, P = 0.036; Fig. 3B ; Supplementary Fig. S5B).


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:24e52eb5a6ef76b99858
claim_id: claim:24e52eb5a6ef76b99858
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
Although STF1 and STF3 clusters exhibited upregulation of FAP , ACTA2 , and TAGLN , the STF2 cluster exhibited upregulation of only CSPG4

summary:
In Homo sapiens gastric cancer, cancer-associated fibroblast clusters STF1 and STF3 exhibit upregulation of FAP, ACTA2, and TAGLN, whereas the STF2 pericyte cluster exhibits upregulation of CSPG4.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:a6f873790a066ffa8e45
claim_id: claim:a6f873790a066ffa8e45
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
Although STF1 and STF3 clusters exhibited upregulation of FAP , ACTA2 , and TAGLN , the STF2 cluster exhibited upregulation of only CSPG4

summary:
In Homo sapiens gastric cancer, the STF2 pericyte cancer-associated fibroblast cluster exhibits upregulation of CSPG4.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:9b2f300051145e0beb30
claim_id: claim:9b2f300051145e0beb30
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal:
INHBA exhibited significant upregulation in tumor-associated STF2 and STF3 clusters compared with normal

summary:
In Homo sapiens gastric cancer, tumor-associated fibroblast clusters STF2 and STF3 exhibit significant upregulation of INHBA compared with normal.


claim_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a:claim:779ac9f7c5c7ad31ec3f
claim_id: claim:779ac9f7c5c7ad31ec3f
paper_key: hca:0315_10.1158_2159-8290.cd-21-0683_4c7216e47a
span_literal: CDH1
summary:
In Homo sapiens gastric cancer, the epithelial metacluster is marked by positive expression of CDH1.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:9489674b923764b3a1ea
claim_id: claim:9489674b923764b3a1ea
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
Pancreatic islets provide the endocrine function of the pancreas and are comprised of at least five hormone-producing cell types: α cells (secreting glucagon, GCG ), β cells (insulin, INS ), γ/PP cells (pancreatic polypeptide, PPY ), δ cells (somatostatin, SST ), and ε cells (ghrelin, GHRL ).

summary:
In Homo sapiens pancreatic islets, alpha cells are marked by GCG (glucagon), beta cells by INS (insulin), gamma/PP cells by PPY (pancreatic polypeptide), delta cells by SST (somatostatin), and epsilon cells by GHRL (ghrelin).


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:a6f5d709c400585f2910
claim_id: claim:a6f5d709c400585f2910
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
mainly pancreatic ductal cells (PDCs) marked by several keratin genes (KRTs), and pancreatic stellate cells (PSCs) marked by collagen genes

summary:
In Homo sapiens pancreatic islets, pancreatic ductal cells are marked by keratin genes (KRTs) and pancreatic stellate cells are marked by collagen genes.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:61d9237183f06d3ff31d
claim_id: claim:61d9237183f06d3ff31d
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
summary: In Homo sapiens, acinar cells are marked by REG1A and PRSS1.
span_literal:
We observed very few acinar cells marked by REG1A and PRSS1 genes, which were identified as PCA outliers but failed to form a distinct cluster in t-SNE due to the scarcity (n = 108, Figures 2A - 2D ).


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:fbd17b25d3e2b47c4833
claim_id: claim:fbd17b25d3e2b47c4833
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
summary: In Homo sapiens, pancreatic ductal cells express keratins, CFTR, and TSPAN8.
span_literal:
As expected, PSCs express collagen genes; ductal cells express keratins, CFTR , and TSPAN8 ; and exocrine acinar cells express REG1A , REG1B , REG3A , and a number of digestive enzymes ( Figures 2E and 2G ).


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:83edb49ec37c45fccfe0
claim_id: claim:83edb49ec37c45fccfe0
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
Interestingly, we also observed duct-exclusive expression of inflammation genes such as CCL2 , CXCL2 , MMP7 , and DEFB1 ( Figures 2E and 2G ).

summary:
In Homo sapiens, pancreatic ductal cells exclusively express inflammation genes CCL2, CXCL2, MMP7, and DEFB1.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:441f164c1cbec6601c3c
claim_id: claim:441f164c1cbec6601c3c
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
we found that the activated PSCs expressed more collagen, TIMPs, and stem cell or cancer signature genes but lost the expression of lipid-processing or adipogenesis genes such as FABP4 and ADIRF ( Figures 2H and 2I ).

summary:
In Homo sapiens, activated pancreatic stellate cells lost the expression of FABP4 and ADIRF compared to quiescent pancreatic stellate cells.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:6dcf0695da1112b62e92
claim_id: claim:6dcf0695da1112b62e92
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
Our top list includes many classically known cell identity master transcription factors, such as PDX1 , MAFA , and NKX6-1 in β cells, ARX and IRX2 in α cells, and HHEX in δ cells ( Figure 3C ).

summary:
In Homo sapiens, beta cells specifically express the master transcription factors PDX1, MAFA, and NKX6-1.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:88b7130d00f068d39ec5
claim_id: claim:88b7130d00f068d39ec5
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
For example, PAX6 , NEUROD1 , and INSM1 are expressed in all four, and MAFB is expressed in three endocrine cell types.

summary:
In Homo sapiens, PAX6, NEUROD1, and INSM1 are expressed in all four endocrine cell types, and MAFB is expressed in three endocrine cell types.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:ef7a6bf6a603deedbe15
claim_id: claim:ef7a6bf6a603deedbe15
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
Some signaling-dependent TFs are also cell-type-specific, such as ESR1 (β cell) and EGR2 , EGR3 , and STAT4 (PP cell) ( Figure 3C ).

summary:
In Homo sapiens, ESR1 is specifically expressed in beta cells, while EGR2, EGR3, and STAT4 are specifically expressed in PP cells.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:8e10886f481d24c31109
claim_id: claim:8e10886f481d24c31109
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
We found 163 GWAS risk genes specifically expressed in one or more endocrine cell types ( Figure 3D ; Data S3 ) including some well-known β cell genes RNF6 , PDX1 , SLC2A2 , MEG3 , and DLK1 .

summary:
In Homo sapiens, well-known beta cell genes RNF6, PDX1, SLC2A2, MEG3, and DLK1 are specifically expressed in beta cells.


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:96b54ebe5da21a62d8e3
claim_id: claim:96b54ebe5da21a62d8e3
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
summary: In Homo sapiens, HHEX, LEPR, and ERBB4 are delta-cell-specific risk genes.
span_literal:
Interestingly, a number of risk genes are δ-cell-specific, including HHEX , LEPR , ERBB4 , etc., suggesting a particularly important role of δ cells to diabetes or obesity ( Figure 3D ).


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:c0e014132c0a86997807
claim_id: claim:c0e014132c0a86997807
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
Interestingly, we noticed that δ cells specifically express several important hormone receptor genes, including LEPR (receptor of leptin), GHSR (receptor of Ghrelin), GHR (receptor of growth hormone), ERBB4 (receptor of EGF), and two GABA receptors ( GABRG2 and GABRA1 ) ( Figure 3E ).

summary:
In Homo sapiens, delta cells specifically express LEPR (leptin receptor), GHSR (ghrelin receptor), GHR (growth hormone receptor), ERBB4 (epidermal growth factor receptor), GABRG2 (GABA receptor), and GABRA1 (GABA receptor).


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:58687e06c2a98ce70da1
claim_id: claim:58687e06c2a98ce70da1
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
summary: In Homo sapiens islets, MAU2 is expressed at higher levels in beta cells than in other cell types.
span_literal:
Our single-cell data demonstrated that in human islets, MAU2 is expressed at higher levels in β cells than in other cell types ( Figure 7C ).


claim_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae:claim:c0c1e419a6ae1f51960d
claim_id: claim:c0c1e419a6ae1f51960d
paper_key: hca:0317_10.1016_j.celrep.2019.02.043_aed04e8aae
span_literal:
Expression levels of KRT19 (duct marker) and COL1A2 (PSC marker) were overlaid onto the t-SNE plot in (B).

summary:
In Homo sapiens, KRT19 is a marker of pancreatic ductal cells and COL1A2 is a marker of pancreatic stellate cells.


claim_key: hca:0318_10.1158_1078-0432.ccr-19-0148_d4eb569329:claim:d8ab72ce7079c1eff389
claim_id: claim:d8ab72ce7079c1eff389
paper_key: hca:0318_10.1158_1078-0432.ccr-19-0148_d4eb569329
summary: In Homo sapiens skin, AIF1 is a marker of macrophages.
span_literal:
Cell types in skin cell suspensions were identified by cell-specific marker as previously described ( 18 ), including AIF1 - macrophages; VWF - endothelial cells; TPSAB1 - mast cells; SCGB1B2P - secretory (glandular) cells; RGS5 - pericytes; PMEL - melanocytes; MS4A1 - B cells; KRT1 - keratinocytes; DES - smooth muscle cells; COL1A1 – fibroblasts; CD3D - T lymphocytes; and CD1C - dendritic cells.


claim_key: hca:0318_10.1158_1078-0432.ccr-19-0148_d4eb569329:claim:b8334acb2759bfbe4a1f
claim_id: claim:b8334acb2759bfbe4a1f
paper_key: hca:0318_10.1158_1078-0432.ccr-19-0148_d4eb569329
span_literal:
TOX (thymus high-mobility group box) is considered a marker of malignant lymphocytes in CTCL tumors ( 9 , 22 , 23 ).

summary:
In Homo sapiens, TOX (thymus high-mobility group box) is considered a marker of malignant lymphocytes in cutaneous T-cell lymphoma tumors.


claim_key: hca:0318_10.1158_1078-0432.ccr-19-0148_d4eb569329:claim:b37781db1e5069bafdc4
claim_id: claim:b37781db1e5069bafdc4
paper_key: hca:0318_10.1158_1078-0432.ccr-19-0148_d4eb569329
span_literal:
CD8 + TILs in cluster 1 expressed markers of skin-residency, such as CD69 and ITGAE, and of memory cells (CD27).

summary:
In Homo sapiens, CD8-positive tumor-infiltrating lymphocytes express skin-residency markers CD69 and ITGAE, and the memory cell marker CD27.


