# claims

claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:2a469474cbe97de7ebdf
claim_id: claim:2a469474cbe97de7ebdf
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
span_literal:
On the other hand, pGC, mural GC, and other cell populations in the ovary expressed CD55 and CD59 , known to protect against targeting and damage by the complement cascade (Fig. 9a ), suggesting a concerted mechanism involving the complement system to allow growth and degeneration of the different follicular compartments in a timely manner.

summary:
In Homo sapiens adult ovary, mural granulosa cells express CD55 and CD59, known to protect against complement cascade damage.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:9440d9a1cfee0d9a1c2c
claim_id: claim:9440d9a1cfee0d9a1c2c
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
span_literal:
Note that some of the innate immune cells expressed high levels of CD68 and IFI30 , as well as complement component C1QA (Fig. 9f, g ).

summary:
In Homo sapiens adult ovary, innate immune cells express high levels of CD68, IFI30, and complement component C1QA.


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:995952d7a7655735b2d3
claim_id: claim:995952d7a7655735b2d3
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
summary: In Homo sapiens adult ovary, B lymphocytes express high levels of JCHAIN and IGKC.
span_literal:
B lymphocytes expressed high levels of JCHAIN and IGKC (Fig. 9h ) and T lymphocytes (and NK cells) expressed IL7R , LTB , CCL5 , and NKG7 (Fig. 9i ).


claim_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f:claim:eb0773c49422800a7280
claim_id: claim:eb0773c49422800a7280
paper_key: hca:0403_10.1038_s41467-019-11036-9_eff650140f
span_literal:
B lymphocytes expressed high levels of JCHAIN and IGKC (Fig. 9h ) and T lymphocytes (and NK cells) expressed IL7R , LTB , CCL5 , and NKG7 (Fig. 9i ).

summary:
In Homo sapiens adult ovary, T lymphocytes and natural killer cells express IL7R, LTB, CCL5, and NKG7.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:cc81bfe262cf953348dc
claim_id: claim:cc81bfe262cf953348dc
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
Germ ( DAZL + ) and supporting ( GATA4 + , WNT6 + ) cells are present exclusively within the gonads, whereas other cell types, including coelomic epithelial ( UPK3B + ) and mesenchymal ( PDGFRA + ) cells, are present in both the gonads and the mesonephros (extragonadal tissue)

summary:
In Homo sapiens, germ cells are marked by DAZL expression, supporting cells by GATA4 and WNT6 expression, coelomic epithelial cells by UPK3B expression, and mesenchymal cells by PDGFRA expression in the developing gonad.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:03b8a407b9788625ed74
claim_id: claim:03b8a407b9788625ed74
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
In humans, the coelomic epithelium and ESGCs are connected through an early somatic cell population that downregulates mesothelial markers ( UPK3B − , LRRN4 − ), upregulates supporting lineage markers ( WNT6 + ) and shares TFs with undifferentiated gonadal interstitial (Gi) cells ( ARX + , TCF21 + ; Fig. 2b ).

summary:
In Homo sapiens, the early somatic cell population downregulates mesothelial markers UPK3B and LRRN4, upregulates the supporting lineage marker WNT6, and shares transcription factors ARX and TCF21 with undifferentiated gonadal interstitial cells.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:0d56a15c5bf1b5b5cd0e
claim_id: claim:0d56a15c5bf1b5b5cd0e
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
Next, human and mouse ESGCs downregulate LHX9 and interstitial TFs ( ARX − , TCF21 − ) while further upregulating the supporting lineage marker WNT6 .

summary:
In Homo sapiens, early supporting gonadal cells downregulate LHX9, ARX, and TCF21 while upregulating the supporting lineage marker WNT6.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:6c6a4c14336360dfd7c1
claim_id: claim:6c6a4c14336360dfd7c1
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
We define a supporting-like PAX8 + population (sPAX8s) expressing gonadal ( GATA4 + , LHX9 + and NR5A1 + ) and supporting ( WNT6 + ) markers that emerges with the first wave of supporting cells in humans and mice

summary:
In Homo sapiens, the supporting-like PAX8-positive population (sPAX8) expresses gonadal markers GATA4, LHX9, and NR5A1, as well as the supporting marker WNT6.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:bf2b96061e2f593076aa
claim_id: claim:bf2b96061e2f593076aa
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
We defined two testis-specific macrophage populations using scRNA-seq and validated them with smFISH: (1) SIGLEC15 + fetal testicular macrophages (ftMs), with an osteoclast-like signature ( SIGLEC15 , ACP5 , ATP6V0D2 ; refs. 24 – 27 ) and (2) TREM2 + ftMs, with a microglia-like signature ( TREM2, P2RY12 , SALL1 ; refs. 28 – 30 )

summary:
In Homo sapiens, SIGLEC15-positive fetal testicular macrophages have an osteoclast-like signature marked by SIGLEC15, ACP5, and ATP6V0D2, while TREM2-positive fetal testicular macrophages have a microglia-like signature marked by TREM2, P2RY12, and SALL1.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:959af0456c66fa451ba4
claim_id: claim:959af0456c66fa451ba4
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
We defined two testis-specific macrophage populations using scRNA-seq and validated them with smFISH: (1) SIGLEC15 + fetal testicular macrophages (ftMs), with an osteoclast-like signature ( SIGLEC15 , ACP5 , ATP6V0D2 ; refs. 24 – 27 ) and (2) TREM2 + ftMs, with a microglia-like signature ( TREM2, P2RY12 , SALL1 ; refs. 28 – 30 )

summary:
In Homo sapiens, TREM2-positive fetal testicular macrophages have a microglia-like signature marked by TREM2, P2RY12, and SALL1.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:15a68412102f9bfc6d25
claim_id: claim:15a68412102f9bfc6d25
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
With the aid of structural gonadal markers, smFISH imaging located tissue-repair macrophages ( CD68 + , F13A1 + ) and SIGLEC15 + ftMs ( CD68 + , SIGLEC15 + ) in the interstitial space ( PDGFRA + or NR2F2 + )

summary:
In Homo sapiens, tissue-repair macrophages are marked by CD68 and F13A1 expression, while SIGLEC15-positive fetal testicular macrophages are marked by CD68 and SIGLEC15 expression in the gonadal interstitial space.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:9d07417c2e1d21039d4b
claim_id: claim:9d07417c2e1d21039d4b
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
With the aid of structural gonadal markers, smFISH imaging located tissue-repair macrophages ( CD68 + , F13A1 + ) and SIGLEC15 + ftMs ( CD68 + , SIGLEC15 + ) in the interstitial space ( PDGFRA + or NR2F2 + )

summary:
In Homo sapiens, SIGLEC15-positive fetal testicular macrophages are marked by CD68 and SIGLEC15 expression in the gonadal interstitial space.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:33f020901b05e06e20ba
claim_id: claim:33f020901b05e06e20ba
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
SIGLEC15 + ftMs express LGALS9 and SPP1, in keeping with a potential immunoregulatory role for this cell type

summary:
In Homo sapiens, SIGLEC15-positive fetal testicular macrophages express LGALS9 and SPP1, consistent with an immunoregulatory role.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:24695fa2ef9d9ebbaf2b
claim_id: claim:24695fa2ef9d9ebbaf2b
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
SIGLEC15 + ftMs also express the remodelling molecule MMP9 and their numbers decrease in later stages of development

summary:
In Homo sapiens, SIGLEC15-positive fetal testicular macrophages express the remodelling molecule MMP9.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:f7263ecf5f7c3116a1c8
claim_id: claim:f7263ecf5f7c3116a1c8
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
SIGLEC15 + ftMs are close to endothelial cells ( CDH5 + ) in the testes (Fig. 5d ) and express COL1A2 , which can potentially interact with the integrins (α1/β1, α2/β1, α10/β1 and α11/β1) expressed by endothelial and mesenchymal cells

summary:
In Homo sapiens, SIGLEC15-positive fetal testicular macrophages express COL1A2, and endothelial cells are marked by CDH5 expression in the testes.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:fb9c9ca92ae01f0c70c9
claim_id: claim:fb9c9ca92ae01f0c70c9
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal: TREM2 + ftMs also have their phagocytosis machinery active ( MERTK , AXL , CYBB , BECN1 , MTOR )
summary:
In Homo sapiens, TREM2-positive fetal testicular macrophages express phagocytosis-related genes MERTK, AXL, CYBB, BECN1, and MTOR.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:e59448441370fa760039
claim_id: claim:e59448441370fa760039
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
TREM2 + ftMs also have their phagocytosis machinery active ( MERTK , AXL , CYBB , BECN1 , MTOR ) (Extended Data Fig. 9l ) and express immunomodulatory molecules ( HAVCR2 , ENTPD1 , CD276 , IL10 , TREM2 )

summary:
In Homo sapiens, TREM2-positive fetal testicular macrophages express immunomodulatory molecules HAVCR2, ENTPD1, CD276, IL10, and TREM2.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:08749b341077239e78b8
claim_id: claim:08749b341077239e78b8
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
ESGCs are the first cells to express the testis-determining factor SRY in XY gonads and, in humans, express stem-cell markers such as TSPAN8 and LGR5 .

summary:
In Homo sapiens, early supporting gonadal cells are the first cells to express the testis-determining factor SRY in XY gonads and express stem-cell markers TSPAN8 and LGR5.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:af768edd72b21c200dfb
claim_id: claim:af768edd72b21c200dfb
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
PreGC-IIa coappear in space (outer cortex) and time (mid-8 PCW) with OSE ( UPK3B + , LHX2 + , IRX3 + ), and express the retinoic acid inhibitor CYP26B1 (meiosis inhibitor) as well as low amounts of FOXL2 .

summary:
In Homo sapiens, ovarian surface epithelium is marked by UPK3B, LHX2, and IRX3 expression, while pregranulosa cell type IIa expresses the retinoic acid inhibitor CYP26B1 and low amounts of FOXL2.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:dacdc3949ef458a64f95
claim_id: claim:dacdc3949ef458a64f95
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
PreGC-IIa coappear in space (outer cortex) and time (mid-8 PCW) with OSE ( UPK3B + , LHX2 + , IRX3 + ), and express the retinoic acid inhibitor CYP26B1 (meiosis inhibitor) as well as low amounts of FOXL2 .

summary:
In Homo sapiens, pregranulosa cell type IIa expresses the retinoic acid inhibitor CYP26B1 and low amounts of FOXL2 in the outer ovarian cortex.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:b24a8132e5f30dcdadf1
claim_id: claim:b24a8132e5f30dcdadf1
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
developing granulosa cells expressing folliculogenesis markers ( NOTCH3 + , HEYL + ) and retinol dehydrogenase ( RDH10

summary:
In Homo sapiens, developing granulosa cells express folliculogenesis markers NOTCH3 and HEYL, as well as retinol dehydrogenase RDH10 in the inner ovarian cortex.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:be0fea497626c1343d52
claim_id: claim:be0fea497626c1343d52
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal: OSE activates the primate-specific TF LHX2 , which is kept active in preGC-IIa (Fig. 4c ).
summary:
In Homo sapiens, ovarian surface epithelium activates the transcription factor LHX2, which remains active in pregranulosa cell type IIa.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:cc1dacb4a41103473ec2
claim_id: claim:cc1dacb4a41103473ec2
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal: OSE activates the primate-specific TF LHX2 , which is kept active in preGC-IIa (Fig. 4c ).
summary:
In Homo sapiens, pregranulosa cell type IIa maintains active expression of the transcription factor LHX2.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:debff740ec16b05855a8
claim_id: claim:debff740ec16b05855a8
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
As they differentiate, preGC-IIb cells upregulate FOXL2 and express WNT-induced TFs ( HIF1A + , FOXO1 + , FOXP1 + ), a programme shared by medullary preGC-Is, suggesting there is a higher WNT environment deeper in the ovary.

summary:
In Homo sapiens, pregranulosa cell type IIb upregulates FOXL2 and expresses WNT-induced transcription factors HIF1A, FOXO1, and FOXP1, a programme shared by medullary pregranulosa cell type I.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:08e08d0f42e481efbbba
claim_id: claim:08e08d0f42e481efbbba
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
In the medulla, preGC-Is upregulate enzymes involved in oestrogen production ( HSD17B6 and CYP19A1 ).

summary:
In Homo sapiens, pregranulosa cell type I upregulates enzymes involved in oestrogen production, HSD17B6 and CYP19A1, in the ovarian medulla.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:e9d6666aba7d64cf08fc
claim_id: claim:e9d6666aba7d64cf08fc
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
Human female ESGCs also upregulate OSR1 , characteristic of preGC-I, which is notably absent in mice

summary:
In Homo sapiens, female early supporting gonadal cells upregulate OSR1, which is characteristic of pregranulosa cell type I.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:45c6ac48cf7ac86f3425
claim_id: claim:45c6ac48cf7ac86f3425
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
PreGC-IIa cells, present in the outer ovarian cortex, express chemoattractants (for example, NRG1 ) and survival factors (for example, KITLG ), with STAT3 downstream of KIT active in PGCs

summary:
In Homo sapiens, pregranulosa cell type IIa expresses the chemoattractant NRG1 and the survival factor KITLG, while STAT3 downstream of KIT is active in primordial germ cells.


claim_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2:claim:e7f381e0b6a72dc7868b
claim_id: claim:e7f381e0b6a72dc7868b
paper_key: hca:0404_10.1038_s41586-022-04918-4_6a15fd8ba2
span_literal:
PreGC-IIb cells, located in the inner cortex, express ligands involved in meiosis initiation (for example, retinoic acid by ALDH1A1 ) and oogenesis (for example, BMP2 ) to support PGC differentiation.