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:bd165a6807232f29c5a0
claim_id: claim:bd165a6807232f29c5a0
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
summary: In Homo sapiens, regulatory T cells express high amounts of the transcription factor FOXP3.
span_literal:
Regulatory T (Treg) cells, expressing high amounts of the transcription factor Foxp3, curtail activity of effector T cells and other immune cell types under physiologic conditions and are found in markedly increased numbers in solid organ tumors


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:b70459ac412300cae0bd
claim_id: claim:b70459ac412300cae0bd
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
span_literal:
Genes most correlated with the component are known to increase upon activation and progressive differentiation, including cytolytic effector molecules granzymes A and K (GZMA and GZMK), pro-inflammatory cytokines (IL-32), cytokine receptor subunits (IL2RB), chemokines (CCL4, CCL5), and their receptors (CXCR4, CCR5)

summary:
In Homo sapiens, activated T cells show increased expression of granzyme A (GZMA), granzyme K (GZMK), interleukin 32 (IL-32), interleukin 2 receptor subunit beta (IL2RB), CCL4, CCL5, CXCR4, and CCR5 upon activation and progressive differentiation.


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:d3a07f7d63ccb24fac75
claim_id: claim:d3a07f7d63ccb24fac75
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
span_literal: Focusing on the first branch, top correlated genes included APOE, CD68, TREM2, and CHIT1
summary:
In Homo sapiens, tumor-associated macrophages are characterized by expression of APOE, CD68, TREM2, and CHIT1 along the macrophage activation branch.


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:964efaf6929313b5d35d
claim_id: claim:964efaf6929313b5d35d
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
span_literal:
Additionally, expression of genes associated with “alternatively activated” (M2) macrophages, including scavenger receptor MARCO, pro-angiogenic receptor NRP2, and inhibitory molecule B7-H3 (CD276), increased along this branch

summary:
In Homo sapiens, alternatively activated (M2) macrophages are associated with expression of scavenger receptor MARCO, pro-angiogenic receptor NRP2, and inhibitory molecule B7-H3 (CD276).


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:83757b76f5c7ce29f543
claim_id: claim:83757b76f5c7ce29f543
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
span_literal:
Concomitantly, immunostimulatory genes associated with “classically activated” (M1) macrophages, including chemokine CCL3 (MIP-1a), increased along the branch.

summary:
In Homo sapiens, classically activated (M1) macrophages are associated with expression of chemokine CCL3 (MIP-1a).


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:250f6469cd3c6fcbf2d1
claim_id: claim:250f6469cd3c6fcbf2d1
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
span_literal:
The fourth branch correlated with canonical plasmacytoid dendritic cell (pDC) markers such as LILRA4, CLEC4C (CD303), and IL3RA.

summary:
In Homo sapiens, plasmacytoid dendritic cells are marked by canonical markers LILRA4, CLEC4C (CD303), and IL3RA.


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:f3b5e494be41dc4b2180
claim_id: claim:f3b5e494be41dc4b2180
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
summary: In Homo sapiens, natural killer cells are typed by markers NCAM1, NCR1, and NKG2.
span_literal:
Markers used to type cells included NCAM1, NCR1, NKG2 (NK-cells), GNLY, PFN1, GZMA, GZMB, GMZM, GZMH (cytotoxic T, NK), FOXP3, CTLA4, TIGIT, TNFRSF4, LAG3, PDCD1 (Exhausted T-cell, T-regulatory Cell), CD8, CD3, CD4 (T-cells), IL7R (Naive T-cells), CD19 (B-cells), ENPP3, KIT (Mast cells), IL3RA, LILRA4 (plasmacytoid DC), HLA-DR, FCGR3A, CD68, ANPEP, ITGAX, CD14, ITGAM, CD33 (Monocytic Lineage).


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:2b1c4402ff15fd227061
claim_id: claim:2b1c4402ff15fd227061
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
span_literal:
Markers used to type cells included NCAM1, NCR1, NKG2 (NK-cells), GNLY, PFN1, GZMA, GZMB, GMZM, GZMH (cytotoxic T, NK), FOXP3, CTLA4, TIGIT, TNFRSF4, LAG3, PDCD1 (Exhausted T-cell, T-regulatory Cell), CD8, CD3, CD4 (T-cells), IL7R (Naive T-cells), CD19 (B-cells), ENPP3, KIT (Mast cells), IL3RA, LILRA4 (plasmacytoid DC), HLA-DR, FCGR3A, CD68, ANPEP, ITGAX, CD14, ITGAM, CD33 (Monocytic Lineage).

summary:
In Homo sapiens, exhausted T cells and regulatory T cells are typed by markers FOXP3, CTLA4, TIGIT, TNFRSF4, LAG3, and PDCD1.


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:9209e5c6fe04abe30729
claim_id: claim:9209e5c6fe04abe30729
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
summary:
In Homo sapiens, regulatory T cells are typed by markers FOXP3, CTLA4, TIGIT, TNFRSF4, LAG3, and PDCD1.


claim_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8:claim:ef3db5f064ea88745281
claim_id: claim:ef3db5f064ea88745281
paper_key: hca:0319_10.1016_j.cell.2018.05.060_d1a05e99e8
summary:
In Homo sapiens, monocytic lineage cells are typed by markers HLA-DR, FCGR3A, CD68, ANPEP, ITGAX, CD14, ITGAM, and CD33.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:69945c7b765475d76822
claim_id: claim:69945c7b765475d76822
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Several AT1 cell markers, including advanced glycosylation end‐product specific receptor (AGER), podoplanin (PDPN), caveolin‐1 (CAV1), and aquaporin (AQP5), have been identified.

summary:
In Homo sapiens, alveolar type I cells are marked by advanced glycosylation end-product specific receptor (AGER), podoplanin (PDPN), caveolin-1 (CAV1), and aquaporin 5 (AQP5).


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:618c33fa4f246cb70da7
claim_id: claim:618c33fa4f246cb70da7
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Cluster 0 was associated with a high expression of SFTPC and SFTPB ; thus, it was annotated as FD‐iAT2 cells.

summary:
In Homo sapiens, fibroblast-dependent induced alveolar type II cells are associated with high expression of SFTPC and SFTPB.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:ea34d1ebf010d1f991b6
claim_id: claim:ea34d1ebf010d1f991b6
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
summary: In Homo sapiens, pulmonary neuroendocrine cells are marked by high expression of ASCL1.
span_literal:
Cluster 2 was annotated as ASCL1 + pulmonary neuroendocrine cells (PNECs) based on the high expression of ASCL1 .


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:bd14a896bea8acb4ffff
claim_id: claim:bd14a896bea8acb4ffff
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Cluster 4 was annotated as iAT1 cells based on the high expression of AGER , CAV1 , and/or PDPN and low or no expression of SFTPC .

summary:
In Homo sapiens, induced alveolar type I cells are defined by high expression of AGER, CAV1, and/or PDPN and low or no expression of SFTPC.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:2cc42b160b4e4fcbef48
claim_id: claim:2cc42b160b4e4fcbef48
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Furthermore, the heatmap of the top 10 genes for each cluster showed that FD‐iAT2 cells expressed AT2 markers ( PGC , SFTPC , SFTPB , and SLC34A2 ), 10 and iAT1 cells expressed EMP2 , an AT1 cell marker 11

summary:
In Homo sapiens, fibroblast-dependent induced alveolar type II cells express the alveolar type II markers PGC, SFTPC, SFTPB, and SLC34A2, and induced alveolar type I cells express EMP2, an alveolar type I cell marker.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:43ff878f6a4b8868d100
claim_id: claim:43ff878f6a4b8868d100
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
summary: In Homo sapiens, alveolar type I cells are marked by AGER and CAV1 in adult donor lung.
span_literal:
we found that 22 254 adult donor lung cells were divided into 12 major types of cells: AT1 cells ( AGER and CAV1 ), AT2 cells ( SFTPB and SFTPC ), ciliated cells ( SNTN1 ), club cells ( SCGB1A1 and SYP2F1 ), fibroblasts ( DCN ), macrophages ( CD68 ), monocytes ( FCN1 ), dendritic cells ( CLEC10A ), endothelial/lymphatic cells ( VWF ), plasma cells ( IGHG4 ), T and NKT cells ( CD3D ), and Mast/B cells ( MS4A1 and TPSB2 )


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:8d74130ff3e8cb83d8c1
claim_id: claim:8d74130ff3e8cb83d8c1
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
iAT1 cells expressed the AT1 marker genes ( AGER , CAV1 , and/or PDPN ) as primary AT1 cells (Figure 3C ).

summary:
In Homo sapiens, induced alveolar type I cells express the alveolar type I marker genes AGER, CAV1, and/or PDPN.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:81480a8d7a6fd8273338
claim_id: claim:81480a8d7a6fd8273338
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
summary: In Homo sapiens, prealveolar type-I transitional cell state-like cells express SFN and KRT17.
span_literal:
In accordance with a recent study reporting that prealveolar type‐I transitional cell state (PATS)‐like cells, expressing SFN and KRT17, accumulated in idiopathic pulmonary fibrosis patients, 20 both COL4A1 + and TP63 + 2D‐iAT1 cell clusters expressed SFN and KRT17, suggesting that some of the 2D‐iAT1 cells had transdifferentiated into abnormal cells, including PATS‐like cells (Figure 4C ).


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:af2ed644f57fad3a0f36
claim_id: claim:af2ed644f57fad3a0f36
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
While we identified the INSM1 + PNEC cluster based on the high expression of INSM1 as well as hepatic‐like cells, based on APOA2 expression, in epithelial clusters

summary:
In Homo sapiens, INSM1-positive pulmonary neuroendocrine cells are identified based on high expression of INSM1, and hepatic-like cells are identified based on APOA2 expression.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:85ce2d909534c78f1d75
claim_id: claim:85ce2d909534c78f1d75
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Among the HFLF clusters, cluster 1, cluster 4, and cluster 6 were annotated as PDGFRA + fibroblasts, WNT5A + /PDGFRA + fibroblasts, and RARRES1 + fibroblasts, based on the gene expression of PDGFRA , WNT5A / PDGFRA , and RARRES1 , respectively.

summary:
In Homo sapiens, PDGFRA-positive fibroblasts are marked by PDGFRA expression in human fetal lung fibroblasts.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:16b356bd8ecf2227979e
claim_id: claim:16b356bd8ecf2227979e
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Among the HFLF clusters, cluster 1, cluster 4, and cluster 6 were annotated as PDGFRA + fibroblasts, WNT5A + /PDGFRA + fibroblasts, and RARRES1 + fibroblasts, based on the gene expression of PDGFRA , WNT5A / PDGFRA , and RARRES1 , respectively.

summary:
In Homo sapiens, WNT5A-positive/PDGFRA-positive fibroblasts are marked by WNT5A and PDGFRA expression in human fetal lung fibroblasts.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:18145be3ff8d94701730
claim_id: claim:18145be3ff8d94701730
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
Among the HFLF clusters, cluster 1, cluster 4, and cluster 6 were annotated as PDGFRA + fibroblasts, WNT5A + /PDGFRA + fibroblasts, and RARRES1 + fibroblasts, based on the gene expression of PDGFRA , WNT5A / PDGFRA , and RARRES1 , respectively.

summary:
In Homo sapiens, RARRES1-positive fibroblasts are marked by RARRES1 expression in human fetal lung fibroblasts.


claim_key: hca:0321_10.1002_stem.3302_bfd2270715:claim:bdb8be8b40d6b446dcad
claim_id: claim:bdb8be8b40d6b446dcad
paper_key: hca:0321_10.1002_stem.3302_bfd2270715
span_literal:
While recent reports indicated that AT1 cells expressed VEGFA and were a heterogeneous population including IGFBP2 + AT1 cells, 22 , 23 we were not able to identify this subpopulation of iAT1 cells, suggesting that XAV‐939 would homogeneously induce iAT1 cells (Figure 7E ).

summary:
In Homo sapiens, alveolar type I cells express VEGFA and include a subpopulation of IGFBP2-positive alveolar type I cells.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:3c5fa0761c1532f499dc
claim_id: claim:3c5fa0761c1532f499dc
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
Except for the marker gene CDKN2A ( 17 ), epithelial-derived KRT18 and KRT7 , type 2 pRCC also differentially expressed SPOCK1 , PTGIS and other genes

summary:
In Homo sapiens, type 2 papillary renal cell carcinoma cells express the marker genes CDKN2A, KRT18, KRT7, SPOCK1, and PTGIS.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:7bb9acb43bb785afa46c
claim_id: claim:7bb9acb43bb785afa46c
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
ccRCC1 and ccRCC2 highly expressed the ccRCC markers CA9 ( 13 ) and NDUFA4L2 ( 49 ), whilst ccRCC3 and ccRCC4 only expressed NDUFA4L2

summary:
In Homo sapiens, clear-cell renal cell carcinoma 1 and clear-cell renal cell carcinoma 2 highly express the markers CA9 and NDUFA4L2.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:07b05287574e62e82e21
claim_id: claim:07b05287574e62e82e21
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
In type 2 pRCC, five significant candidate genes were identified ( SPOCK1 , PTGIS , NDUFA4L2 , C5orf46 and WISP1 ); they were generally highly expressed in type 2 pRCC

summary:
In Homo sapiens, type 2 papillary renal cell carcinoma cells highly express the tumor-specific candidate genes SPOCK1, PTGIS, NDUFA4L2, C5orf46, and WISP1.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:4a9b80c9eb21afb56fb9
claim_id: claim:4a9b80c9eb21afb56fb9
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal: Three specific candidate genes ( REG1A , CP and FABP7 ) were also identified in ccRCC
summary:
In Homo sapiens, clear-cell renal cell carcinoma cells express the tumor-specific candidate genes REG1A, CP, and FABP7.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:0ed5c07cd7635c53c3f4
claim_id: claim:0ed5c07cd7635c53c3f4
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal: In a previous study, RHCG and LINC01187 are identified as marker genes for chRCC ( 42 ).
summary:
In Homo sapiens, RHCG and LINC01187 are identified as marker genes for chromophobe renal cell carcinoma.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:8eab8ec53d0d80a9f390
claim_id: claim:8eab8ec53d0d80a9f390
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
In addition, a novel tumor-specific gene marker called SPAG4 was discovered in chRCC and it was more specifically expressed in chRCC3

summary:
In Homo sapiens, SPAG4 is a novel tumor-specific gene marker for chromophobe renal cell carcinoma, more specifically expressed in chromophobe renal cell carcinoma 3.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:582591cf26f56bb1d381
claim_id: claim:582591cf26f56bb1d381
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal: And NDUFA4L2 both highly expressed in tumor cells of ccRCC and type 2 pRCC.
summary:
In Homo sapiens, NDUFA4L2 is highly expressed in tumor cells of both clear-cell renal cell carcinoma and type 2 papillary renal cell carcinoma.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:1c63ab3913871997e657
claim_id: claim:1c63ab3913871997e657
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal: And NDUFA4L2 both highly expressed in tumor cells of ccRCC and type 2 pRCC.
summary:
In Homo sapiens, NDUFA4L2 is highly expressed in tumor cells of type 2 papillary renal cell carcinoma.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:3908259bee3a9caac3a8
claim_id: claim:3908259bee3a9caac3a8
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
The quiescent fibroblast highly expressed the markers of fibroblast, namely, SFRP2 ( 51 ) and MMP2 ( 52 , 53 ), but did not express the markers of CAF, namely, ACTA2 ( 52 ) and TAGLN ( 53 )

summary:
In Homo sapiens, quiescent fibroblast highly expresses the fibroblast markers SFRP2 and MMP2 but does not express the cancer-associated fibroblast markers ACTA2 and TAGLN.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:232f395625a494ce7b3e
claim_id: claim:232f395625a494ce7b3e
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal: All the CAFs in type 2 pRCC expressed TGFB1I1
summary:
In Homo sapiens, all cancer-associated fibroblasts in type 2 papillary renal cell carcinoma express TGFB1I1.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:3dd0855e9dda93fb8d32
claim_id: claim:3dd0855e9dda93fb8d32
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
Two subpopulations of CAFs, which expressed ACTA2 ( 52 ) and TAGLN ( 53 ), the markers of CAF, were discovered in ccRCC

summary:
In Homo sapiens, cancer-associated fibroblasts in clear-cell renal cell carcinoma express the markers ACTA2 and TAGLN.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:d92cb7c64ceec56db2c0
claim_id: claim:d92cb7c64ceec56db2c0
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
CAF 1 highly expressed ACTA2 and TAGLN , whilst CAF 2 specifically expressed SFRP2 , MMP2 , TGFBI and TNC

summary:
In Homo sapiens, cancer-associated fibroblast 1 in clear-cell renal cell carcinoma highly expresses ACTA2 and TAGLN.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:2d312f4bd9409c827a38
claim_id: claim:2d312f4bd9409c827a38
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
CAF 1 highly expressed ACTA2 and TAGLN , whilst CAF 2 specifically expressed SFRP2 , MMP2 , TGFBI and TNC

summary:
In Homo sapiens, cancer-associated fibroblast 2 in clear-cell renal cell carcinoma specifically expresses SFRP2, MMP2, TGFBI, and TNC.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:1ae7410d81af829ed808
claim_id: claim:1ae7410d81af829ed808
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal: The fibroblast that specifically expressed the proliferation factor MKI67 in ccRCC was discovered.
summary:
In Homo sapiens, proliferative fibroblast in clear-cell renal cell carcinoma specifically expresses the proliferation factor MKI67.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:ad3d0a53195002b61423
claim_id: claim:ad3d0a53195002b61423
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
Although both types of EC expressed classical endothelial cell markers, such as PECAM1 ( 50 ), CDH5 ( 50 ) and KDR ( 50 )

summary:
In Homo sapiens, endothelial cells in type 2 papillary renal cell carcinoma express the classical endothelial cell markers PECAM1, CDH5, and KDR.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:7a9fd036229b88fa13c1
claim_id: claim:7a9fd036229b88fa13c1
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
The endothelial cell 1 of type 2 pRCC (pEC1) specifically expressed VEGFC , whilst pEC2 significantly expressed VEGFA

summary:
In Homo sapiens, endothelial cell 1 of type 2 papillary renal cell carcinoma specifically expresses VEGFC, while endothelial cell 2 significantly expresses VEGFA.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:5a14f1ed40ab4c7d31e6
claim_id: claim:5a14f1ed40ab4c7d31e6
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
The endothelial cell 1 of type 2 pRCC (pEC1) specifically expressed VEGFC , whilst pEC2 significantly expressed VEGFA

summary:
In Homo sapiens, endothelial cell 2 of type 2 papillary renal cell carcinoma significantly expresses VEGFA.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:5684461bbdc77bfec252
claim_id: claim:5684461bbdc77bfec252
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
A type of EC with fibroblast characteristics was identified in ccRCC. It expressed COL3A1 ( 55 ) and POSTN

summary:
In Homo sapiens, a type of endothelial cell with fibroblast characteristics in clear-cell renal cell carcinoma expresses COL3A1 and POSTN.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:36d155867f04de41a151
claim_id: claim:36d155867f04de41a151
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
summary: In Homo sapiens, tumor-associated macrophage is defined by the markers GPNMB, SLC40A1, and MSR1.
span_literal:
TAM was present in three pathologic RCC, which was defined by GPNMB ( 58 ), SLC40A1 ( 58 ) and MSR1 ( 64 ).