summary:
In Homo sapiens, pregranulosa cell type IIb expresses ALDH1A1 involved in retinoic acid production for meiosis initiation and BMP2 for oogenesis.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:04e37ec634183465a1e3
claim_id: claim:04e37ec634183465a1e3
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
We detected 5 CD8 + T cell clusters ( Figure 2D ), with three characterized by expression of activation and exhaustion markers PDCD1 , LAG3 , HAVCR2 , and TOX among others

summary:
In Homo sapiens clear cell renal cell carcinoma, CD8-positive T cell clusters are characterized by expression of the activation and exhaustion markers PDCD1, LAG3, HAVCR2, and TOX.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:b75768eaeb37a4d2cedc
claim_id: claim:b75768eaeb37a4d2cedc
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
CD8A + Proliferating”) expressed genes associated with cell cycling and proliferation, e.g. MKI67 , TOP2A , and STMN1

summary:
In Homo sapiens clear cell renal cell carcinoma, CD8A-positive proliferating T cells express genes associated with cell cycling and proliferation such as MKI67, TOP2A, and STMN1.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:d78f7cc3281195e72f2a
claim_id: claim:d78f7cc3281195e72f2a
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
CD8A + Exhausted Immediate Early Genes (IEG)”) was distinguished by expression of genes induced early after activation, e.g. JUNB , FOS , ATF3 , HSPA1A , and DNAJB1

summary:
In Homo sapiens clear cell renal cell carcinoma, CD8A-positive exhausted immediate early genes T cells are distinguished by expression of JUNB, FOS, ATF3, HSPA1A, and DNAJB1.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:a8d2559ff9da9ad1f73b
claim_id: claim:a8d2559ff9da9ad1f73b
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
This third cluster also demonstrated high expression of the transcription factor NR4A1 , previously linked to T cell dysfunction

summary:
In Homo sapiens clear cell renal cell carcinoma, CD8A-positive exhausted immediate early genes T cells demonstrate high expression of the transcription factor NR4A1.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:155a869ff0d8e1a52d05
claim_id: claim:155a869ff0d8e1a52d05
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal: One expressed the tissue-residency markers CD69 and ZNF683 and was termed CD8A + tissue-resident.
summary:
In Homo sapiens clear cell renal cell carcinoma, CD8A-positive tissue-resident T cells express the tissue-residency markers CD69 and ZNF683.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:9639ab0da559f4bb466c
claim_id: claim:9639ab0da559f4bb466c
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
we observed a CD3D + CD8 + T cell cluster marked by high expression of genes typically associated with NK cell activity, e.g. KLRB1 , FCGR3A , GZMH , and GNLY

summary:
In Homo sapiens clear cell renal cell carcinoma, NK-like T cells are marked by high expression of KLRB1, FCGR3A, GZMH, and GNLY.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:5b33c52a71c115f19c1a
claim_id: claim:5b33c52a71c115f19c1a
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
We identified a cluster of regulatory T cells (“CD4 + Treg”) characterized by expression of the transcription factor FOXP3 , as well BATF , CTLA4 , and TIGIT

summary:
In Homo sapiens clear cell renal cell carcinoma, CD4-positive regulatory T cells are characterized by expression of FOXP3, BATF, CTLA4, and TIGIT.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:6ebfa0bdda87d8e8ef97
claim_id: claim:6ebfa0bdda87d8e8ef97
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal: CD4 + effector”) was distinguished by expression of cytotoxic markers GZMA , GZMK , and NKG7
summary:
In Homo sapiens clear cell renal cell carcinoma, CD4-positive effector T cells are distinguished by expression of cytotoxic markers GZMA, GZMK, and NKG7.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:c212641928fd25c190d1
claim_id: claim:c212641928fd25c190d1
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
we observed a CD4 + naïve cluster primarily restricted to the blood, expressing high levels of TCF7 , CCR7 , and SELL

summary:
In Homo sapiens clear cell renal cell carcinoma, CD4-positive naïve T cells express high levels of TCF7, CCR7, and SELL.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:230decbf4204f07be7ad
claim_id: claim:230decbf4204f07be7ad
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
TAM HLA hi ”) demonstrated a classically immunosuppressive phenotype, with the highest expression of HLA-DR among all TAM clusters, complement genes (e.g. C1QA/B ), APOE , and TREM2

summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage HLA-high cells demonstrate the highest expression of HLA-DR, complement genes C1QA/B, APOE, and TREM2 among all tumor-associated macrophage clusters.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:05a6c24481ac3342cd1f
claim_id: claim:05a6c24481ac3342cd1f
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
The second demonstrated intermediate expression of HLA-DR (“TAM HLA int ”), and also expressed the immunosuppressive CD163 as well as CSF1R and heat shock proteins

summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage HLA-intermediate cells express CD163 and CSF1R.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:88c346fcee646dbc6dfd
claim_id: claim:88c346fcee646dbc6dfd
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal: We also observed expression of IL1A , SIGLEC1 ( CD169 ) and MRC1 ( CD206 ) in this cluster
summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage HLA-intermediate cells express IL1A, SIGLEC1, and MRC1.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:69d6b30e5c99451bf3c3
claim_id: claim:69d6b30e5c99451bf3c3
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
The third and fourth clusters (“TAM ISG hi ” and “TAM ISG int ) were defined by low expression of HLA-DR and varying levels of interferon signaling (ISG) genes, i.e. IFITM1 , IFITM3 , and IL1B

summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage interferon-stimulated gene-high cells are defined by varying levels of IFITM1, IFITM3, and IL1B.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:15b743c850f60a64cd51
claim_id: claim:15b743c850f60a64cd51
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
The third and fourth clusters (“TAM ISG hi ” and “TAM ISG int ) were defined by low expression of HLA-DR and varying levels of interferon signaling (ISG) genes, i.e. IFITM1 , IFITM3 , and IL1B

summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage interferon-stimulated gene-intermediate cells are defined by varying levels of IFITM1, IFITM3, and IL1B.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:c12e362d05f1deccb81f
claim_id: claim:c12e362d05f1deccb81f
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
TAM ISG hi and ISG int also expressed markers of genes associated with angiogenesis, e.g. FLT1 , SPARC , and RGS5

summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage interferon-stimulated gene-high cells express angiogenesis-associated genes FLT1, SPARC, and RGS5.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:ede75b583bea02b6f913
claim_id: claim:ede75b583bea02b6f913
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
TAM ISG hi and ISG int also expressed markers of genes associated with angiogenesis, e.g. FLT1 , SPARC , and RGS5

summary:
In Homo sapiens clear cell renal cell carcinoma, tumor-associated macrophage interferon-stimulated gene-intermediate cells express angiogenesis-associated genes FLT1, SPARC, and RGS5.


claim_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6:claim:99b6ae453cb35cce6d02
claim_id: claim:99b6ae453cb35cce6d02
paper_key: hca:0405_10.1016_j.ccell.2021.03.007_50f32173d6
span_literal:
We also found expression of the effector molecules IFNG , GZMH , PRF1 , and KLRG1 on these cells as well as CD44 , a hallmark of tissue-resident memory cells

summary:
In Homo sapiens clear cell renal cell carcinoma, CD8A-positive tissue-resident T cells express the effector molecules IFNG, GZMH, PRF1, and KLRG1 as well as CD44, a hallmark of tissue-resident memory cells.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:4831dcc088b394759124
claim_id: claim:4831dcc088b394759124
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
summary: In Homo sapiens midbrain, oligodendrocytes are characterized by the expression of MOBP.
span_literal:
Oligodendrocytes, the most abundant cell type in the midbrain ( Fig. 1F ), were characterized by the expression of MOBP .


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:fd75b4e3de91283a9e64
claim_id: claim:fd75b4e3de91283a9e64
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
summary: In Homo sapiens midbrain, astrocytes are characterized by expression of AQP4.
span_literal:
Expression of AQP4 was characteristic for astrocytes 37 and FOXJ1 for ependymal cells ( Fig. 1E–G and Supplementary Fig. 1C–I ).


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:049193d14e52b68e5eff
claim_id: claim:049193d14e52b68e5eff
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
summary: In Homo sapiens midbrain, microglia are marked by expression of CD74.
span_literal:
CD74 in microglia, 39 CLDN5 in endothelial cells, 40 , 41 and GFRB in pericytes 42 ( Fig. 1E–G and Supplementary Fig. 1C ).


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:514801c925252501851a
claim_id: claim:514801c925252501851a
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
summary: In Homo sapiens midbrain, excitatory neurons are marked by expression of SLC17A6.
span_literal:
Regarding neuronal cells, we identified four cell types: excitatory ( SLC17A6 ), 43 inhibitory ( GAD2 ), 43 GABAergic ( GAD2 / GRIK1 ) 44 , 45 and, dopaminergic neurons ( TH ) ( Fig. 1E–G and Supplementary Fig. 1C–I ).


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:ad7035e4d1874d8af7bd
claim_id: claim:ad7035e4d1874d8af7bd
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
we also found a neuronal cluster of 120 cells, which we could not annotate initially based on known marker genes, that was characterized by high expression of CADPS2 (CADPS2 high cells) ( Fig. 1E–F and H–I and Supplementary Fig. 1C and I ).

summary:
In Homo sapiens midbrain, the CADPS2 high neuronal cell cluster is characterized by high expression of CADPS2.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:66a694973c4810aca930
claim_id: claim:66a694973c4810aca930
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
summary: In Homo sapiens midbrain, CADPS2 high cells show low TH abundance compared to dopaminergic neurons.
span_literal:
With regard to neuronal markers, these cells show a similar profile to DaNs, except for low TH abundance ( Fig. 1I ).


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:9b216b7ab3206059705e
claim_id: claim:9b216b7ab3206059705e
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal: Moreover, CADPS2 high cells express even higher levels of TIAM1 than DaNs ( Fig. 1I ).
summary:
In Homo sapiens midbrain, CADPS2 high cells express higher levels of TIAM1 than dopaminergic neurons.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:f5bb4fb83246b7cb3d49
claim_id: claim:f5bb4fb83246b7cb3d49
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
The three biggest subpopulations are defined by the high expression of P2RY12 , GPNMB , and HSP90AA1 ( Fig. 3B ).

summary:
In Homo sapiens midbrain, the three biggest microglia subpopulations are defined by the high expression of P2RY12, GPNMB, and HSP90AA1.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:b867f9d9c45591d5c6b4
claim_id: claim:b867f9d9c45591d5c6b4
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
While P2RY12 is highly abundant in the resting microglia, 51 GPNMB, 52 HSP90, 53 and IL-1β 54 are involved in the inflammatory response and have previously been linked to neurodegeneration 53 , 55 , 56 supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation.

summary:
In Homo sapiens, P2RY12 is highly abundant in resting microglia, while GPNMB and HSP90AA1 are markers of microglial activation.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:54af2f046578d4fe8023
claim_id: claim:54af2f046578d4fe8023
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
While P2RY12 is highly abundant in the resting microglia, 51 GPNMB, 52 HSP90, 53 and IL-1β 54 are involved in the inflammatory response and have previously been linked to neurodegeneration 53 , 55 , 56 supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation.

summary:
In Homo sapiens, GPNMB and HSP90AA1 are markers of activated microglia in idiopathic Parkinson's disease.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:c50b389700ca6da0f8bc
claim_id: claim:c50b389700ca6da0f8bc
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
First, we identified five astrocyte subpopulations characterized by high expression of VAV3 , LRRC4C , ELMO1 , ADGRV1 and CD44 ( Fig. 4A and B ).

summary:
In Homo sapiens midbrain, five astrocyte subpopulations are characterized by high expression of VAV3, LRRC4C, ELMO1, ADGRV1, and CD44.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:ca8e82323ad0a33f5104
claim_id: claim:ca8e82323ad0a33f5104
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
We identified five subpopulations characterized by the expression of ATP6V02 , OPALIN , TRPM3 , ST6GAL1 , and RBFOX1 ( Fig. 4G and H ).

summary:
In Homo sapiens midbrain, five oligodendrocyte subpopulations are characterized by the expression of ATP6V02, OPALIN, TRPM3, ST6GAL1, and RBFOX1.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:03cb59c8ffb8a10ae06c
claim_id: claim:03cb59c8ffb8a10ae06c
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
OPALIN (also denominated as Tmem ) is a marker of myelinating oligodendrocytes, 63 while S100B has been associated with glial stress response in Parkinson’s disease post-mortem midbrain.

summary:
In Homo sapiens, OPALIN is a marker of myelinating oligodendrocytes, while S100B is associated with glial stress response.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:6aa053e0f58a44624d04
claim_id: claim:6aa053e0f58a44624d04
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson’s disease microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B , GPNMB and HSP90AA1 .

summary:
In Homo sapiens, reactive astrocytes show CD44 overexpression, while idiopathic Parkinson's disease microglia show elevated levels of IL1B, GPNMB, and HSP90AA1.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:3e0cfcca0f2046fafe37
claim_id: claim:3e0cfcca0f2046fafe37
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson’s disease microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B , GPNMB and HSP90AA1 .

summary:
In Homo sapiens, idiopathic Parkinson's disease microglia show a pro-inflammatory trajectory characterized by elevated levels of IL1B, GPNMB, and HSP90AA1.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:7d29b41b752d75865c70
claim_id: claim:7d29b41b752d75865c70
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
We discovered a neuronal cell cluster characterized by CADPS2 overexpression and low TH levels, which was exclusively present in idiopathic Parkinson’s disease midbrains.

summary:
In Homo sapiens midbrain, a neuronal cell cluster exclusively present in idiopathic Parkinson's disease is characterized by CADPS2 overexpression and low TH levels.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:65ff26ee1bfa2fbc60ac
claim_id: claim:65ff26ee1bfa2fbc60ac
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal:
We also discovered a reduction in idiopathic Parkinson’s disease oligodendrocyte numbers with the remaining cells being characterized by a stress-induced upregulation of S100B .