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:805d3cc4f58ea16a0712
claim_id: claim:805d3cc4f58ea16a0712
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
Pro-TAM not only expressed TAM markers but also specifically expressed the proliferation factor MKI67

summary:
In Homo sapiens, proliferative tumor-associated macrophage specifically expresses the proliferation factor MKI67.


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:d4f867d35c569918fc92
claim_id: claim:d4f867d35c569918fc92
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
summary: In Homo sapiens, proliferative T cells specifically express MKI67.
span_literal:
In accordance with the characteristics of gene expression, a type of T cells specifically expressing MKI67 was found and regarded as proliferative T cells


claim_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753:claim:fdca027160e01f721622
claim_id: claim:fdca027160e01f721622
paper_key: hca:0322_10.3389_fonc.2021.719564_a0cfb67753
span_literal:
An endothelial cell in ccRCC may be associated with fibroblasts and significantly expressed fibroblast markers, such as POSTN and COL3A1

summary:
In Homo sapiens, an endothelial cell in clear-cell renal cell carcinoma significantly expresses fibroblast markers such as POSTN and COL3A1.


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:654f8d56e12f08237d3c
claim_id: claim:654f8d56e12f08237d3c
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
summary: In Homo sapiens glioblastoma, neoplastic cells are marked by overexpression of EGFR and SOX9.
span_literal:
these cells significantly overexpressed EGFR ( Figure 2B ), a gene upregulated in 30%–50% of all GBMs ( Libermann et al., 1984 , 1985a , 1985b ), as well as SOX9, a transcription factor with an established oncogenic role in gliomas ( Wang et al., 2012 ).


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:6e9de1c23a8b9d895b27
claim_id: claim:6e9de1c23a8b9d895b27
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
span_literal: Unsurprisingly, EGFR showed the highest enrichment of any gene.
summary:
In Homo sapiens glioblastoma, EGFR is the most enriched gene in neoplastic cells compared to non-neoplastic cells.


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:d383d8334d027348228e
claim_id: claim:d383d8334d027348228e
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
summary: In Homo sapiens glioblastoma, CHL1 is among the most enriched genes in neoplastic cells.
span_literal:
In addition, among the highest enriched genes, we found CHL1 , a member of the L1 family of neural cell adhesion molecules that is involved in migration and positioning of neurons in the developing neocortex.


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:c2155396355c934c0351
claim_id: claim:c2155396355c934c0351
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
span_literal:
Furthermore, we found upregulation of the transcription factors SOX2 and SOX9 , which are also involved in brain development and lineage specification.

summary:
In Homo sapiens glioblastoma, the transcription factors SOX2 and SOX9 are upregulated in neoplastic cells.


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:3da13234ac14a6492ffe
claim_id: claim:3da13234ac14a6492ffe
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
summary: In Homo sapiens, SOX2, POU3F2, OLIG2, and SALL2 are markers of glioma stem cells.
span_literal:
Notably, SOX2 has been reported as a marker of glioma stem cells, along with the genes POU3F2 , OLIG2 , and SALL2 ( Suvà et al., 2014 ), whereas SOX9 has been shown to correlate with poor clinical outcome ( Wang et al., 2012 ).


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:9fe89230993af525eb1c
claim_id: claim:9fe89230993af525eb1c
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
summary: In Homo sapiens glioblastoma, NFIB is a neoplastic cell-specific transcription factor.
span_literal:
NFIB was another neoplastic-specific transcription factor that has been implicated in brain development ( Campbell et al., 2008 ; Steele-Perkins et al., 2005 ) with an important role in the induction of quiescence in neural stem cells ( Martynoga et al., 2013 ) and promotion of metastasis ( Denny et al., 2016 ).


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:d4e7815b760a823bb9c9
claim_id: claim:d4e7815b760a823bb9c9
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
summary: In Homo sapiens, MBP and OPALIN are markers of oligodendrocytes.
span_literal:
Unsurprisingly, many of these markers were genes known to define mature, differentiated CNS cell types: MBP and OPALIN (oligodendrocytes), GPR17 (OPCs), and L1CAM (neurons), as well as ALDH1L1, WIF1, and NTSR2 (astrocytes).


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:4ec5d903d0bce9dcd581
claim_id: claim:4ec5d903d0bce9dcd581
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
span_literal:
Two of the largest tSNE clusters that we observed were composed of immune cells, defined by the specific expression of numerous myeloid-specific genes, including PTPRC (CD45) and MHC class II genes ( Figure 2B ).

summary:
In Homo sapiens glioblastoma, immune cells are defined by specific expression of PTPRC (CD45) and major histocompatibility complex class II genes.


claim_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c:claim:5707d12fa512a0175409
claim_id: claim:5707d12fa512a0175409
paper_key: hca:0325_10.1016_j.celrep.2017.10.030_a9d12a5d7c
summary: In Homo sapiens, microglia are marked by TMEM119, P2RY12, GPR34, OLFML3, SLC2A5, SALL1, and ADORA3.
span_literal:
we correlated gene expression of each cell with a panel of established macrophage and microglia specific genes ( TMEM119 , P2RY12 , GPR34 , OLFML3 , SLC2A5 , SALL1 , and ADORA3 for microglia and CRIP1 , S100A8 , S100A9 , ANXA1 , and CD14 for macrophages) ( Bennett et al., 2016 ).


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:9ec2723dcce6ec95a7fe
claim_id: claim:9ec2723dcce6ec95a7fe
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
span_literal:
two clusters corresponding to exocrine acinar (n = 185) and ductal (n = 386) cells based on expression of their respective markers, PRSS1 and KRT19

summary:
In Homo sapiens, acinar cells are marked by PRSS1 and ductal cells are marked by KRT19 in the pancreas.


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:d7af084c95ec9a693cb3
claim_id: claim:d7af084c95ec9a693cb3
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, pancreatic stellate cells show high expression of TIMP1, FN1, POSTN, and ACTA2.
span_literal:
pancreatic stellate cells (PSCs; n = 54, high expression of collagen genes, matrix metalloproteinases, TIMP1 , FN1 , POSTN , and ACTA2 )


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:b7b2868995a8a2de3adb
claim_id: claim:b7b2868995a8a2de3adb
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
span_literal:
antigen-presenting MHC class II cells (n = 5, high expression of CD74 , CD86 , HLA-DPA1 , HLA-DPB1 , and HLA-DRA )

summary:
In Homo sapiens, antigen-presenting MHC class II cells show high expression of CD74, CD86, HLA-DPA1, HLA-DPB1, and HLA-DRA.


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:f0aa2d07e06fa4e07fa7
claim_id: claim:f0aa2d07e06fa4e07fa7
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
span_literal:
In β cells, we found elevated expression levels of, e.g., INS , IAPP , ADCYAP1 , PDX1 , MAFA , NKX6-1 , and MEG3

summary:
In Homo sapiens, beta cells show elevated expression of INS, IAPP, ADCYAP1, PDX1, MAFA, NKX6-1, and MEG3.


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:c62891d67797de3bd5fd
claim_id: claim:c62891d67797de3bd5fd
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, LINC01099 expression is restricted mainly to beta cells.
span_literal:
We also detected long non-coding RNAs, e.g., LINC01099 , with expression restricted mainly to β cells


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:c71ac9d09c5e457c634b
claim_id: claim:c71ac9d09c5e457c634b
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
span_literal:
We noted that many receptors were highest or exclusively expressed in δ cells (e.g., UNC5B , GABRB3 , GABRG2 , CASR , FFAR4/GPR120 , and KCNJ2 )

summary:
In Homo sapiens, delta cells show highest or exclusive expression of UNC5B, GABRB3, GABRG2, CASR, FFAR4, and KCNJ2.