summary:
In Homo sapiens, idiopathic Parkinson's disease oligodendrocytes are characterized by a stress-induced upregulation of S100B.


claim_key: hca:0406_10.1093_brain_awab446_1c9ee67691:claim:59e919128a6c9f73e5d0
claim_id: claim:59e919128a6c9f73e5d0
paper_key: hca:0406_10.1093_brain_awab446_1c9ee67691
span_literal: They express MAP2 , SCN2A , and TIAM1 , but have low levels of TH .
summary:
In Homo sapiens midbrain, CADPS2 high cells express MAP2, SCN2A, and TIAM1, but have low levels of TH.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:a56564861a79b925e239
claim_id: claim:a56564861a79b925e239
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
span_literal:
The annotations were performed using differential gene expression analysis supported by known gene markers such as ACTA2 , CNN1 for SMCs, VWF and PECAM for endothelial cells (Endo), PDPN Lymphatic ECs, DCN and LUM for fibroblasts (Fibro), CD3D for T cells, MS4A1 and CD79A for B cells, GNLY and NKG7 for NK cells and CD14 and S100A8 for myeloid cells

summary:
In Homo sapiens, smooth muscle cells are marked by ACTA2 and CNN1 in myometrium and leiomyoma tissues.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:515064f0ce83272abe68
claim_id: claim:515064f0ce83272abe68
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
span_literal:
The annotations were performed using differential gene expression analysis supported by known gene markers such as ACTA2 , CNN1 for SMCs, VWF and PECAM for endothelial cells (Endo), PDPN Lymphatic ECs, DCN and LUM for fibroblasts (Fibro), CD3D for T cells, MS4A1 and CD79A for B cells, GNLY and NKG7 for NK cells and CD14 and S100A8 for myeloid cells

summary:
In Homo sapiens, lymphatic endothelial cells are marked by PDPN in myometrium and leiomyoma tissues.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:ed42d053d12d1942e1be
claim_id: claim:ed42d053d12d1942e1be
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
summary:
In Homo sapiens, natural killer cells are marked by GNLY and NKG7 in myometrium and leiomyoma tissues.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:b180cf8f580b8d9b5716
claim_id: claim:b180cf8f580b8d9b5716
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
span_literal:
The following signature markers were used to identify the cell clusters: SMCs ( MYH11 , TAGLN , ACTA2 , CNN1 , DES , CALD1 ), fibroblast cells ( VIM , ALDH1 , CD90 , FN1 , DCN , OGN , MGP , COL1A1 , COL1A2 , COL3A1 ), endothelial cells ( PECAM1 , CD31 , CDH11 , VWF ) and immune cells ( CD3D , CD3E , FCER1G , MS4A1 , CD79B , CST7 , GZMB , FCGF3A , MS4A7 ).

summary:
In Homo sapiens, smooth muscle cells are identified by the markers MYH11, TAGLN, ACTA2, CNN1, DES, and CALD1.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:d192f66fd5d07885b72b
claim_id: claim:d192f66fd5d07885b72b
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
span_literal:
The following signature markers were used to identify the cell clusters: SMCs ( MYH11 , TAGLN , ACTA2 , CNN1 , DES , CALD1 ), fibroblast cells ( VIM , ALDH1 , CD90 , FN1 , DCN , OGN , MGP , COL1A1 , COL1A2 , COL3A1 ), endothelial cells ( PECAM1 , CD31 , CDH11 , VWF ) and immune cells ( CD3D , CD3E , FCER1G , MS4A1 , CD79B , CST7 , GZMB , FCGF3A , MS4A7 ).

summary:
In Homo sapiens, fibroblast cells are identified by the markers VIM, ALDH1, CD90, FN1, DCN, OGN, MGP, COL1A1, COL1A2, and COL3A1.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:40bcee5f0d7985fe8f5a
claim_id: claim:40bcee5f0d7985fe8f5a
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
summary:
In Homo sapiens, immune cells are identified by the markers CD3D, CD3E, FCER1G, MS4A1, CD79B, CST7, GZMB, FCGF3A, and MS4A7.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:8a1f87fc41222507f35c
claim_id: claim:8a1f87fc41222507f35c
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
span_literal:
Fibro cluster 0 identified by the expression of SERPINE1 , IER2 and NR4A1 significantly resembled myofibroblast due to co-expression of SMC markers ( CARMN , DES) as well as fibroblast cell markers ( DCN ) .

summary:
In Homo sapiens, fibroblast cluster 0 is identified by the expression of SERPINE1, IER2, NR4A1, CARMN, DES, and DCN.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:ace92b2ae0263f9268ac
claim_id: claim:ace92b2ae0263f9268ac
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
span_literal:
Fibro cluster 1 (expressing FAP gene) was linked to integrin pathway and axon guidance, while fibro cluster 2 (expressing SFRP2 and PI16 genes) was enriched in terms related to the regulation of extracellular matrix organization, regulation of insulin growth factor transport and uptake by insulin growth factor binding proteins

summary:
In Homo sapiens, fibroblast cluster 1 is marked by expression of FAP, while fibroblast cluster 2 is marked by expression of SFRP2 and PI16.


claim_key: hca:0407_10.1093_humrep_deac183_7b0f560d74:claim:6001d9d134124cd12c5c
claim_id: claim:6001d9d134124cd12c5c
paper_key: hca:0407_10.1093_humrep_deac183_7b0f560d74
summary: In Homo sapiens, vein endothelial cells (Cluster 0 and 4) are marked by ACKR1.
span_literal:
Based on the differential gene expression, we identified these endothelial cell clusters as veins (Cluster 0 and 4; ACKR1 +), arteries (Cluster 1; GJA5 ), Lymphatic ECs (Cluster 2 and 8; PDPN ), capillaries (Cluster 5; RGCC ), tip cells (Cluster 7; CXCR4 ) and vascular endothelial cells (Cluster 3 and 6; MYH11 , FLNA ).


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:0f5016ea4ff1b02984d7
claim_id: claim:0f5016ea4ff1b02984d7
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Hereditary CP cells mainly consisted of CD4+ helper T cell (Th) subpopulations including CCR6+, TNF+ (Th1), regulatory T (Treg) cells, and HLA-DA+ CD8+ T cells.

summary:
In Homo sapiens hereditary chronic pancreatitis pancreas, CCR6 is a positive marker of a CD4+ helper T cell subpopulation.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:924de1752f158ce0817d
claim_id: claim:924de1752f158ce0817d
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Hereditary CP cells mainly consisted of CD4+ helper T cell (Th) subpopulations including CCR6+, TNF+ (Th1), regulatory T (Treg) cells, and HLA-DA+ CD8+ T cells.

summary:
In Homo sapiens hereditary chronic pancreatitis pancreas, TNF is a positive marker of T helper 1 cells.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:ad016b9a34be6dc3daeb
claim_id: claim:ad016b9a34be6dc3daeb
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Hereditary CP cells mainly consisted of CD4+ helper T cell (Th) subpopulations including CCR6+, TNF+ (Th1), regulatory T (Treg) cells, and HLA-DA+ CD8+ T cells.

summary:
In Homo sapiens hereditary chronic pancreatitis pancreas, HLA-DA is a positive marker of CD8+ T cells.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:28d484d35a2d39134563
claim_id: claim:28d484d35a2d39134563
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
However, FTH1+ CD4+ or CD8+ T cells were predominant T cells in idiopathic CP (online supplemental figure 6D, E).

summary:
In Homo sapiens idiopathic chronic pancreatitis pancreas, FTH1 is a positive marker of CD4+ T cells and CD8+ T cells.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:3d920693d18cf24e64fb
claim_id: claim:3d920693d18cf24e64fb
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
However, FTH1+ CD4+ or CD8+ T cells were predominant T cells in idiopathic CP (online supplemental figure 6D, E).

summary:
In Homo sapiens idiopathic chronic pancreatitis pancreas, FTH1 is a positive marker of CD8+ T cells.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:ca8b3c5af53bf11fbfd5
claim_id: claim:ca8b3c5af53bf11fbfd5
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Importantly, the frequency of CD68+ and CD163+ macrophages and S100A8+ monocytes (clusters #3, 8) were significantly higher in controls compared with CP

summary:
In Homo sapiens pancreas, CD68 is a positive marker of macrophages. In Homo sapiens pancreas, CD163 is a positive marker of macrophages.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:f876f0fd8d0320bd746b
claim_id: claim:f876f0fd8d0320bd746b
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
summary: In Homo sapiens hereditary chronic pancreatitis pancreas, CCL20 is a positive marker of monocytes.
span_literal:
The most noticeable finding was a significantly higher frequency of CCL20+ monocytes in hereditary CP compared with control or idiopathic CP.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:5c541d8f097478a2282b
claim_id: claim:5c541d8f097478a2282b
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Overall, single-cell transcriptional analysis of pancreatic myeloid populations revealed distinct myeloid subpopulation enrichment in each group; macrophages in controls, CCL20+ monocytes and IL1B+ DCs in hereditary CP, and FTH1+ or S100A8+ monocytes in idiopathic CP.

summary:
In Homo sapiens hereditary chronic pancreatitis pancreas, CCL20 is a positive marker of monocytes and IL1B is a positive marker of dendritic cells.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:2048481293442c155fca
claim_id: claim:2048481293442c155fca
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Overall, single-cell transcriptional analysis of pancreatic myeloid populations revealed distinct myeloid subpopulation enrichment in each group; macrophages in controls, CCL20+ monocytes and IL1B+ DCs in hereditary CP, and FTH1+ or S100A8+ monocytes in idiopathic CP.

summary:
In Homo sapiens hereditary chronic pancreatitis pancreas, IL1B is a positive marker of dendritic cells.


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:9aabab53f824f771d2e3
claim_id: claim:9aabab53f824f771d2e3
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
summary: In Homo sapiens control pancreas, GZMA is a positive marker of cytotoxic CD8+ T cells.
span_literal:
Control cells comprised predominantly GZMA+ cytotoxic CD8+ T cells while distinct CD4+ or CD8+ T cell subpopulations constituted CP T cells


claim_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36:claim:fd09dc0534610fc2fee1
claim_id: claim:fd09dc0534610fc2fee1
paper_key: hca:0408_10.1101_2021.04.05.438347_e17dfd8c36
span_literal:
Furthermore, T cell analyses revealed a significant portion of CD4+ T cell subsets (CCD6+ Th, TNF+ Th1, and Treg) were enriched in the hereditary CP pancreas highlighting the immune signature of hereditary CP pancreas is largely conserved across heterogeneous CD4+ T cell subsets.

summary:
In Homo sapiens hereditary chronic pancreatitis pancreas, CCR6 is a positive marker of CD4+ helper T cells and TNF is a positive marker of T helper 1 cells.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:267527589208b42f6861
claim_id: claim:267527589208b42f6861
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
Hereditary CP cells mainly consisted of CD4 + helper T-cell (Th) subpopulations, including CCR6 + , TNF + (Th1), regulatory T (Treg) cells and HLA-DA + CD8 + T cells.

summary:
In Homo sapiens hereditary chronic pancreatitis, CCR6 is a positive marker of a CD4+ helper T cell subpopulation in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:ed33aaba7f42ba25973f
claim_id: claim:ed33aaba7f42ba25973f
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
Hereditary CP cells mainly consisted of CD4 + helper T-cell (Th) subpopulations, including CCR6 + , TNF + (Th1), regulatory T (Treg) cells and HLA-DA + CD8 + T cells.

summary:
In Homo sapiens hereditary chronic pancreatitis, TNF is a positive marker of Th1 cells in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:a623e91da49ed4d8b45f
claim_id: claim:a623e91da49ed4d8b45f
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
Hereditary CP cells mainly consisted of CD4 + helper T-cell (Th) subpopulations, including CCR6 + , TNF + (Th1), regulatory T (Treg) cells and HLA-DA + CD8 + T cells.

summary:
In Homo sapiens hereditary chronic pancreatitis, HLA-DA is a positive marker of CD8+ T cells in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:fc406a27468c9b460b51
claim_id: claim:fc406a27468c9b460b51
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
However, FTH1 + CD4 + and BAG3 + CD8 + T cells were the predominant T cells in idiopathic CP samples

summary:
In Homo sapiens idiopathic chronic pancreatitis, FTH1 is a positive marker of CD4+ T cells in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:09a83eeb6d68316f9d59
claim_id: claim:09a83eeb6d68316f9d59
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
However, FTH1 + CD4 + and BAG3 + CD8 + T cells were the predominant T cells in idiopathic CP samples

summary:
In Homo sapiens idiopathic chronic pancreatitis, BAG3 is a positive marker of CD8+ T cells in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:580d181bdb1081f35ec6
claim_id: claim:580d181bdb1081f35ec6
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
summary: In Homo sapiens, GZMA is a positive marker of cytotoxic CD8+ T cells in control pancreas tissues.
span_literal:
Control cells comprised predominantly GZMA + cytotoxic CD8 + T cells, while distinct CD4 + or CD8 + T-cell subpopulations constituted CP T cells


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:86f7ad43a2bb5a032b4f
claim_id: claim:86f7ad43a2bb5a032b4f
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
summary: In Homo sapiens, CD68 and CD163 are positive markers of macrophages in the pancreas.
span_literal:
Importantly, the frequency of CD68 + and CD163 + macrophages and S100A8 + monocytes (clusters 3 and 8) were significantly higher in controls compared with patients with CP


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:1e8909150057b3a95cd7
claim_id: claim:1e8909150057b3a95cd7
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
The most notable finding was a significantly higher frequency of CCL20 + monocytes in hereditary CP compared with control or idiopathic CP samples.