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:af348d7cb283801b043c
claim_id: claim:af348d7cb283801b043c
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, gamma cells specifically express SERTM1, SPOCK1, ABCC9, and SLITRK6.
span_literal:
We also identified genes specifically expressed in γ cells, e.g., SERTM1 , SPOCK1 , ABCC9 , and SLITRK6


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:69eb9b64241dbe24c0e4
claim_id: claim:69eb9b64241dbe24c0e4
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, epsilon cells show elevated expression of GHRL and GHRLOS.
span_literal:
Analysis of these cells allowed us to identify elevated expression of 39 genes, including the expression of GHRL and GHRLOS


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:85d7e548bcf39e4e24dd
claim_id: claim:85d7e548bcf39e4e24dd
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, epsilon cells uniquely express NPY1R, OPRK1, PTGER4, ASGR1, and PCSK6.
span_literal:
The ε cells uniquely expressed several interesting receptors like NPY1R , OPRK1 , PTGER4 , and ASGR1 , and processing enzymes such as PCSK6


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:a665e96c80cde3be608a
claim_id: claim:a665e96c80cde3be608a
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
span_literal: restricted expression of MAFA in β cells and IRX2 in α cells
summary:
In Homo sapiens, MAFA expression is restricted to beta cells and IRX2 expression is restricted to alpha cells.


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:3477645f58838f713406
claim_id: claim:3477645f58838f713406
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, ARX is expressed in alpha cells and gamma cells.
span_literal:
ARX expression in α and γ cells, in line with the increase in γ and α cell numbers after forced ARX expression in mouse embryonic islets


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:d3ab47fd943742ad709d
claim_id: claim:d3ab47fd943742ad709d
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
summary: In Homo sapiens, HHEX is expressed in ductal cells.
span_literal:
We found HHEX expression in both δ and ductal cells while MAFB expression was restricted to α, β, and δ cells


claim_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3:claim:e38ba996369363e537b4
claim_id: claim:e38ba996369363e537b4
paper_key: hca:0326_10.1016_j.cmet.2016.08.020_b710322bb3
span_literal: GCG-like peptide receptor 1 ( GLP1R ), expressed in β and δ cells
summary:
In Homo sapiens, glucagon-like peptide receptor 1 (GLP1R) is expressed in beta cells and delta cells.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:ffaea7643fcc60f1f4b9
claim_id: claim:ffaea7643fcc60f1f4b9
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
A unique cell type termed LAM CORE was identified, which was distinct from, but closely related to, lung mesenchymal cells. LAM CORE cells expressing signature genes included known LAM markers such as PMEL , FIGF , CTSK , and MLANA and novel biomarkers validated by aptamer screening, ELISA, and immunofluorescence microscopy.

summary:
In Homo sapiens, LAM CORE cells express known lymphangioleiomyomatosis markers PMEL, FIGF, CTSK, and MLANA.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:475361203db30da52b24
claim_id: claim:475361203db30da52b24
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
A small cluster of unique cells expressed multiple known LAM-associated genes, including PMEL ( 18 , 19 ), ACTA2 ( 19 ), ESR1 ( 20 ), and FIGF (VEGFD) ( 21 ), hereafter termed LAM CORE cells ( Figure 2A , magenta; Figure E1).

summary:
In Homo sapiens, LAM CORE cells express known lymphangioleiomyomatosis-associated genes PMEL, ACTA2, ESR1, and FIGF (vascular endothelial growth factor D).


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:82e3155eaa84f5e68c3f
claim_id: claim:82e3155eaa84f5e68c3f
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
A total of 777 LAM CORE signature genes were identified, including well-known LAM markers, such as PMEL , MLANA ( 22 ), FIGF , ESR1 , and many new and more selective markers, including HOXD11 , HOXA11 , VGLL2 , and SLC35F1 ( Figures 2D and 2E and Table E2).

summary:
In Homo sapiens, LAM CORE cells express well-known markers PMEL, MLANA, FIGF, and ESR1, as well as novel selective markers HOXD11, HOXA11, VGLL2, and SLC35F1.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:80b786ecbfa98537f9b0
claim_id: claim:80b786ecbfa98537f9b0
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
LAM CORE signature genes RAMP1 and MYH11 were coexpressed with ACTA2 in LAM nodules ( Figures 3G–3I and E6G), supporting RAMP1 as a new marker for LAM CORE cells.

summary:
In Homo sapiens, LAM CORE cells express RAMP1, MYH11, and ACTA2, with RAMP1 identified as a new marker for LAM CORE cells.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:3f1091d8cb7d0bda60b0
claim_id: claim:3f1091d8cb7d0bda60b0
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
Expression of known LAM CORE signature RNAs ( CTSK , FIGF , PGR , and MYH11 ) and novel LAM CORE signatures ( KCNAB1 and PALLD ) were validated by qPCR and immunofluorescence staining (Figure E6).

summary:
In Homo sapiens, LAM CORE cells express known signature genes CTSK, FIGF, PGR, and MYH11, as well as novel signature genes KCNAB1 and PALLD.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:a1aedea4cd0766ea8396
claim_id: claim:a1aedea4cd0766ea8396
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
Expression of genes associated with metastatic invasion of lymphatic vessels ( UNC5B , NECTIN2 , CD200 , ESAM , and ENG ) ( 39 ) was increased in LAM-associated lymphatic endothelial cells (Figures E11A and E11B).

summary:
In Homo sapiens, LAM-associated lymphatic endothelial cells show increased expression of UNC5B, NECTIN2, CD200, ESAM, and ENG, genes associated with metastatic invasion of lymphatic vessels.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:725e3789c46d1df6ee1f
claim_id: claim:725e3789c46d1df6ee1f
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
PROX1 , NR2F2 , NRP2 , FLT4 (VEGFR3) , and TBX1 , were abundantly expressed in lymphatic endothelial cells

summary:
In Homo sapiens, lymphatic endothelial cells in lymphangioleiomyomatosis samples abundantly express PROX1, NR2F2, NRP2, FLT4 (VEGFR3), and TBX1.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:731470b3ebe6e085ee2f
claim_id: claim:731470b3ebe6e085ee2f
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
expression of genes involved in host defense and innate immunity ( DMBT1 , LCN2 , and SFTPD ) and cytokine/IL signaling ( IFI27 and IL20RA ) was increased in LAM-associated AT2 cells.

summary:
In Homo sapiens, LAM-associated alveolar type 2 cells show increased expression of DMBT1, LCN2, SFTPD, IFI27, and IL20RA.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:585fad25fb0e79bfc5d5
claim_id: claim:585fad25fb0e79bfc5d5
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
summary: In Homo sapiens, monocytes express IL1B, CSF1R, and TLR2 in lymphangioleiomyomatosis lung.
span_literal:
The expression of multiple cytokines and chemokines involved in the recruitment of monocytes ( IL1B , CSF1R , and TLR2 ), T cells ( CD8A and CD3D ), B cells ( CD79A and CD19 ), mast cells ( KIT and FCER1A ), natural killer cells ( NKG7 and KLRF1 ), and other inflammatory cells was noted.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:f84d37b76a9387c84428
claim_id: claim:f84d37b76a9387c84428
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
LAM CORE cells expressed multiple growth factors, including VEGFD , PDFGRA/B , FGF7 , IGFBP2/4/6 , and TGFB1I1 , that likely mediate active crosstalk among pulmonary LAM CORE and surrounding cells ( Figure 6A and Table E2).

summary:
In Homo sapiens, LAM CORE cells express multiple growth factors including VEGFD, PDGFRA/B, FGF7, IGFBP2/4/6, and TGFB1I1.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:56a5ae6976240c52a358
claim_id: claim:56a5ae6976240c52a358
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal: LAM CORE cells selectively expressed VEGF-D (FIGF) in the lung
summary:
In Homo sapiens, LAM CORE cells selectively express VEGF-D (FIGF) in the lung, supporting its use as a biomarker.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:d41a731db129a348872a
claim_id: claim:d41a731db129a348872a
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
LAM CORE cells expressed a unique panel of uterine-selective transcription factors, including HOXD11 , HOXA11 , and EMX2

summary:
In Homo sapiens, LAM CORE cells express uterine-selective transcription factors HOXD11, HOXA11, and EMX2.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:bccf400b8773a95fa148
claim_id: claim:bccf400b8773a95fa148
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
summary: In Homo sapiens, PTGER3 (prostaglandin E receptor 3) is selectively expressed in LAM CORE cells.
span_literal:
EP3 (PTGER3) ( 28 ), a regulator of tumor-associated lymphangiogenesis that enhances expression of VEGFC/VEGFD and VEGFR-3 in tumor stromal tissues ( 50 ), is selectively expressed in LAM CORE cells.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:aac97c4f44637fae78cd
claim_id: claim:aac97c4f44637fae78cd
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
PROX1 ( 45 ), NR2F2 ( 46 ), TBX1 ( 47 ), and SOX18 ( 48 ), known regulators of lymphatic morphogenesis, are expressed in the LAM-associated lymphatic endothelial cells

summary:
In Homo sapiens, LAM-associated lymphatic endothelial cells express PROX1, NR2F2, TBX1, and SOX18, known regulators of lymphatic morphogenesis.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:4a4463d2c5763d07aa05
claim_id: claim:4a4463d2c5763d07aa05
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal: LAM CORE cells express VEGFD, CCBE1
summary:
In Homo sapiens, LAM CORE cells express VEGFD and CCBE1, while lymphatic endothelial cells express VEGFR3, KDR, NRP2, and ITGB1.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:edd35592f5776f6fb8d4
claim_id: claim:edd35592f5776f6fb8d4
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
LAM CORE cells express VEGFD, CCBE1, ECM, and collagens, which are known to activate VEGF signaling in lymphatic endothelial cells via multiple ligand–receptor interactions, including VEGFR3, KDR, NRP2, and ITGB1

summary:
In Homo sapiens, lymphatic endothelial cells express VEGFR3, KDR, NRP2, and ITGB1, which are activated by LAM CORE cell-derived ligands.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:dbf035ad6fe36e65cce1
claim_id: claim:dbf035ad6fe36e65cce1
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal: FLT4 (VEGFR3) RNA is highly expressed in lymphatic endothelial cells
summary:
In Homo sapiens, lymphatic endothelial cells highly express FLT4 (VEGFR3) in lymphangioleiomyomatosis.


claim_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02:claim:46d71bfcc8e5ce33b2b4
claim_id: claim:46d71bfcc8e5ce33b2b4
paper_key: hca:0328_10.1164_rccm.201912-2445oc_4927636a02
span_literal:
LAM CORE cells express a unique panel of signature genes characteristic of normal uterus and known to be important in sex steroid action; these included homeobox transcription factors HOXA9 , HOXA11 , HOXD11 , and EMX2

summary:
In Homo sapiens, LAM CORE cells express homeobox transcription factors HOXA9, HOXA11, HOXD11, and EMX2, characteristic of normal uterus.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:f3b79ef73df247d1fc94
claim_id: claim:f3b79ef73df247d1fc94
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
Epithelial cells contained clusters representing the major known lung epithelial cell types: ciliated epithelial cells ( FOXJ1 ), club cells ( SCGB1A1 ), alveolar type I cells ( AGER ), and alveolar type II cells ( SFTPC and LAMP3 ).

summary:
In Homo sapiens lung, ciliated epithelial cells are marked by FOXJ1, club cells by SCGB1A1, alveolar type I cells by AGER, and alveolar type II cells by SFTPC and LAMP3.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:34b51dd8c8ee2054690c
claim_id: claim:34b51dd8c8ee2054690c
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
In a patient with IPF (IPF 2), we were able to resolve FOXP3 - and CD4 -expressing regulatory T cells and ITGAE - and CD8 -expressing lung-resident T-cell subsets

summary:
In Homo sapiens lung, regulatory T cells express FOXP3 and CD4, while lung-resident T cells express ITGAE and CD8.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:f73f68ae03914f83972c
claim_id: claim:f73f68ae03914f83972c
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
summary: In Homo sapiens, plasmacytoid dendritic cells are marked by CLEC4C, TCL1A, IRF8, and TLR7.
span_literal:
The first cluster (30 cells) expressed CLEC4C , TCL1A , IRF8 , and TLR7 , markers associated with plasmacytoid dendritic cells.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:cb497e14dbc3f8bb0eb8
claim_id: claim:cb497e14dbc3f8bb0eb8
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
summary: In Homo sapiens, conventional dendritic cell type 1 is marked by CLEC9A.
span_literal:
The second cluster (31 cells) expressed CLEC9A , a typical marker of a subset of conventional dendritic cells (DC1).


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:ad4cf436536030866638
claim_id: claim:ad4cf436536030866638
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
Consistent with the hypothesis that cells in cluster 0 represent homeostatic tissue-resident alveolar macrophages, they expressed higher levels of PPARG , MRC1 , and MARCO , and lower levels of APOE and MAFB , which we and others have reported rise and fall, respectively, as monocytes differentiate into alveolar macrophages

summary:
In Homo sapiens, homeostatic tissue-resident alveolar macrophages express higher levels of PPARG, MRC1, and MARCO, and lower levels of APOE and MAFB.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:524d2e6c5308067557de
claim_id: claim:524d2e6c5308067557de
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
Using selective marker genes ( CD68 for alveolar macrophages and SFTPC for alveolar type II cells), we were able to confirm the predicted emergence of CHI3L1- and SPP1 -positive alveolar macrophages and increased expression of CHI3L1 in alveolar type 2 cells in patients with pulmonary fibrosis

summary:
In Homo sapiens, CD68 is a marker gene for alveolar macrophages and SFTPC is a marker gene for alveolar type II cells.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:c50ce96bce55a47f4606
claim_id: claim:c50ce96bce55a47f4606
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
Feature plots demonstrating differential expression of selected epithelial marker genes: SFTPC (alveolar type II cells), AGER (alveolar type I cells), SCGB1A1 (club cells), FOXJ1, and RFX2 (ciliated airway epithelial cells).

summary:
In Homo sapiens lung, SFTPC marks alveolar type II cells, AGER marks alveolar type I cells, SCGB1A1 marks club cells, and FOXJ1 and RFX2 mark ciliated airway epithelial cells.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:6dc3705584a8bdab6929
claim_id: claim:6dc3705584a8bdab6929
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
we identified a cluster of cells expressing many of the genes distinctly associated with these cells including KRT5 , TP63 , and SOX2 with variable expression of ITGA6 , NGF , and MYC

summary:
In Homo sapiens lung, airway basal stem cells express KRT5, TP63, and SOX2, with variable expression of ITGA6, NGF, and MYC.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:c1b9263cfeb1ae892665
claim_id: claim:c1b9263cfeb1ae892665
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
Among the detected cells, we were able to resolve several populations of endothelial cells (characterized by expression of VWF ) including a distinct population of cells characterized by expression of PROX1 , MMRN1 , TBX1 , and RELN , suggesting that these cells represent lymphatic progenitors

summary:
In Homo sapiens lung, endothelial cells are characterized by expression of VWF, and lymphatic progenitors are characterized by expression of PROX1, MMRN1, TBX1, and RELN.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:2ade6a1a7439bd0f2999
claim_id: claim:2ade6a1a7439bd0f2999
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
span_literal:
Among the detected cells, we were able to resolve several populations of endothelial cells (characterized by expression of VWF ) including a distinct population of cells characterized by expression of PROX1 , MMRN1 , TBX1 , and RELN , suggesting that these cells represent lymphatic progenitors

summary:
In Homo sapiens lung, lymphatic progenitors are characterized by expression of PROX1, MMRN1, TBX1, and RELN.


claim_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097:claim:b8d8bc56778835a606c2
claim_id: claim:b8d8bc56778835a606c2
paper_key: hca:0329_10.1164_rccm.201712-2410oc_fdd97d9097
summary: In Homo sapiens lung, airway progenitor cells (basal cells) express TP63 and KRT5.
span_literal:
We identified a likely population of TP63 - and KRT5 -expressing airway progenitor cells (basal cells) in the normal and fibrotic lung


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:b6bf8463fce03e419e71
claim_id: claim:b6bf8463fce03e419e71
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
The two predominant cell types in the retina at this stage are retinal progenitors in the neuroblast layer (NBL; SOX2+/PAX6+) and retinal ganglion cells (RGCs;HUC/D+).

summary:
In Homo sapiens fetal retina, retinal progenitor cells are marked by SOX2 and PAX6, while retinal ganglion cells are marked by HUC/D.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:5a0a786eef5b3350b1d1
claim_id: claim:5a0a786eef5b3350b1d1
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
summary: In Homo sapiens fetal retina, amacrine cells are marked by TFAP2A.
span_literal:
Smallernumbers of amacrine cells and horizontal cells (TFAP2A+ and ONECUT2+, respectively) and some photoreceptors (OTX2+) are also present at this stage.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:f941964a9d4403e32f8e
claim_id: claim:f941964a9d4403e32f8e
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
The T1 population is characterized by expression of a high level of ATOH7 , so we used the expression of this gene to better define this population of cells.

summary:
In Homo sapiens fetal retina, the transition cell population 1 is characterized by high expression of ATOH7.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:a65061114f4c5f717516
claim_id: claim:a65061114f4c5f717516
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
In addition to high ATOH7 expression, cells in the T1 population have high levels of the Notch pathway components HES6 and DLL3 ( Figure 1F ; Table S2 ).

summary:
In Homo sapiens fetal retina, transition cell population 1 expresses high levels of ATOH7, HES6, and DLL3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:04b25dfb04ca1fbc28d6
claim_id: claim:04b25dfb04ca1fbc28d6
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
The T2 cells lead to ACs; the cells in this cluster express PRDM13 , a gene that promotes AC identity ( Bessodes et al., 2017 ; Goodson et al., 2018 ; Watanabe et al., 2015 ).

summary:
In Homo sapiens fetal retina, transition cell population 2 cells express PRDM13, which promotes amacrine cell identity.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:71e5aaded24dc8ed515a
claim_id: claim:71e5aaded24dc8ed515a
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
summary: In Homo sapiens fetal retina, transition cell population 3 expresses high levels of FABP7.
span_literal:
In contrast, T3 cells lie between T1 cells and PR cells or BCs; T3 cells express high levels of FABP7 ( Su et al., 2016 ).