summary:
In Homo sapiens hereditary chronic pancreatitis, CCL20 is a positive marker of monocytes in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:c64d8e812722ec2d3440
claim_id: claim:c64d8e812722ec2d3440
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
Overall, single-cell transcriptional analysis of pancreatic myeloid populations revealed distinct myeloid subpopulation enrichment in each group: macrophages in controls, CCL20 + monocytes and IL1B + DCs in hereditary patients with CP, and FTH1 + or S100A8 + monocytes in idiopathic patients with CP.

summary:
In Homo sapiens hereditary chronic pancreatitis, IL1B is a positive marker of dendritic cells in the pancreas.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:796c1e1cfce7cdd42c61
claim_id: claim:796c1e1cfce7cdd42c61
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
Some of the genes noted to be upregulated in hereditary compared with idiopathic CP included chemotactic receptors and ligands, such as CCR6, CXCR4, GPR183 and CCL20 , suggesting their involvement in CD4 + T-cell recruitment in hereditary CP.

summary:
In Homo sapiens hereditary chronic pancreatitis, CCR6, CXCR4, GPR183 and CCL20 are upregulated in CD4+ T cells compared with idiopathic chronic pancreatitis.


claim_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482:claim:2277d4efd3ca182446c6
claim_id: claim:2277d4efd3ca182446c6
paper_key: hca:0409_10.1136_gutjnl-2021-324546_a227082482
span_literal:
However, idiopathic CP showed evenly distributed CD4 + and CD8 + T-cell subsets uniquely expressing FTH1 and PCBP2 , which indicates that human idiopathic CP is highly associated with iron metabolism in immune cells, and this aligns with previous reports of dysregulated iron metabolism in pancreatitis.

summary:
In Homo sapiens idiopathic chronic pancreatitis, FTH1 and PCBP2 are uniquely expressed in CD4+ and CD8+ T-cell subsets in the pancreas.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:aa5b4d0a999353fae24c
claim_id: claim:aa5b4d0a999353fae24c
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
We selected the marker genes from the published literature to identify the four types of immune cells, such as CD79A and CD27 for B cells

summary:
In Homo sapiens, B cells are identified by the marker genes CD79A and CD27 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:c7331fb012d0cb0f449b
claim_id: claim:c7331fb012d0cb0f449b
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: TRAC, NKG7, and CD3D for T cells
summary:
In Homo sapiens, T cells are identified by the marker genes TRAC, NKG7, and CD3D in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:93b13abd04a81e2f23e2
claim_id: claim:93b13abd04a81e2f23e2
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: CD14 and CD68 for monocytes
summary:
In Homo sapiens, monocytes are identified by the marker genes CD14 and CD68 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:3bed83c5740eb6790b34
claim_id: claim:3bed83c5740eb6790b34
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: TPSB2, TPSAB1 and CPA3 for mast cells
summary:
In Homo sapiens, mast cells are identified by the marker genes TPSB2, TPSAB1, and CPA3 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:a5f23bf8eff822faad3b
claim_id: claim:a5f23bf8eff822faad3b
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: OMD, COL1A1, and TNFRSF11B for osteocytes
summary:
In Homo sapiens, osteocytes are identified by the marker genes OMD, COL1A1, and TNFRSF11B in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:941ef80725cb089cd9f6
claim_id: claim:941ef80725cb089cd9f6
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: ODAM (odontogenesis), KRT19, and KRT14 for epithelial cells
summary:
In Homo sapiens, epithelial cells are identified by the marker genes ODAM, KRT19, and KRT14 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:0ec822b633974f4bcdbc
claim_id: claim:0ec822b633974f4bcdbc
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: BCAM, RGS5, and TAGLN for basal/stromal cells
summary:
In Homo sapiens, basal/stromal cells are identified by the marker genes BCAM, RGS5, and TAGLN in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:bd1f1cbcd053c15055eb
claim_id: claim:bd1f1cbcd053c15055eb
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: ACKR1, VWF, and CDH5 for endothelial cells
summary:
In Homo sapiens, endothelial cells are identified by the marker genes ACKR1, VWF, and CDH5 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:d9e481f7621b497b9559
claim_id: claim:d9e481f7621b497b9559
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
In immune cells, CD3, CD19, CD14, and CD117 were respectively marked for T cells, B cells, monocytes, and mast cells

summary:
In Homo sapiens, T cells are marked by CD3 in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:452dfb120ce8d0810cf5
claim_id: claim:452dfb120ce8d0810cf5
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
In immune cells, CD3, CD19, CD14, and CD117 were respectively marked for T cells, B cells, monocytes, and mast cells

summary:
In Homo sapiens, B cells are marked by CD19 in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:80afc997e10727d88b8f
claim_id: claim:80afc997e10727d88b8f
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
In immune cells, CD3, CD19, CD14, and CD117 were respectively marked for T cells, B cells, monocytes, and mast cells

summary:
In Homo sapiens, monocytes are marked by CD14 in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:94cbdf74174f5fb3d733
claim_id: claim:94cbdf74174f5fb3d733
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
summary:
In Homo sapiens, mast cells are marked by CD117 in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:e8bcba208a0c5acb4cc3
claim_id: claim:e8bcba208a0c5acb4cc3
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
In nonimmune cells, CTSK, BCAM, VWF, and ODAM were respectively coded for osteo-like cells, basal/stromal cells, endothelial cells, and epithelial cells

summary:
In Homo sapiens, osteo-like cells are marked by CTSK in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:68654a47c2c5e885594d
claim_id: claim:68654a47c2c5e885594d
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
In nonimmune cells, CTSK, BCAM, VWF, and ODAM were respectively coded for osteo-like cells, basal/stromal cells, endothelial cells, and epithelial cells

summary:
In Homo sapiens, basal/stromal cells are marked by BCAM in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:c414158367c5d3b89590
claim_id: claim:c414158367c5d3b89590
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
In nonimmune cells, CTSK, BCAM, VWF, and ODAM were respectively coded for osteo-like cells, basal/stromal cells, endothelial cells, and epithelial cells

summary:
In Homo sapiens, endothelial cells are marked by VWF in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:86bcdc9697db02a58658
claim_id: claim:86bcdc9697db02a58658
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
summary:
In Homo sapiens, epithelial cells are marked by ODAM in chronic apical periodontitis tissue by immunohistochemistry.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:846218e7ee8e263d9291
claim_id: claim:846218e7ee8e263d9291
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Cells in Bs2 coexpressed smooth muscle cells and myofibroblasts, as previously suggested by their expression of MYH11, ACTG2, and DES of smooth muscle cells and TAGLN and ACTA2 of myofibroblasts.

summary:
In Homo sapiens, smooth muscle cells express MYH11, ACTG2, and DES, while myofibroblasts express TAGLN and ACTA2, as shown in basal/stromal cell subcluster Bs2 in chronic apical periodontitis.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:29c39410de0d544c45fb
claim_id: claim:29c39410de0d544c45fb
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Cells in Bs2 coexpressed smooth muscle cells and myofibroblasts, as previously suggested by their expression of MYH11, ACTG2, and DES of smooth muscle cells and TAGLN and ACTA2 of myofibroblasts.

summary:
In Homo sapiens, myofibroblasts express TAGLN and ACTA2, as shown in basal/stromal cell subcluster Bs2 in chronic apical periodontitis.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:18c542255a0480d50661
claim_id: claim:18c542255a0480d50661
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Bs1, predominantly expressed FGF7, was annotated as inflammation-associated fibroblasts (IAFs) according to the high expression of CCL2, IL6, and IRF1.

summary:
In Homo sapiens, inflammation-associated fibroblasts (basal/stromal cell subcluster Bs1) predominantly express FGF7 and show high expression of CCL2, IL6, and IRF1 in chronic apical periodontitis.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:1e4cc975bdcbec1781db
claim_id: claim:1e4cc975bdcbec1781db
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal: RGS5 and TAGLN are fibroblast cell markers.
summary:
In Homo sapiens, RGS5 and TAGLN are fibroblast cell markers in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:9ebea38256849b989b9e
claim_id: claim:9ebea38256849b989b9e
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed1, with expression of the cell cycling marker RGCC, hematopoietic stem cell marker CD34, and endothelial progenitor cell marker KDR, were supposed to be immature endothelial cells differentiated from hematopoietic stem cells.

summary:
In Homo sapiens, endothelial cell subcluster Ed1 expresses the cell cycling marker RGCC, the hematopoietic stem cell marker CD34, and the endothelial progenitor cell marker KDR, and is considered to represent immature endothelial cells.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:7fda2cb39bf7c71dd765
claim_id: claim:7fda2cb39bf7c71dd765
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed1, with expression of the cell cycling marker RGCC, hematopoietic stem cell marker CD34, and endothelial progenitor cell marker KDR, were supposed to be immature endothelial cells differentiated from hematopoietic stem cells.

summary:
In Homo sapiens, hematopoietic stem cells are marked by CD34 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:7791ca1752e157064446
claim_id: claim:7791ca1752e157064446
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed1, with expression of the cell cycling marker RGCC, hematopoietic stem cell marker CD34, and endothelial progenitor cell marker KDR, were supposed to be immature endothelial cells differentiated from hematopoietic stem cells.

summary:
In Homo sapiens, endothelial progenitor cells are marked by KDR in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:01821ef6d8d6204d3f66
claim_id: claim:01821ef6d8d6204d3f66
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed2, characterized by lymphatic endothelial cell marker LYVE-1 and growth factor IGFBP5, were considered a population of early differentiating lymphatic endothelial cells.

summary:
In Homo sapiens, lymphatic endothelial cells are characterized by the marker LYVE-1 and the growth factor IGFBP5 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:0c66b2af48da43f866cf
claim_id: claim:0c66b2af48da43f866cf
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed7, with pericyte marker (RGS5), fibroblast markers (LUM and DCN), and smooth muscle cell markers (TAGLN and ACTA2), were reckoned to be critical for vascular repair.

summary:
In Homo sapiens, endothelial cell subcluster Ed7 expresses pericyte marker RGS5, fibroblast markers LUM and DCN, and smooth muscle cell markers TAGLN and ACTA2 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:8485db99e82db2aea780
claim_id: claim:8485db99e82db2aea780
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed7, with pericyte marker (RGS5), fibroblast markers (LUM and DCN), and smooth muscle cell markers (TAGLN and ACTA2), were reckoned to be critical for vascular repair.

summary:
In Homo sapiens, fibroblasts are marked by LUM and DCN as shown in endothelial cell subcluster Ed7 in chronic apical periodontitis periapical tissue.


claim_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f:claim:6b5b7151d7e588b7d71c
claim_id: claim:6b5b7151d7e588b7d71c
paper_key: hca:0410_10.3389_fcell.2021.820274_b0973e038f
span_literal:
Ed7, with pericyte marker (RGS5), fibroblast markers (LUM and DCN), and smooth muscle cell markers (TAGLN and ACTA2), were reckoned to be critical for vascular repair.

summary:
In Homo sapiens, smooth muscle cells are marked by TAGLN and ACTA2 as shown in endothelial cell subcluster Ed7 in chronic apical periodontitis periapical tissue.


claim_key: hca:0411_10.1016_j.immuni.2019.06.027_4a3b9ca5c7:claim:8f19973c925845927b03
claim_id: claim:8f19973c925845927b03
paper_key: hca:0411_10.1016_j.immuni.2019.06.027_4a3b9ca5c7
span_literal:
LECs lining the subcapsular sinus (SCS) of LNs abundantly expressed neutrophil chemoattractants, whereas LECs lining the medullary sinus (MS) expressed a C-type lectin CD209.

summary:
In Homo sapiens lymph nodes, lymphatic endothelial cells lining the medullary sinus expressed CD209, a C-type lectin.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:3d66a21a1e6c751c271b
claim_id: claim:3d66a21a1e6c751c271b
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal: We identify two FAP cell clusters that both express the canonical FAP cell markers PDGFRA and CD34
summary:
In Homo sapiens skeletal muscle, fibro-adipogenic progenitor cells express the canonical markers PDGFRA and CD34.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:1dcea1aea3fa220724a2
claim_id: claim:1dcea1aea3fa220724a2
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal: we refer to the subtypes as fibrillin 1+ (FBN1+) and lumican+ (LUM+) FAP subtypes
summary:
In Homo sapiens skeletal muscle, fibro-adipogenic progenitor cell subtypes are distinguished as fibrillin 1-positive (FBN1-positive) and lumican-positive (LUM-positive) subtypes.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:72100ea6725311c04dcf
claim_id: claim:72100ea6725311c04dcf
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal: we refer to the subtypes as fibrillin 1+ (FBN1+) and lumican+ (LUM+) FAP subtypes
summary:
In Homo sapiens skeletal muscle, the lumican-positive fibro-adipogenic progenitor cell subtype is marked by expression of LUM.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:a26a49e4927cb0b0c3a7
claim_id: claim:a26a49e4927cb0b0c3a7
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal:
PCV endothelial cells: DARC, PLVAP and CCL14, are not expressed in the remaining endothelial cell population

summary:
In Homo sapiens skeletal muscle, post-capillary venule endothelial cells are marked by DARC, PLVAP, and CCL14, which are not expressed in the remaining endothelial cell population.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:6be05d28433361db3b67
claim_id: claim:6be05d28433361db3b67
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal: Type I fibers express MYH7, whereas Type IIa fibers express MYH2
summary:
In Homo sapiens skeletal muscle, Type I muscle fibers express MYH7, whereas Type IIa muscle fibers express MYH2.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:a4dd3169b58cf23b737d
claim_id: claim:a4dd3169b58cf23b737d
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal: Type I fibers express MYH7, whereas Type IIa fibers express MYH2
summary:
In Homo sapiens skeletal muscle, Type IIa muscle fibers express MYH2, whereas Type I muscle fibers express MYH7.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:9588f946891868633828
claim_id: claim:9588f946891868633828
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
summary: In Homo sapiens, fibro-adipogenic progenitor cells are marked by expression of PDGFRA and CD34.
span_literal:
FAPs are non-myogenic mesenchymal stem cells that reside in muscle interstitium, are marked by expression of PDGFRA and CD34, and do not originate from bone marrow


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:2796c62dff891672bdc9
claim_id: claim:2796c62dff891672bdc9
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
summary: In Homo sapiens, TEK is not highly expressed in either fibro-adipogenic progenitor cell subtype.
span_literal:
Although TEK, the gene precursor of the Tie2 protein, is not highly expressed in either FAP subtype in human, the FBN1+ FAP subtype in mouse co-expresses the TEK gene.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:967052d119c50a364572
claim_id: claim:967052d119c50a364572
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal:
the FBN1+ FAP cells specifically express elastin, MFAP5 and LOXL1 (Supplementary Table S1 ), three critical components of elastic fiber formation in the extracellular matrix, suggesting that these cells may play a role in elastic fiber assembly

summary:
In Homo sapiens skeletal muscle, fibrillin 1-positive fibro-adipogenic progenitor cells specifically express ELN, MFAP5, and LOXL1.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:72261b8d821380d80bd5
claim_id: claim:72261b8d821380d80bd5
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal:
We also divided cluster 8 into separate T and B cell populations based upon their expression of CD3D vs MS4A1.

summary:
In Homo sapiens skeletal muscle, T cells and B cells were distinguished based upon their expression of CD3D versus MS4A1.


claim_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a:claim:8ef149300044da0337d7
claim_id: claim:8ef149300044da0337d7
paper_key: hca:0412_10.1038_s41598-019-57110-6_5feef6086a
span_literal:
We also divided cluster 8 into separate T and B cell populations based upon their expression of CD3D vs MS4A1.

summary:
In Homo sapiens skeletal muscle, B cells were distinguished from T cells based upon expression of MS4A1 versus CD3D.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:78b091eef2a22d2f47c8
claim_id: claim:78b091eef2a22d2f47c8
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
summary: In Homo sapiens, Langerhans cells in the skin are marked by specific expression of CD207 and CD1A.
span_literal:
A group of Langerhans cells were identified in the skin sample (1% of all skin cells) with specific expression of CD207 and CD1A [ 21 ].


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:d0f53066520e7f1d2331
claim_id: claim:d0f53066520e7f1d2331
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
An even smaller group of 26 sweat gland epithelial cells (0.31%) were also identified in the skin sample, which had specific expression of DCD , SCGB2A2 , KRT19 , MUCL1 , and PIP genes

summary:
In Homo sapiens, sweat gland epithelial cells in the skin are marked by specific expression of DCD, SCGB2A2, KRT19, MUCL1, and PIP.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:e7d3323fdbc285458fda
claim_id: claim:e7d3323fdbc285458fda
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
summary: In Homo sapiens, FibSmo cells are marked by co-expression of MMP2 and ACTA2.
span_literal:
another novel group of cells were assigned as FibSmo with a co-expression of MMP2 and ACTA2 , which are marker genes for fibroblasts and smooth muscle cells


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:506d426fde46fed77717
claim_id: claim:506d426fde46fed77717
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
TCL1A was significantly expressed in two naïve B cell clusters with distinct gene expression profiles, TCL1A_ly_naive_B from the lymph nodes and TCL1A_naive_B from multiple tissues, compared with the other B and plasma cell clusters

summary:
In Homo sapiens, TCL1A is significantly expressed in naïve B cells compared with other B cell and plasma cell clusters.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:87bcc3f14d23828f28aa
claim_id: claim:87bcc3f14d23828f28aa
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
We identified a total of 6932 ECs, including 6681 blood endothelial cells (BECs, marked with VWF ) and 251 lymphatic endothelial cells (LECs, marked with LYVE1 ).

summary:
In Homo sapiens, blood endothelial cells are marked by VWF and lymphatic endothelial cells are marked by LYVE1.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:40b3ae37c9afeb3841e3
claim_id: claim:40b3ae37c9afeb3841e3
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
These cells were further grouped into 14 fibroblast clusters (11,697 cells, MMP2 ), four smooth muscle cell clusters (3165 cells, ACTA2 ), and another five novel clusters assigned as FibSmo (2828 cells; marked with MMP2 and ACTA2 ;

summary:
In Homo sapiens, fibroblasts are marked by MMP2, smooth muscle cells are marked by ACTA2, and FibSmo cells are marked by both MMP2 and ACTA2.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:a4d716617dea10c09302
claim_id: claim:a4d716617dea10c09302
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
summary: In Homo sapiens, B cells are marked by CD20 (MS4A1) and plasma cells are marked by SDC1.
span_literal:
Cluster analysis revealed 14 distinct cell clusters among 10,100 B and plasma cells from 11 organ samples, including nine B ( CD20 ) and six plasma cell ( SDC1 ) clusters


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:9442fe6eaccfbe12ece4
claim_id: claim:9442fe6eaccfbe12ece4
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
t-SNE plots of the normalized expression of marker genes for monocytes ( S100A8/9/12 and VCAN ) and macrophages (pan-marker: C1QC , C1QB , and VSIG4 ), cDC1 ( CLEC9A ), cDC2 ( FCER1A ), and Langerhans ( CD207 ) as well as subpopulation-specific genes ( CD14 and FCGR3A ).

summary:
In Homo sapiens, monocytes are marked by S100A8, S100A9, S100A12, and VCAN; macrophages are marked by C1QC, C1QB, and VSIG4; conventional dendritic cell type 1 is marked by CLEC9A; conventional dendritic cell type 2 is marked by FCER1A; and Langerhans cells are marked by CD207.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:a4e7ed5ff1adf0b782fa
claim_id: claim:a4e7ed5ff1adf0b782fa
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
Notably, high expression of proliferation marker genes including MKI67 and PCNA were exclusively detected in the HISTIH4C_Mac macrophages (C12) in the bladder, esophagus, heart, and rectum

summary:
In Homo sapiens, HIST1H4C_Mac macrophages show high expression of proliferation markers MKI67 and PCNA.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:2a1b0c95cf8bd8df3553
claim_id: claim:2a1b0c95cf8bd8df3553
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
Although CD27 is a canonical marker of memory B cells [ 30 ], we observed a low transcription level of CD27 in memory B cells, but a higher level in plasma cells

summary:
In Homo sapiens, CD27 is a canonical marker of memory B cells, though its transcription level was observed to be low in memory B cells and higher in plasma cells.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:8541d0082a0ec93078b8
claim_id: claim:8541d0082a0ec93078b8
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
Interestingly, a group of LECs (FCN3_LEC) were strictly identified in the liver and expressed only two of the four genes for LECs ( PECAM1 and LYVE1 ; but not PDPN and PROX1 [ 43 ]

summary:
In Homo sapiens, FCN3_LEC lymphatic endothelial cells in the liver express PECAM1 and LYVE1 but do not express PDPN and PROX1.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:350e15edeb70d80ef680
claim_id: claim:350e15edeb70d80ef680
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
Fibroblasts have specific enrichment of genes that are involved in the “extracellular structure organization,” which is consistent with their strong expression of extracellular matrix protein genes ( DCN and FBLN2 ) and genes related to matrix assembly ( MFAP5 and SFRP2 ) and matrix remodeling ( MMP2 ;

summary:
In Homo sapiens, fibroblasts strongly express extracellular matrix protein genes DCN and FBLN2, matrix assembly genes MFAP5 and SFRP2, and matrix remodeling gene MMP2.


claim_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e:claim:2b6ea60d84935ab85b77
claim_id: claim:2b6ea60d84935ab85b77
paper_key: hca:0414_10.1186_s13059-020-02210-0_30c1533a3e
span_literal:
Smooth muscle cells have specific enrichment of genes related to muscle system processing, including MYH11 , MYLK , CAV1 , and MEF2C

summary:
In Homo sapiens, smooth muscle cells have specific enrichment of muscle system processing genes including MYH11, MYLK, CAV1, and MEF2C.


claim_key: hca:0415_10.1038_s41467-020-20358-y_582bbd075a:claim:d55f9b30a984279c8841
claim_id: claim:d55f9b30a984279c8841
paper_key: hca:0415_10.1038_s41467-020-20358-y_582bbd075a
summary: In Homo sapiens, TAGLN is a well-known marker for smooth muscle cells.
span_literal:
well-known cell type markers, such as LUM for fibroblasts 28 , TAGLN for smooth muscle cells 29 , and AIF1 for macrophages 30 , 31 , were used to determine the cellular identity of the clusters


claim_key: hca:0415_10.1038_s41467-020-20358-y_582bbd075a:claim:729c6b9004f657d985af
claim_id: claim:729c6b9004f657d985af
paper_key: hca:0415_10.1038_s41467-020-20358-y_582bbd075a
summary: In Homo sapiens, FBLN1 is an additional marker for fibroblasts.
span_literal:
we also identified multiple additional markers, for example, FBLN1 for fibroblasts and MT1A and PLN for smooth muscle cells


claim_key: hca:0416_10.1126_science.aat1699_46d73cdfcb:claim:63ba9484e04c5a7962c7
claim_id: claim:63ba9484e04c5a7962c7
paper_key: hca:0416_10.1126_science.aat1699_46d73cdfcb
span_literal:
To validate the identity of the PT1 signature in RCC, we exploited the fact that they were defined by SLC17A3 and VCAM1 with absence of SLC7A13 within our data

summary:
In Homo sapiens, proximal convoluted tubular cell subtype PT1 is defined by positive expression of SLC17A3 and VCAM1 and negative expression of SLC7A13.


claim_key: hca:0416_10.1126_science.aat1699_46d73cdfcb:claim:25ccd402a838b8d7e690
claim_id: claim:25ccd402a838b8d7e690
paper_key: hca:0416_10.1126_science.aat1699_46d73cdfcb
span_literal:
Confocal microscopy demonstrated co-localization of VCAM1 and SLC17A3 in CA9+ cells, CA9 being a specific marker of ccRCC cells

summary:
In Homo sapiens, CA9 is a specific marker of clear cell renal cell carcinoma cells, and VCAM1 and SLC17A3 co-localize in CA9-positive cells.


claim_key: hca:0416_10.1126_science.aat1699_46d73cdfcb:claim:1809967e0edcd66f1bd4
claim_id: claim:1809967e0edcd66f1bd4
paper_key: hca:0416_10.1126_science.aat1699_46d73cdfcb
span_literal:
Furthermore, tE2 endothelial cells expressed high levels of ACKR1, a marker of venular endothelium promoting tissue migration of immune cells

summary:
In Homo sapiens, ACKR1 is a marker of venular endothelial cells, and tE2 endothelial cells express high levels of ACKR1.


claim_key: hca:0416_10.1126_science.aat1699_46d73cdfcb:claim:211a1e72e0b0069e45f8
claim_id: claim:211a1e72e0b0069e45f8
paper_key: hca:0416_10.1126_science.aat1699_46d73cdfcb
summary: In Homo sapiens, tumor infiltrating macrophages express VEGFA in renal cell carcinoma tissue.
span_literal:
Measuring expression of the key components of VEGF signaling, we identified tumor infiltrating macrophages as a further source of VEGFA


claim_key: hca:0416_10.1126_science.aat1699_46d73cdfcb:claim:430ce29eef540289e0dc
claim_id: claim:430ce29eef540289e0dc
paper_key: hca:0416_10.1126_science.aat1699_46d73cdfcb
span_literal:
VEGF-signaling receptors (KDR, FLT1, FLT4) were mainly expressed by one population of ascending vasa recta cells

summary:
In Homo sapiens, ascending vasa recta cells express the VEGF-signaling receptors KDR, FLT1, and FLT4.


claim_key: hca:0416_10.1126_science.aat1699_46d73cdfcb:claim:ed7fdc1cd5f3c1ad8bfc
claim_id: claim:ed7fdc1cd5f3c1ad8bfc
paper_key: hca:0416_10.1126_science.aat1699_46d73cdfcb
summary: In Homo sapiens, the ascending vasa recta cluster tE2 expresses VEGFC and FLT1.
span_literal:
The other ascending vasa recta cluster, tE2, ( Fig. S18A ) exhibited lymphangiogenic VEGFC and FLT1.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:93d3e20d9f29582c1361
claim_id: claim:93d3e20d9f29582c1361
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
Five islet endocrine cell types have been assigned based on exclusive and robust expression of the peptide hormone genes INS (beta), GCG (alpha), SST (delta), PPY (PP/gamma), and GHRL (epsilon)

summary:
In Homo sapiens, beta cells are identified by expression of INS, alpha cells by GCG, delta cells by SST, pancreatic polypeptide/gamma cells by PPY, and epsilon cells by GHRL.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:95656c02d268011b131d
claim_id: claim:95656c02d268011b131d
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, acinar cells are identified by expression of the serine peptidase gene PRSS1.
span_literal:
Each also has been identified by specific marker gene expression, including the serine peptidase gene PRSS1 (acinar)


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:7a6a8b61d5b6a22e6cca
claim_id: claim:7a6a8b61d5b6a22e6cca
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal: the extracellular matrix protein gene COL1A1 (stellate)
summary:
In Homo sapiens, stellate cells are identified by expression of the extracellular matrix protein gene COL1A1.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:7aa6bbf34915707001bb
claim_id: claim:7aa6bbf34915707001bb
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, IRX2, LOXL4, and DPP4 are alpha cell-specific genes.
span_literal:
alpha cell–specific genes like IRX2 , LOXL4 , and DPP4 , a cell surface receptor and diabetes drug target