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:9a11696053b5e0b0734a
claim_id: claim:9a11696053b5e0b0734a
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
For example, in addition to ATOH7 , T1 cells express HES6 , whereas PRDM13 + cells express PTF1A and HSPB1 , and T3 cells express high levels of FABP7 , OTX2 , and DLL3 ( Figure S2A ).

summary:
In Homo sapiens fetal retina, transition cell population 1 expresses ATOH7 and HES6, transition cell population 2 (PRDM13-positive) expresses PTF1A and HSPB1, and transition cell population 3 expresses FABP7, OTX2, and DLL3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:c999fc73a615a98d4d90
claim_id: claim:c999fc73a615a98d4d90
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
For example, in addition to ATOH7 , T1 cells express HES6 , whereas PRDM13 + cells express PTF1A and HSPB1 , and T3 cells express high levels of FABP7 , OTX2 , and DLL3 ( Figure S2A ).

summary:
In Homo sapiens fetal retina, transition cell population 2 (PRDM13-positive cells) expresses PTF1A and HSPB1.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:fa2dfdaa38d480cb18fb
claim_id: claim:fa2dfdaa38d480cb18fb
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
For example, in addition to ATOH7 , T1 cells express HES6 , whereas PRDM13 + cells express PTF1A and HSPB1 , and T3 cells express high levels of FABP7 , OTX2 , and DLL3 ( Figure S2A ).

summary:
In Homo sapiens fetal retina, transition cell population 3 expresses high levels of FABP7, OTX2, and DLL3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:47cc2a719934163724eb
claim_id: claim:47cc2a719934163724eb
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
T3 cells express FABP7 and are positioned between the progenitors, the BCs, and the PRs, whereas T2 cells still express PRDM13 and are positioned between the progenitor cells and the ACs.

summary:
In Homo sapiens fetal retina, transition cell population 3 expresses FABP7 and transition cell population 2 expresses PRDM13.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:8952a4b9853f8e5f6901
claim_id: claim:8952a4b9853f8e5f6901
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
there is now a large number of cells we identified as Müller glia ( Figure 6A , dark blue), based on their expression of RLBP1 , AQP4 , and SLC1A3 ( Figure 6B ; Figure S5D ).

summary:
In Homo sapiens retinal organoids, Müller glia are identified by expression of RLBP1, AQP4, and SLC1A3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:ef00e8d9ae479348809d
claim_id: claim:ef00e8d9ae479348809d
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
Also at this age, D205 organoids have substantial numbers of BCs, as evidenced by their expression of VSX1 , CABP5 , and GRM6 ( Figure 6B ; Figure S5C )

summary:
In Homo sapiens retinal organoids, bipolar cells are evidenced by expression of VSX1, CABP5, and GRM6.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:0b1fd7523eda4999e35d
claim_id: claim:0b1fd7523eda4999e35d
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
summary: In Homo sapiens fetal retina, transition cell population 1 is characterized by expression of ATOH7.
span_literal:
The T1 cell population is characterized by expression of ATOH7 ; this gene is known in the mouse to be primarily expressed in newly generated postmitotic cells that can differentiate into diverse retinal cell types ( Brzezinski et al., 2012 ).


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:1a97a6de88dac5b967f1
claim_id: claim:1a97a6de88dac5b967f1
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
The T2 cell cluster represents cells that lie midway between progenitor cells and differentiated ACs or HCs. These cells are characterized by expression of PRDM13 and PTF1A , a previously described transcription factor known to be critical for development of these cell types ( Bessodes et al., 2017 ; Goodson et al., 2018 ; Hanotel et al., 2014 ; Watanabe et al., 2015 ; Hori et al., 2008 ; Xiao et al., 2018 ).

summary:
In Homo sapiens fetal retina, transition cell population 2 is characterized by expression of PRDM13 and PTF1A.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:b9f39cad408421530af8
claim_id: claim:b9f39cad408421530af8
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
Last, the analysis identified a cluster of transition cells that appear to serve as precursors for PR cells and BCs, characterized by high levels of FABP7 , OTX2 , and DLL3 .

summary:
In Homo sapiens fetal retina, transition cell population 3 is characterized by high levels of FABP7, OTX2, and DLL3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:eaa69835b4d2d0b4d91a
claim_id: claim:eaa69835b4d2d0b4d91a
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
It is therefore quite interesting that one of the most characteristic genes of the T1 cell population is HES6 , which inhibits the function of HES1/5 ( Bae et al., 2000 ; Jhas et al., 2006 ).

summary:
In Homo sapiens fetal retina, one of the most characteristic genes of transition cell population 1 is HES6.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:a1f0f621527bbd13e8b8
claim_id: claim:a1f0f621527bbd13e8b8
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
T1 and T3 cells also express DLL3 , which inhibits Notch in a cell-autonomous manner by targeting it for lysosomal degradation in the late endocytic compartment ( Chapman et al., 2011 ).

summary:
In Homo sapiens fetal retina, transition cell population 1 and transition cell population 3 express DLL3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:cf6667e73d9f5a836f20
claim_id: claim:cf6667e73d9f5a836f20
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
summary: In Homo sapiens fetal retina, transition cell population 2 expresses PTF1A.
span_literal:
In addition, T2 cells express PTF1A , which is critical for the specification of inhibitory neurons in many areas of the CNS, including the retina, and functions in part by competing with Notch for RBPJ ( Hori et al., 2008 ) a necessary co-factor for Notch signaling.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:9cc95a7b1f51754a60c0
claim_id: claim:9cc95a7b1f51754a60c0
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
IF analysis shows that most of the ATOH7+ cells (red) are not positive for VSX2 (blue, white arrows), a progenitor marker, but occasionally overlap with the ganglion cell marker SNCG (green).

summary:
In Homo sapiens fetal retina, VSX2 is a progenitor cell marker and SNCG is a retinal ganglion cell marker.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:f832932b8102710b08b6
claim_id: claim:f832932b8102710b08b6
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
now amacrine cells (ACs) and horizontal cells (HCs) form distinct clusters ( TFAP2A, ONECUT2 ; feature plots in Figure S2A ).

summary:
In Homo sapiens fetal retina, amacrine cells and horizontal cells form distinct clusters identified by TFAP2A and ONECUT2.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:d6e9971fb4d43328eae4
claim_id: claim:d6e9971fb4d43328eae4
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
Although there are still some cells with a progenitor profile of gene expression in late-staged organoids ( Figure 6B , ASCL1 ), there is now a large number of cells we identified as Müller glia ( Figure 6A , dark blue), based on their expression of RLBP1 , AQP4 , and SLC1A3 ( Figure 6B ; Figure S5D ).

summary:
In Homo sapiens retinal organoids, retinal progenitor cells express ASCL1, while Müller glia are identified by expression of RLBP1, AQP4, and SLC1A3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:0eab2effb53ed1c6b8e1
claim_id: claim:0eab2effb53ed1c6b8e1
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal: ATOH7 T1 cells
summary:
In Homo sapiens fetal retina, ATOH7 marks transition cell population 1, PRDM13 marks transition cell population 2, and FABP7 marks transition cell population 3.


claim_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119:claim:47874061dc627a111791
claim_id: claim:47874061dc627a111791
paper_key: hca:0330_10.1016_j.celrep.2020.01.007_2459125119
span_literal:
Feature plots showing the T1 marker ATOH7 , bipolar markers ( VSX1 and GRM6 ), Mùller glia markers ( RLBP1 and SLC1A3 ), and rods ( NRL ).

summary:
In Homo sapiens retina, ATOH7 is a marker of transition cell population 1, VSX1 and GRM6 are markers of bipolar cells, RLBP1 and SLC1A3 are markers of Müller glia, and NRL is a marker of rod photoreceptors.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:d7d34d4b4885f051ca9b
claim_id: claim:d7d34d4b4885f051ca9b
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
We identified a population of fibroblasts by the expression of THY1, MCAM and that of odontoblasts by the expression of ALPL, OMD , and CCL2 , which were exclusively found in the dental pulp

summary:
In Homo sapiens dental pulp, fibroblasts are identified by the expression of THY1 and MCAM, and odontoblasts are identified by the expression of ALPL, OMD, and CCL2.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:35dab054153965a3f98f
claim_id: claim:35dab054153965a3f98f
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
the immune cells such as T cells ( CD3D ), NK cells ( GNLY and FCGR3A ) cells and monocytes ( CD14 ) were found in all the three tissues

summary:
In Homo sapiens, T cells are identified by the expression of CD3D, natural killer cells by GNLY and FCGR3A, and monocytes by CD14.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:80d621c76050e9367cc8
claim_id: claim:80d621c76050e9367cc8
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
we were also able to identify hematopoietic stem cells (HSCs) based on the expression of CD34, ENG and VCAM1 in both the dental pulp and bone marrow samples, but not in the PBMCs

summary:
In Homo sapiens, hematopoietic stem cells are identified by the expression of CD34, ENG, and VCAM1 in dental pulp and bone marrow.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:51dff48e238cd935fb82
claim_id: claim:51dff48e238cd935fb82
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
in our study we identified fibroblasts by the expression of THY1 , and MCAM , which were also considered markers for mesenchymal stem cells (MSCs) in earlier studies

summary:
In Homo sapiens, fibroblasts are identified by the expression of THY1 and MCAM, which were also considered markers for mesenchymal stem cells.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:023e6ec1e7a6586bc71b
claim_id: claim:023e6ec1e7a6586bc71b
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
summary: In Homo sapiens, odontoblasts express odontogenesis-associated genes such as OMD, ALPL, and DMP1.
span_literal:
We found heterogeneous populations of odontoblasts with varying degrees of gene expression associated with odontogenesis, such as OMD, ALPL and DMP1