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:14c926764f4ab39d7bd5
claim_id: claim:14c926764f4ab39d7bd5
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, HHEX is exclusively expressed in delta cells as a signature gene.
span_literal:
Among delta cell signature genes, we detected exclusive expression of HHEX, a transcription factor reported to govern delta cell identity and function and linked to T2D GWAS


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:0c13fe6c92d481933455
claim_id: claim:0c13fe6c92d481933455
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
PP/gamma cell–specific transcriptomes included CTD-2008P7.8 , a lincRNA of unknown function; CNTNAP5 , a member of the neurexin family of cell adhesion molecules; and ID4 , which encodes an inhibitor of DNA-binding protein.

summary:
In Homo sapiens, pancreatic polypeptide/gamma cell-specific transcriptomes include CTD-2008P7.8, CNTNAP5, and ID4.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:e9b0929111e4dbb2ada1
claim_id: claim:e9b0929111e4dbb2ada1
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, MAFA, SLC2A2, SIX3, and DLK1 were confirmed as beta cell signature genes.
span_literal:
Several genes previously reported to be enriched in the major islet cell types, such as MAFA , SLC2A2 , SIX3 , and DLK1 in beta cells and IRX2 , DPP4 , and ADORA2A in alpha cells, were confirmed to be signature genes.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:04b08db66dabef517298
claim_id: claim:04b08db66dabef517298
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
Notable examples included beta and delta cell expression of the congenital hyperinsulinemia (CHI) gene HADH and alpha and PP/gamma cell expression of the ARX transcription factor

summary:
In Homo sapiens, the congenital hyperinsulinemia gene HADH is expressed in beta cells and delta cells.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:8c6eb59771d726d95466
claim_id: claim:8c6eb59771d726d95466
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
Notable examples included beta and delta cell expression of the congenital hyperinsulinemia (CHI) gene HADH and alpha and PP/gamma cell expression of the ARX transcription factor

summary:
In Homo sapiens, the congenital hyperinsulinemia gene HADH is expressed in delta cells as well as beta cells.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:6b7a96fcc34c9b04eae1
claim_id: claim:6b7a96fcc34c9b04eae1
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
GSIS pathway genes associated with glucose sensing and uptake displayed highly beta cell–specific expression, including SLC2A2 , which encodes the glucose transporter GLUT2; G6PC2 , which encodes a subunit of glucose-6-phosphatase; and PFKFB2 , which encodes an enzyme involved in regulation of glycolysis

summary:
In Homo sapiens, SLC2A2, G6PC2, and PFKFB2 display highly beta cell-specific expression as glucose-stimulated insulin secretion pathway genes.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:faa3b4e4a9b41309eec0
claim_id: claim:faa3b4e4a9b41309eec0
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, GPD1 is a beta cell signature gene, and GPD2 is also expressed in beta cells.
span_literal:
Both components of the glycerol-3-phosphate shuttle, cytoplasmic GPD1 and mitochondrial GPD2 , were expressed in beta cells, with the former representing a beta cell signature gene


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:70461e3d4121e06bd607
claim_id: claim:70461e3d4121e06bd607
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
Among the top 100 differentially expressed (FDR < 5%) genes in delta versus other islet endocrine cells are receptors for the appetite-regulating hormones leptin ( LEPR ) and ghrelin ( GHSR ), the growth factor neuregulin 4 ( ERBB4 ), and the neurotransmitter dopamine ( DRD2 )

summary:
In Homo sapiens, delta cells specifically express LEPR, GHSR, ERBB4, and DRD2 compared to other islet endocrine cells.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:0ded91dbfca128d7a141
claim_id: claim:0ded91dbfca128d7a141
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
We report expression of FEV , a serotonergic transcription factor and necessary driver of neuronal maturation previously reported in mouse beta cells ( Ohta et al. 2011 ), in PP/gamma cells (average log 2 CPM of 2.172).

summary:
In Homo sapiens, FEV, a serotonergic transcription factor, is expressed in pancreatic polypeptide/gamma cells.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:aa47570d8b035b17c7b2
claim_id: claim:aa47570d8b035b17c7b2
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, TPH1 and SLC6A4 are signature genes of pancreatic polypeptide/gamma cells.
span_literal:
Other related signature genes in PP/gamma cells include TPH1 , encoding a tryptophan hydroxylase essential for the initial catalysis of serotonin, and SLC6A4 , a serotonin reuptake transporter.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:634c3470946aabb5fff1
claim_id: claim:634c3470946aabb5fff1
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
We also observed high PP/gamma expression of muscarinic acetylcholine receptor M3, CHRM3 , which stimulates exocrine pancreatic amylase

summary:
In Homo sapiens, pancreatic polypeptide/gamma cells exhibit high expression of CHRM3, the muscarinic acetylcholine receptor M3.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:08fb1a42edda626f8ce3
claim_id: claim:08fb1a42edda626f8ce3
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, the congenital hyperinsulinism-associated gene UCP2 is enriched in delta cells.
span_literal:
Another CHI-associated gene, UCP2 ( González-Barroso et al. 2008 ; Senniappan et al. 2013 ), which was reported to be highly expressed in human beta cells ( Liu et al. 2013 ) and to suppress insulin secretion ( Krauss et al. 2003 ), was enriched in delta cells


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:b372bb5cf9f2e1a5d563
claim_id: claim:b372bb5cf9f2e1a5d563
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal:
Ten genes were uniquely expressed in beta cells, including MEG3 , a type 1 diabetes (T1D)–associated lincRNA with reported expression in mouse beta cells and potential tumor suppressor activity

summary:
In Homo sapiens, MEG3, a type 1 diabetes-associated long intergenic noncoding RNA, is uniquely expressed in beta cells.


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:d2b146979cbfa11873c7
claim_id: claim:d2b146979cbfa11873c7
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
summary: In Homo sapiens, IAPP is uniquely expressed in beta cells.
span_literal:
and IAPP , whose protein product, when aggregated, possesses cytotoxic properties that may contribute to beta cell death and dysfunction in T2D


claim_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab:claim:1075ec4d5da78c82eb86
claim_id: claim:1075ec4d5da78c82eb86
paper_key: hca:0417_10.1101_gr.212720.116_ba8d2583ab
span_literal: beta cell maturation transcription factor PDX1 , and the sulfonylurea drug target ABCC8
summary:
In Homo sapiens, the beta cell maturation transcription factor PDX1 and the sulfonylurea drug target ABCC8 are enriched in beta cells.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:fa97c279da96c51afea0
claim_id: claim:fa97c279da96c51afea0
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
While epidermal stem cells (EpSC) and other undifferentiated progenitors (#7 and #15) expressed markers such as KRT5 , KRT14 , TP63 , ITGA6 , and ITGB1 , differentiated keratinocytes (#5) were defined by KRT1 , KRT10 , SBSN , and KRTDAP expression

summary:
In Homo sapiens skin, epidermal stem cells and other undifferentiated progenitors express KRT5, KRT14, TP63, ITGA6, and ITGB1.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:c72b4b642ad8712f4b2e
claim_id: claim:c72b4b642ad8712f4b2e
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
While epidermal stem cells (EpSC) and other undifferentiated progenitors (#7 and #15) expressed markers such as KRT5 , KRT14 , TP63 , ITGA6 , and ITGB1 , differentiated keratinocytes (#5) were defined by KRT1 , KRT10 , SBSN , and KRTDAP expression

summary:
In Homo sapiens skin, differentiated keratinocytes are defined by KRT1, KRT10, SBSN, and KRTDAP expression.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:201b1deae9790d3c140e
claim_id: claim:201b1deae9790d3c140e
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal: Fibroblasts were identified by their archetypal markers LUM , DCN , VIM , PDGFRA , and COL1A2
summary:
In Homo sapiens skin, fibroblasts are identified by their archetypal markers LUM, DCN, VIM, PDGFRA, and COL1A2.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:99b1de5ba2da7a7f973b
claim_id: claim:99b1de5ba2da7a7f973b
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal: fibroblasts in cluster #3 express COL13A1 and COL23A1 , two known markers of papillary fibroblasts
summary:
In Homo sapiens skin, secretory-papillary fibroblasts express COL13A1 and COL23A1, two known markers of papillary fibroblasts.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:afd6bf3fae86f0e9f9ea
claim_id: claim:afd6bf3fae86f0e9f9ea
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
While the most representative markers of the papillary fibroblasts comprise APCDD1 , AXIN2 , COLEC12 , PTGDS , and COL18A1 , the reticular fibroblast signature is typically defined by a group of ten genes, including MGP or MFAP5

summary:
In Homo sapiens skin, the most representative markers of papillary fibroblasts comprise APCDD1, AXIN2, COLEC12, PTGDS, and COL18A1.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:0b56aeee80cedcb3e478
claim_id: claim:0b56aeee80cedcb3e478
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
While the most representative markers of the papillary fibroblasts comprise APCDD1 , AXIN2 , COLEC12 , PTGDS , and COL18A1 , the reticular fibroblast signature is typically defined by a group of ten genes, including MGP or MFAP5

summary:
In Homo sapiens skin, the reticular fibroblast signature is typically defined by genes including MGP and MFAP5.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:560655c60bc54ee2e789
claim_id: claim:560655c60bc54ee2e789
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
the collagen genes COL11A1 and COL24A1 , associated with cartilage and bone development 38 , 39 , respectively, were specifically expressed in the fibroblasts of cluster #9

summary:
In Homo sapiens skin, mesenchymal fibroblasts specifically express the collagen genes COL11A1 and COL24A1.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:a0ecf76da9038d7377af
claim_id: claim:a0ecf76da9038d7377af
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
Collagen Triple Helix Repeat-Containing 1 ( CTHRC1 ), and Adenomatosis polyposis coli downregulated 1 ( APCDD1 ) were selected to detect the secretory-reticular and secretory-papillary fibroblasts, respectively.

summary:
In Homo sapiens skin, Collagen Triple Helix Repeat-Containing 1 (CTHRC1) was selected to detect secretory-reticular fibroblasts.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:fe1c892058b3c2ee8fa4
claim_id: claim:fe1c892058b3c2ee8fa4
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
Collagen Triple Helix Repeat-Containing 1 ( CTHRC1 ), and Adenomatosis polyposis coli downregulated 1 ( APCDD1 ) were selected to detect the secretory-reticular and secretory-papillary fibroblasts, respectively.

summary:
In Homo sapiens skin, Adenomatosis polyposis coli downregulated 1 (APCDD1) was selected to detect secretory-papillary fibroblasts.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:48085627a0c59a76710c
claim_id: claim:48085627a0c59a76710c
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
C-C motif chemokine ligand 19 ( CCL19 ) and Apolipoprotein E ( APOE ), were used to detect the pro-inflammatory fibroblasts, and Asporin ( ASPN ) was chosen as a marker for the mesenchymal subpopulation.

summary:
In Homo sapiens skin, C-C motif chemokine ligand 19 (CCL19) and Apolipoprotein E (APOE) were used to detect pro-inflammatory fibroblasts.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:512039a3252dcacc8c35
claim_id: claim:512039a3252dcacc8c35
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
C-C motif chemokine ligand 19 ( CCL19 ) and Apolipoprotein E ( APOE ), were used to detect the pro-inflammatory fibroblasts, and Asporin ( ASPN ) was chosen as a marker for the mesenchymal subpopulation.

summary:
In Homo sapiens skin, Asporin (ASPN) was chosen as a marker for the mesenchymal fibroblast subpopulation.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:90709388a09a1980a6bd
claim_id: claim:90709388a09a1980a6bd
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal: Platelet-derived growth factor receptor alpha ( PDGFRA) was included as a pan-fibroblast control
summary:
In Homo sapiens skin, Platelet-derived growth factor receptor alpha (PDGFRA) was included as a pan-fibroblast control marker.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:eb9b6d981cdaff382988
claim_id: claim:eb9b6d981cdaff382988
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
dermal papilla-associated fibroblasts, which are characterized by high CRABP1 and TNN expression levels

summary:
In Homo sapiens skin, dermal papilla-associated fibroblasts are characterized by high CRABP1 and TNN expression levels.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:8fbfb104f54f9771946c
claim_id: claim:8fbfb104f54f9771946c
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
KRT5 , KRT14 , TP63 , ITGB1 , and ITGA6 (epidermal stem cells and other undifferentiated progenitors, clusters #7 and #15)

summary:
In Homo sapiens skin, epidermal stem cells and other undifferentiated progenitors are identified by KRT5, KRT14, TP63, ITGB1, and ITGA6.


claim_key: hca:0418_10.1038_s42003-020-0922-4_8904851286:claim:36db07d3be63664e0310
claim_id: claim:36db07d3be63664e0310
paper_key: hca:0418_10.1038_s42003-020-0922-4_8904851286
span_literal:
AIF1 , LYZ , HLA-DRA , CD68 , and ITGAX (macrophages and dendritic cells (DC), clusters #0, #13 and #16)

summary:
In Homo sapiens skin, macrophages and dendritic cells are identified by AIF1, LYZ, HLA-DRA, CD68, and ITGAX.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:fd97763fe70a850e5b88
claim_id: claim:fd97763fe70a850e5b88
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
SCPs were marked by the expression of CDH19 , SOX10 , PLP1 and ERBB3 and split into a cluster comprising cells from 7 and 8 weeks postconception and a cluster comprising cells from later time points (11, 14, 17 weeks postconception; late SCPs)

summary:
In Homo sapiens developing adrenal gland, Schwann cell precursors are marked by the expression of CDH19, SOX10, PLP1 and ERBB3.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:633ecac3659e95fd3664
claim_id: claim:633ecac3659e95fd3664
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal: Expression of the chromaffin markers TH , DBH, DDC and CHGA marked adrenal chromaffin cells.
summary:
In Homo sapiens developing adrenal gland, TH, DBH, DDC and CHGA are markers of adrenal chromaffin cells.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:41804f680c9d8f2f9f28
claim_id: claim:41804f680c9d8f2f9f28
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
summary: In Homo sapiens developing adrenal gland, late chromaffin cells additionally express PNMT.
span_literal:
Chromaffin cells from later developmental time points formed a distinct cluster harboring cells that additionally expressed PNMT , encoding the enzyme catalyzing methylation of norepinephrine to form epinephrine