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:5e1312f08dc92a3ed3d8
claim_id: claim:5e1312f08dc92a3ed3d8
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
Endothelial cells were identified by the expression of SELE and PECAM1 and hematopoietic stem cells (HSCs) in the adjacent cluster were annotated by the expression of CD34, ENG and VCAM1

summary:
In Homo sapiens dental pulp, endothelial cells are identified by the expression of SELE and PECAM1, and hematopoietic stem cells are annotated by the expression of CD34, ENG, and VCAM1.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:95161e1a60f0927460fb
claim_id: claim:95161e1a60f0927460fb
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
Endothelial cells were identified by the expression of SELE and PECAM1 and hematopoietic stem cells (HSCs) in the adjacent cluster were annotated by the expression of CD34, ENG and VCAM1

summary:
In Homo sapiens dental pulp, hematopoietic stem cells are annotated by the expression of CD34, ENG, and VCAM1.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:2365d3a879ce4e893f6f
claim_id: claim:2365d3a879ce4e893f6f
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
Global differential gene expression analysis showed the upregulation of B cell and plasma cell-related genes such as IGHG1, IGHG2, IGLC1 and IGKC in the deep dental caries, which fell in line with the enriched B-cell and plasma cell numbers

summary:
In Homo sapiens dental pulp with deep dental caries, B cells and plasma cells show upregulation of IGHG1, IGHG2, IGLC1, and IGKC.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:3922f36785df6a8abcfb
claim_id: claim:3922f36785df6a8abcfb
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
Global differential gene expression analysis showed the upregulation of B cell and plasma cell-related genes such as IGHG1, IGHG2, IGLC1 and IGKC in the deep dental caries, which fell in line with the enriched B-cell and plasma cell numbers

summary:
In Homo sapiens dental pulp with deep dental caries, plasma cells show upregulation of IGHG1, IGHG2, IGLC1, and IGKC.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:421be604f277a06768ee
claim_id: claim:421be604f277a06768ee
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
HSCs also showed the upregulation of proinflammatory mediators, including IL6 and CXCL8 specifically in the deep dental caries

summary:
In Homo sapiens dental pulp with deep dental caries, hematopoietic stem cells show upregulation of the proinflammatory mediators IL6 and CXCL8.


claim_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6:claim:3fd072ba4a9ab5312e33
claim_id: claim:3fd072ba4a9ab5312e33
paper_key: hca:0331_10.3389_fdmed.2021.806294_aea78ef1b6
span_literal:
Macrophage activation was also evident by the upregulation of genes related to antigen presentation such as HLA-DPA1, HLA-DPB1, HLA-DQA2 and CD74

summary:
In Homo sapiens dental pulp, macrophage activation is evident by the upregulation of antigen presentation genes HLA-DPA1, HLA-DPB1, HLA-DQA2, and CD74.


claim_key: hca:0333_10.1101_2022.03.25.485846_ff3d78f96d:claim:e302ee3927a30384be7d
claim_id: claim:e302ee3927a30384be7d
paper_key: hca:0333_10.1101_2022.03.25.485846_ff3d78f96d
summary: In Homo sapiens, a subtype of dopaminergic neuron in the substantia nigra is enriched for RIT2.
span_literal:
we identified three molecularly distinct subtypes of DA-related neurons, including a RIT2 -enriched population, in human aged SN.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:2decbe37e589341c3ba3
claim_id: claim:2decbe37e589341c3ba3
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
Monocyte 1 strongly expressed FCGR3A (CD16) and was most similar to CD16-positive, proinflammatory, nonclassic monocytes.

summary:
In Homo sapiens, nonclassical monocytes strongly express FCGR3A (CD16) in a kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:382d484aed0fab9e4147
claim_id: claim:382d484aed0fab9e4147
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
Interestingly, ABCA1 , which mediates sterol efflux in activated dendritic cells (DCs), 20 , 21 was uniquely detected in monocyte 1

summary:
In Homo sapiens, ABCA1 was uniquely detected in monocyte 1, a nonclassical monocyte subtype differentiating toward a dendritic cell phenotype in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:cf79d3f514ae0e99e1ce
claim_id: claim:cf79d3f514ae0e99e1ce
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
a panel of DC maturation markers, including APOE , 22 PDE3A , IGKC , 23 LGMN , and i CD83 , 24 suggesting differentiation into DC in situ

summary:
In Homo sapiens, monocyte 1 expressed dendritic cell maturation markers including APOE, PDE3A, IGKC, LGMN, and CD83, suggesting differentiation into dendritic cells.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:031b93794324b6eff7f1
claim_id: claim:031b93794324b6eff7f1
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
Violin plot showing that FCGR3A (CD16) distinguishes monocyte 1 from monocyte 2, whereas FCN1 is expressed in monocyte 2 but not monocyte 1.

summary:
In Homo sapiens, FCGR3A (CD16) distinguishes monocyte 1 from monocyte 2, whereas FCN1 is expressed in monocyte 2 but not monocyte 1 in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:c9537b105e19d434b11e
claim_id: claim:c9537b105e19d434b11e
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal: MSR1 is expressed in both clusters.
summary:
In Homo sapiens, MSR1 is expressed in both monocyte 1 and monocyte 2 clusters in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:46eedaa94d209674e14e
claim_id: claim:46eedaa94d209674e14e
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal: MSR1 is expressed in both clusters.
summary:
In Homo sapiens, MSR1 is expressed in both monocyte 2 and monocyte 1 clusters in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:67beb3fc1ef48cff7d24
claim_id: claim:67beb3fc1ef48cff7d24
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
collecting duct epithelia express KITLG , also known as stem cell factor, which binds the transmembrane receptor encoded by KIT and is expressed on mast cells in the biopsy

summary:
In Homo sapiens, collecting duct epithelial cells express KITLG (stem cell factor), and mast cells express KIT in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:55fd3eb74ab442fe2c93
claim_id: claim:55fd3eb74ab442fe2c93
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
collecting duct epithelia express KITLG , also known as stem cell factor, which binds the transmembrane receptor encoded by KIT and is expressed on mast cells in the biopsy

summary:
In Homo sapiens, mast cells express KIT in the kidney allograft biopsy, and collecting duct epithelial cells express its ligand KITLG.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:b787c16df7f393b64ce2
claim_id: claim:b787c16df7f393b64ce2
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
the predominant EC cluster was in the resting state, because it expressed EC markers ( PECAM1 , VWF , and ENG ) but no transcripts previously associated with ABMR or angiogenesis

summary:
In Homo sapiens, resting endothelial cells express the markers PECAM1, VWF, and ENG in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:d4bbbf76298b6d9c655d
claim_id: claim:d4bbbf76298b6d9c655d
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal: The genes SEMA3G , IGFBP3 , SERPINE2 , and AQP1 indicate activation of an angiogenic program.
summary:
In Homo sapiens, the genes SEMA3G, IGFBP3, SERPINE2, and AQP1 indicate activation of an angiogenic program in angiogenic endothelial cells of the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:eda874def0a25bafc1b3
claim_id: claim:eda874def0a25bafc1b3
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
A separate EC subcluster expresses Igs as well as markers of endoplasmic reticulum stress (XBP1) and cold shock (RBM3).

summary:
In Homo sapiens, a separate endothelial cell subcluster expresses markers of endoplasmic reticulum stress XBP1 and cold shock gene RBM3 in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:65ccee94d6cdc2e1c2e9
claim_id: claim:65ccee94d6cdc2e1c2e9
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal: Consistent with this, FYN is highly expressed in this EC subcluster.
summary:
In Homo sapiens, FYN is highly expressed in the immunoglobulin-internalizing endothelial cell subcluster of the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:ab456d140d7c2ae50170
claim_id: claim:ab456d140d7c2ae50170
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
summary: In Homo sapiens, pericytes highly express RGS5 and CACNA1C in the kidney allograft biopsy.
span_literal:
Cluster 1 highly expresses RSG5 , a pericyte marker, 39 as well as CACNA1C , which is expressed in a pericyte pattern.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:bef4ba705478df80ec46
claim_id: claim:bef4ba705478df80ec46
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
summary: In Homo sapiens, fibroblasts (stromal cluster 2) express MOXD1 in the kidney allograft biopsy.
span_literal:
Stromal cluster 2 expresses MoxD1 , a gene upregulated in early kidney transplant biopsies and associated with subsequent fibrosis.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:50a1fe1521b6dd362a8e
claim_id: claim:50a1fe1521b6dd362a8e
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
summary: In Homo sapiens, myofibroblasts uniquely express COL8A1 and COL12A1 in the kidney allograft biopsy.
span_literal:
The third stromal cluster uniquely expressed COL8A1 and COL12A1 , two genes that we have previously shown to be strongly upregulated in kidney myofibroblasts during fibrotic injury, suggesting a myofibroblast identity for this cluster.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:3d12fea0dbc01960e1c7
claim_id: claim:3d12fea0dbc01960e1c7
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
The B cell cluster expressed few Ig genes but did express genes involved in antigen presentation ( CD86 ) and T cell regulation (indoleamine 2,3-dioxygenase, IDO1 ), thus behaving like a naïve B cell.

summary:
In Homo sapiens, the naïve B cell cluster expressed CD86 (involved in antigen presentation) and IDO1 (indoleamine 2,3-dioxygenase, involved in T cell regulation) in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:e6ad0e53cd2bc11fb505
claim_id: claim:e6ad0e53cd2bc11fb505
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
In addition, DCN and COL6A1 are expressed in both fibroblast and myofibroblast populations, whereas SPARC , BGN , and COL6A2 are expressed in all three stromal cell types.

summary:
In Homo sapiens, DCN and COL6A1 are expressed in both fibroblast and myofibroblast populations, whereas SPARC, BGN, and COL6A2 are expressed in all three stromal cell types (pericyte, fibroblast, and myofibroblast) in the kidney allograft biopsy.


claim_key: hca:0334_10.1681_asn.2018020125_804c4742d9:claim:c01358e81f041822cc1f
claim_id: claim:c01358e81f041822cc1f
paper_key: hca:0334_10.1681_asn.2018020125_804c4742d9
span_literal:
In addition, DCN and COL6A1 are expressed in both fibroblast and myofibroblast populations, whereas SPARC , BGN , and COL6A2 are expressed in all three stromal cell types.

summary:
In Homo sapiens, DCN and COL6A1 are expressed in both myofibroblast and fibroblast populations, whereas SPARC, BGN, and COL6A2 are expressed in all three stromal cell types in the kidney allograft biopsy.