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:1e7874dd07287d914f1b
claim_id: claim:1e7874dd07287d914f1b
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal: An ERBB4 + , ASCL1 + bridge population connected SCPs and chromaffin cells.
summary:
In Homo sapiens developing adrenal gland, the bridge population is marked by ERBB4 and ASCL1 expression.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:4b67214bd85a91369e80
claim_id: claim:4b67214bd85a91369e80
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Expression of the neuroblast markers NEFM , GAP43 , STMN2 , ISL1 and ALK identified sympathetic neuroblasts.

summary:
In Homo sapiens developing adrenal gland, NEFM, GAP43, STMN2, ISL1 and ALK are markers that identify sympathetic neuroblasts.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:9b9c64881a992126e648
claim_id: claim:9b9c64881a992126e648
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
At later time points, neuroblasts showed increased expression of the differentiation markers SYN3 and IL7 , whereas expression of the early neuroblast marker ALK declined.

summary:
In Homo sapiens developing adrenal gland, late neuroblasts show increased expression of the differentiation markers SYN3 and IL7, whereas expression of the early neuroblast marker ALK declines.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:3bd02e93c89df1c18caf
claim_id: claim:3bd02e93c89df1c18caf
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Remarkably, neuroblasts and SCPs harbored distinct subpopulations of cycling cells, marked by the expression of MKI67 and TOP2A , whereas no such population was present in chromaffin or bridge cells

summary:
In Homo sapiens developing adrenal gland, cycling neuroblasts and cycling Schwann cell precursors are marked by the expression of MKI67 and TOP2A.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:6099571926d4930622db
claim_id: claim:6099571926d4930622db
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Remarkably, neuroblasts and SCPs harbored distinct subpopulations of cycling cells, marked by the expression of MKI67 and TOP2A , whereas no such population was present in chromaffin or bridge cells

summary:
In Homo sapiens developing adrenal gland, cycling Schwann cell precursors are marked by the expression of MKI67 and TOP2A.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:e3d7e51a146daa25f99b
claim_id: claim:e3d7e51a146daa25f99b
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
While PHOX2B was expressed during SCP to bridge transition, HAND2 was expressed starting in the bridge population and GATA3 late during bridge to neuroblast transition

summary:
In Homo sapiens developing adrenal gland, PHOX2B is expressed during Schwann cell precursor to bridge cell transition, HAND2 is expressed starting in the bridge cell population, and GATA3 is expressed late during bridge cell to neuroblast transition.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:f9d3abc0eabcc4b35bbc
claim_id: claim:f9d3abc0eabcc4b35bbc
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Expression of the cell cycle inhibitor CDKN1C was specific to chromaffin cells, while CCND1 , which encodes a promoter of cell cycle transition, was expressed in the neuroblast lineage.

summary:
In Homo sapiens developing adrenal gland, expression of the cell cycle inhibitor CDKN1C is specific to chromaffin cells, while CCND1 is expressed in the neuroblast lineage.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:3d3021217ca38bff16f5
claim_id: claim:3d3021217ca38bff16f5
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal: In neuroblasts, GATA3, SOX11 and TFAP2B showed high transcription factor activities.
summary:
In Homo sapiens developing adrenal gland, neuroblasts show high transcription factor activities of GATA3, SOX11 and TFAP2B.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:698f0705ac13ff19c5c2
claim_id: claim:698f0705ac13ff19c5c2
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal: PRPH , SYN3 , GAP43 , NTRK1 and SOX4 , which defined the most differentiated normal neuroblast
summary:
In Homo sapiens, PRPH, SYN3, GAP43, NTRK1 and SOX4 define the most differentiated normal late neuroblast state.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:d89eb703ea77c10ead22
claim_id: claim:d89eb703ea77c10ead22
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Conversely, the neuronal markers NPY , PRPH , NTRK1 and ISL1 are used to annotate chromaffin cells; these were clearly expressed in neuroblasts in our analyses.

summary:
In Homo sapiens developing adrenal gland, the neuronal markers NPY, PRPH, NTRK1 and ISL1 are clearly expressed in neuroblasts.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:65bd9718cbb310e85c49
claim_id: claim:65bd9718cbb310e85c49
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Expression of many other sympathetic neuronal marker genes in our neuroblasts supports our cell type annotation, including NEFM , STMN2 , SYN3 and ALK 27 , 29 , 30 , 31 .

summary:
In Homo sapiens developing adrenal gland, neuroblasts express the sympathetic neuronal marker genes NEFM, STMN2, SYN3 and ALK.


claim_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99:claim:480a9aa1f145ea8b1159
claim_id: claim:480a9aa1f145ea8b1159
paper_key: hca:0419_10.1038_s41588-021-00806-1_d66603cd99
span_literal:
Importantly, a subpopulation of mature chromaffin cells in our study expressed the well-established chromaffin marker PNMT , which encodes the enzyme that catalyzes the methylation of norepinephrine to form epinephrine 32 .

summary:
In Homo sapiens developing adrenal gland, a subpopulation of mature chromaffin cells expresses the well-established chromaffin marker PNMT.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:531c43d1018cb3c76c49
claim_id: claim:531c43d1018cb3c76c49
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, regulatory T cells are marked by high expression of FOXP3 and IL2RA.
span_literal:
Cells in C4 were predominantly Tregs, as evidenced by high levels of expression of Treg‐specific markers, FOXP3 and IL2RA .


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:dee759970ebf1f33553b
claim_id: claim:dee759970ebf1f33553b
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
C6 was enriched with cells expressing high levels of NK cell marker ( NCAM1 ) and killer cell lectin‐like receptor D1 ( KLRD1 ) (Figure 3C ), thus representing NK T cells.

summary:
In Homo sapiens, natural killer T cells are marked by high expression of NCAM1 and killer cell lectin‐like receptor D1 (KLRD1).


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:92eec2508d4751211ae6
claim_id: claim:92eec2508d4751211ae6
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, double negative T cells lack expression of FOXP3, NCAM1, CD4, and CD8.
span_literal:
In concordance with previous reports, 15 this T cell subpopulation lacked expression of FOXP3 as well as natural killer cell marker ( NCAM1 ), thus representing DN T cells ( CD4 − CD8 − NCAM1 − ).


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:1b6518aa8265d9c51cce
claim_id: claim:1b6518aa8265d9c51cce
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, double negative T cells show high expression of PLCG2.
span_literal:
These DN T cells also showed high expression of PLCG2 which is known to play an important role in T cell receptor signal transduction and T cell selection 16 (Figure 3D ).


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:9cb93650de1ba5e9eac4
claim_id: claim:9cb93650de1ba5e9eac4
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Cells in C5 ( CD8 + and CD4 + T cells) and C9 (DN T cells) expressed high levels of cell proliferation markers MKI67 and TOP2A , representing proliferative T cells.

summary:
In Homo sapiens, proliferative T cells express high levels of the cell proliferation markers MKI67 and TOP2A.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:3e710b953bce50e7d65d
claim_id: claim:3e710b953bce50e7d65d
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, naïve T cells are marked by high expression of ILR7 and CCR7.
span_literal:
C0, C7, and C8 showed enrichment of cells expressing high levels of naïve T cell markers ILR7 and CCR7 , representing naïve T cells.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:c5d122b0e0351210fde2
claim_id: claim:c5d122b0e0351210fde2
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
C1 showed enrichment of cells expressing high levels of cytotoxicity‐related genes ( GZMA , GZMB , GZMK , PRF1 , and NKG7 ), representing CD8 + cytotoxic T cells.

summary:
In Homo sapiens, CD8-positive cytotoxic T cells express high levels of cytotoxicity-related genes GZMA, GZMB, GZMK, PRF1, and NKG7.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:34d1aa0680323006534d
claim_id: claim:34d1aa0680323006534d
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Cells in C3 ( CD8 + T cells) expressed cytotoxicity‐related genes ( GZMA , GZMB , GZMK , PRF1 , and NKG7 ) and CTLA4 , LAG3 , PDCD1 ( PD1 ), HAVCR2 ( TIM3 ), TIGIT , and LAYN , suggestive of cytotoxic and exhausted CD8 + T cells 19 (Figure 3B,H,I ).

summary:
In Homo sapiens, cytotoxic and exhausted CD8-positive T cells express GZMA, GZMB, GZMK, PRF1, NKG7, CTLA4, LAG3, PDCD1, HAVCR2, TIGIT, and LAYN.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:5aff159ce4522e027c76
claim_id: claim:5aff159ce4522e027c76
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, plasma B cells express CD38 and CD27 but do not express MS4A1 (CD20) or CD24.
span_literal:
Plasma B cells were represented by C0, C3, C6, and C8, which expressed CD38 and CD27 but did not express MS4A1 / CD20 or CD24 .


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:aaebbe2c36c8f907eab6
claim_id: claim:aaebbe2c36c8f907eab6
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, memory B cells express MS4A1 (CD20), CD19, and CD27 but do not express CD38.
span_literal:
C1, C2, C4, C5, and C7 comprised memory B cells that expressed MS4A1 / CD20 , CD19 , and CD27 but did not express CD38 .


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:6da531f4d4c1c1c419bf
claim_id: claim:6da531f4d4c1c1c419bf
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Additionally, C6 was found to be enriched with cells expressing high levels of CCL5 , interleukins including IL32 and IL7R , and GNLY , indicating their cytotoxic potential.

summary:
In Homo sapiens, a cytotoxic plasma B cell subpopulation expresses high levels of CCL5, IL32, IL7R, and GNLY.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:ae4b397cce11fbf72ba8
claim_id: claim:ae4b397cce11fbf72ba8
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Cells in C0 showed high expression of immunoglobulin genes including IGKC , IGHG2 , IGLC3 , IGLC2 , and JCHAIN .

summary:
In Homo sapiens, plasma B cells show high expression of immunoglobulin genes IGKC, IGHG2, IGLC3, IGLC2, and JCHAIN.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:d701b53215f26ed58458
claim_id: claim:d701b53215f26ed58458
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, marginal zone B cells are marked by expression of MZB1.
span_literal:
C8 was enriched with cells expressing MZB1 , suggestive of a marginal zone (MZ) B cell subpopulation.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:8b50d012a499f81a921b
claim_id: claim:8b50d012a499f81a921b
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, macrophages express CD14, CD68, and FCGR3A (CD16).
span_literal:
The myeloid cell population (14% of the total cell population) was represented by 13 major clusters mostly consisting of macrophages (Clusters 0, 3, 4, 5, 6, and 10) expressing CD14 , CD68 , and FCGR3A ( CD16 ) (Figure 4A,B,E ).


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:fe99efe4c164a35afa17
claim_id: claim:fe99efe4c164a35afa17
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
C1 was enriched with cells expressing CD1C and CLEC10A , indicative of myeloid dendritic cells, whereas C2 and C12 were enriched with cells expressing CLEC4C and IL3RA , suggestive of plasmacytoid dendritic cells.

summary:
In Homo sapiens, myeloid dendritic cells express CD1C and CLEC10A, whereas plasmacytoid dendritic cells express CLEC4C and IL3RA.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:0f47fecbde8687b89f7d
claim_id: claim:0f47fecbde8687b89f7d
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Cells expressing APOBEC3A , which is involved in promoting pro‐inflammatory M1 macrophage polarization, 21 were enriched in C5.

summary:
In Homo sapiens, M1 macrophages are marked by expression of APOBEC3A, which promotes pro-inflammatory M1 macrophage polarization.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:eb1bb95cd230c485bfe8
claim_id: claim:eb1bb95cd230c485bfe8
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Cells in C0 and C4 were enriched with the expression of LGMN that was earlier reported to be involved in inducing M2 phenotype.

summary:
In Homo sapiens, M2 macrophages are marked by expression of LGMN, which is involved in inducing the M2 phenotype.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:693c94daa62b205311f5
claim_id: claim:693c94daa62b205311f5
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, lipid-laden foam macrophages are marked by expression of FABP5.
span_literal:
Cells expressing FABP5 , a marker for lipid‐rich foamy macrophages, 23 were enriched in C3, suggesting that they could be lipid‐laden foam macrophages.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:53876a0127e0e3b56eae
claim_id: claim:53876a0127e0e3b56eae
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
Cells started with an M1 phenotype expressing M1 marker genes ( CD86 ) and traveled through branch points one to four whereas cells with an M2 phenotype expressing M2 marker genes ( CD163 ) traveled through branch points two to four (Figure 4H,I ).

summary:
In Homo sapiens, M1 macrophages express the marker gene CD86 and M2 macrophages express the marker gene CD163.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:037efebc9578124a617a
claim_id: claim:037efebc9578124a617a
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, lymphatic endothelial cells are marked by expression of PDPN and PROX1.
span_literal:
PDPN was earlier reported to be expressed in lymphatic endothelium 27 and PROX1 is widely used as a marker for lymphatic endothelial cells.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:ecfdb973bc6ece5f8338
claim_id: claim:ecfdb973bc6ece5f8338
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, venous endothelial cells are marked by expression of ACKR1.
span_literal:
C0 and C6 were enriched with cells expressing ACKR1 , 30 suggestive of being enriched with venous endothelial cells.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:b2ab28d20cc8c9f34f4b
claim_id: claim:b2ab28d20cc8c9f34f4b
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, pericytes are marked by expression of PDGFRB.
span_literal:
C7 was enriched with cells expressing PDGFRB , a pericyte marker, 31 suggesting that these cells were pericytes.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:d3fc3321abb2661e5492
claim_id: claim:d3fc3321abb2661e5492
paper_key: hca:0420_10.1111_cas.15979_052ebae233
summary: In Homo sapiens, proliferative endothelial cells express the proliferation markers MKI67 and TOP2A.
span_literal:
C8 was enriched with cells expressing proliferation markers MKI67 and TOP2A , representing proliferative endothelial cells.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:92c9efac79fe2dd8a721
claim_id: claim:92c9efac79fe2dd8a721
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
The first group consisted of cells (C0, C3, and C7) with an enriched expression of ECM‐related genes, including the fibroblast activation protein ( FAP ), podoplanin ( PDPN ), and MMP‐related genes ( MMP2 , MMP1 , and MMP3 ) (Figure 5A,B,D–G ), thus, representing CAFs.

summary:
In Homo sapiens, cancer-associated fibroblasts are marked by enriched expression of fibroblast activation protein (FAP), podoplanin (PDPN), MMP2, MMP1, and MMP3.


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:fa9da0ce16951df1423b
claim_id: claim:fa9da0ce16951df1423b
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
The second group consists of cells (C1, C4, C5, and C6) with an enriched expression of alpha‐smooth muscle actin ( ACTA2 ) and myosin light chain proteins ( MYLK ) (Figure 5A,C,E,F,H ), thus representing myCAFs.

summary:
In Homo sapiens, cancer-associated myofibroblasts are marked by enriched expression of alpha-smooth muscle actin (ACTA2) and myosin light chain kinase (MYLK).


claim_key: hca:0420_10.1111_cas.15979_052ebae233:claim:7de4335061943996b4dc
claim_id: claim:7de4335061943996b4dc
paper_key: hca:0420_10.1111_cas.15979_052ebae233
span_literal:
In concordance with a previous report, 9 C7 cells were characterized by the expression of elastic fibroblasts markers ( MFAP4 , MFAP5 , and FBLN1 ), representing the elastic fibroblasts (Figure 5D ).

summary:
In Homo sapiens, elastic fibroblasts are characterized by expression of the markers MFAP4, MFAP5, and FBLN1.


claim_key: hca:0421_10.1101_2022.02.14.480397_c10e165496:claim:240bc1bf494155d485fb
claim_id: claim:240bc1bf494155d485fb
paper_key: hca:0421_10.1101_2022.02.14.480397_c10e165496
summary: In Homo sapiens, excitatory neuron subcluster 1 is marked by CUX2, CBLN2, and HS6ST3.
span_literal:
We found unique or enriched RNA markers for each of the cell types, including CUX2, CBLN2, HS6ST3 for excitatory neuron subcluster 1; TSHZ2, POU6F2, FOXP2 for excitatory neuron subcluster 2; NRG1, NEFL, CADPS2 for excitatory neuron subcluster 3; ADARB2, GALNTL6, RGS12 for inhibitory neuron subcluster 1; NXPH1, KIAA1217, SOX6 for inhibitory neuron subcluster 2; FGF13, TMEM132D, UNC13C for inhibitory neuron subcluster 3; ST18, PLP1, MBP for oligodendrocytes; AQP4, GFAP, RYR3 for astrocytes; SPP1, RUNX1, DOCK8 for microglia; LHFPL3, TNR, MEGF11 for oligodendrocyte precursor cells; EBF1, ADGRF5, TFPI for endothelial cells; SKAP1, GNLY, CD96 for brain-resident T cells ([Fig. 1D](480397v1_fig1.tif)).


claim_key: hca:0421_10.1101_2022.02.14.480397_c10e165496:claim:47e241b1ac6326ed6a69
claim_id: claim:47e241b1ac6326ed6a69
paper_key: hca:0421_10.1101_2022.02.14.480397_c10e165496
span_literal:
excitatory neuron-specific RNA markers were enriched in synapse related module M1 (e.g., HPCAL1, NPTX1, and SYN2), M2 (e.g., ERC2, CDH13, and CCK), and M11 (e.g., HPCA, and DCLK1).

summary:
In Homo sapiens, excitatory neuron-specific RNA markers include HPCAL1, NPTX1, SYN2, ERC2, CDH13, CCK, HPCA, and DCLK1.


claim_key: hca:0421_10.1101_2022.02.14.480397_c10e165496:claim:bb75a5b726ea5660f362
claim_id: claim:bb75a5b726ea5660f362
paper_key: hca:0421_10.1101_2022.02.14.480397_c10e165496
span_literal:
The M4 module was enriched for microglia markers (PADI2, CD14, and CD163) and endothelial cell markers (ANXA1, and CFH).

summary:
In Homo sapiens, microglia are marked by PADI2, CD14, and CD163, and endothelial cells are marked by ANXA1 and CFH.


claim_key: hca:0421_10.1101_2022.02.14.480397_c10e165496:claim:f41fbfc6191b8841b5b1
claim_id: claim:f41fbfc6191b8841b5b1
paper_key: hca:0421_10.1101_2022.02.14.480397_c10e165496
summary: In Homo sapiens, astrocytes are marked by SLC14A1, AQP4, and AGT.
span_literal:
The M7 module was associated with both astrocyte markers (SLC14A1, AQP4, and AGT) and endothelial cell markers (COL1A2, CAVIN2, and FN1).


claim_key: hca:0421_10.1101_2022.02.14.480397_c10e165496:claim:3ffc1d84660267644adc
claim_id: claim:3ffc1d84660267644adc
paper_key: hca:0421_10.1101_2022.02.14.480397_c10e165496
summary: In Homo sapiens, oligodendrocytes are marked by ANLN, ERMN, and CNP.
span_literal:
Oligodendrocyte markers were over-represented in the M5 module, including ANLN, ERMN, and CNP ([Fig. 5F](480397v1_fig5.tif)).


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:3af397db2425b42d26b1
claim_id: claim:3af397db2425b42d26b1
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
Expression of PDGFRB , MCAM and SUSD2 (Extended Data Fig. 2f–h ) suggests that this smooth muscle cell type contains previously identified endometrial cells with mesenchymal stem cell characteristics

summary:
In Homo sapiens endometrium, smooth muscle cells express PDGFRB, MCAM, and SUSD2, suggesting they contain cells with mesenchymal stem cell characteristics.


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:a7bf49bed047859a0d6e
claim_id: claim:a7bf49bed047859a0d6e
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
Four genes were selected for RNA staining, as these were highly discriminatory for the cell type (Fig. 1b ) but either had no previous functional annotation ( C11orf88 , C20orf85 , FAM183A ) or were annotated with noncilia-associated functionality ( CDHR3 )

summary:
In Homo sapiens endometrium, C11orf88, C20orf85, FAM183A, and CDHR3 are highly discriminatory markers for ciliated epithelial cells.


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:58ca0a9c22a7c9a75d2d
claim_id: claim:58ca0a9c22a7c9a75d2d
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
In unciliated epithelia, the dynamics demonstrated an overall continuous feature across phases 1–3 until an abrupt and uniform activation of a gene module marked the entrance into phase 4. Genes in this module included PAEP , GPX3 and CXCL14

summary:
In Homo sapiens endometrium, unciliated epithelial cells activate PAEP, GPX3, and CXCL14 at the entrance into the window of implantation (phase 4).


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:b9e2d6b98295100dd31c
claim_id: claim:b9e2d6b98295100dd31c
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
In phase 4 stromal fibroblasts the upregulated gene module includes DKK1 and CRYAB , among a few others that were recapitulated by consensus among whole-tissue analysis, and further confirms the identity of the WOI

summary:
In Homo sapiens endometrium, stromal fibroblasts in the window of implantation (phase 4) upregulate DKK1 and CRYAB.


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:c27f08b4bcc1ba4ffd65
claim_id: claim:c27f08b4bcc1ba4ffd65
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
In the same module we noticed the decidualization-initiating transcriptional factor FOXO1 (ref. 20 ) and decidualization stromal marker IL15 (ref. 21 ).

summary:
In Homo sapiens endometrium, stromal fibroblasts express the decidualization-initiating transcription factor FOXO1 and the decidualization stromal marker IL15.


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:2c39d5a0f7d5c1a9bf1e
claim_id: claim:2c39d5a0f7d5c1a9bf1e
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
Compared to their counterparts in nondecidualized endometrium, lymphocytes in decidualizing endometrium (phase 4) had increased expression of markers characteristic of uterine natural killer (NK) cells during pregnancy ( CD69 , ITGA1 , CD56 )

summary:
In Homo sapiens decidualizing endometrium, lymphocytes have increased expression of CD69, ITGA1, and CD56, which are markers characteristic of uterine natural killer cells.


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:89aefdf970db7b9d461e
claim_id: claim:89aefdf970db7b9d461e
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
summary: In Homo sapiens endometrium, WNT7A is exclusively expressed in luminal epithelial cells.
span_literal:
For example, WNT7A was overexpressed in one subpopulation in all proliferative phases (Fig. 5c ), and its exclusive expression in the luminal epithelia of human 29 , primate 30 and mouse 31 endometrium has been demonstrated in situ.


claim_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866:claim:4c4c9e9594d72d357b99
claim_id: claim:4c4c9e9594d72d357b99
paper_key: hca:0422_10.1038_s41591-020-1040-z_d966e12866
span_literal:
Similarly, we observed differential expression of LGR5 , ITGA1 and FOXA2 in one of the two subpopulations across multiple phases (Fig. 5c,d ), and previous in situ studies have reported their differential expression between luminal and glandular epithelia in both humans ( LGR5 (ref. 32 ), ITGA1 (ref. 33 ), FOXA2 (ref. 34 )) and mice ( FOXA2 (refs. 35 , 36 )).

summary:
In Homo sapiens endometrium, LGR5, ITGA1, and FOXA2 are differentially expressed between luminal epithelial cells and glandular epithelial cells.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:22124442f1a3274d6068
claim_id: claim:22124442f1a3274d6068
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
summary: In Homo sapiens, cone photoreceptors in the retina express GNAT2, OPN1SW, OPN1MW, and OPN1LW.
span_literal:
Cone photoreceptors expressed the cone-specific alpha subunit of transducin (GNAT2), and the short-wavelength (OPN1SW; blue), medium-wavelength, (OPN1MW; green), and long-wavelength (OPN1LW; red) opsins.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:d8b635509ed985eaee4c
claim_id: claim:d8b635509ed985eaee4c
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Rod photoreceptors were distinguished based on expression of phosphodiesterase 6-alpha (PDE6A), protein phosphatase with EF-hand domain 2 (PPEF2), the nuclear receptor transcription factor (NR2E3) (Fig. 1d, e ).

summary:
In Homo sapiens, rod photoreceptors in the retina are distinguished by expression of phosphodiesterase 6-alpha (PDE6A), protein phosphatase with EF-hand domain 2 (PPEF2), and the nuclear receptor transcription factor NR2E3.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:3ea9eeca4aa2c9620919
claim_id: claim:3ea9eeca4aa2c9620919
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Retinal ganglion cells were identified based on the expression of the neurofilament medium polypeptide (NEFM) and the solute carrier family 17 member 6 (SLC17A6).

summary:
In Homo sapiens, retinal ganglion cells are identified by expression of neurofilament medium polypeptide (NEFM) and solute carrier family 17 member 6 (SLC17A6).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:44cedeef7967d5503fd3
claim_id: claim:44cedeef7967d5503fd3
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Bipolar cells were marked based on expression of the marker Calcium/Calmodulin-dependent protein kinase II (CAMK2B), the glutamate metabotropic receptor 6 (GRM6), the transmembrane protein 215 (TMEM215), and the transient receptor potential cation channel subfamily M member 1 (TRPM1).

summary:
In Homo sapiens, bipolar cells in the retina are marked by expression of calcium/calmodulin-dependent protein kinase II (CAMK2B), glutamate metabotropic receptor 6 (GRM6), transmembrane protein 215 (TMEM215), and transient receptor potential cation channel subfamily M member 1 (TRPM1).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:9758e30bdc4c3ce151b0
claim_id: claim:9758e30bdc4c3ce151b0
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal: Glutamate decarboxylase 1 (GAD1) and complement C1q like 2 (C1QL2) labeled amacrine cells.
summary:
In Homo sapiens, amacrine cells in the retina are labeled by glutamate decarboxylase 1 (GAD1) and complement C1q like 2 (C1QL2).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:566816571d2db481c5e8
claim_id: claim:566816571d2db481c5e8
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal: The transcription factors (ONECUT1, ONECUT2, and LHX1) allowed identification of horizontal cells.
summary:
In Homo sapiens, horizontal cells in the retina are identified by expression of the transcription factors ONECUT1, ONECUT2, and LHX1.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:3dad0f56abb0d0cbd9c3
claim_id: claim:3dad0f56abb0d0cbd9c3
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
The cell group corresponding to Müller glia and astrocytes was identified based on expression of glutamine synthetase (GLUL), clusterin (CLU), and apolipoprotein E (APOE).

summary:
In Homo sapiens, the macroglia group comprising Müller glia and astrocytes in the retina is identified by expression of glutamine synthetase (GLUL), clusterin (CLU), and apolipoprotein E (APOE).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:90d06c3e9c8d67db24b1
claim_id: claim:90d06c3e9c8d67db24b1
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
The group of cells corresponding to resident microglia was identified based on the expression of complement protein (C1QA), transmembrane protein 119 (TMEM119), allograft inflammatory factor 1 (AIF1) and CD163.

summary:
In Homo sapiens, resident microglia in the retina are identified by expression of complement protein C1QA, transmembrane protein 119 (TMEM119), allograft inflammatory factor 1 (AIF1), and CD163.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:ddd5044f6e2b73ee373e
claim_id: claim:ddd5044f6e2b73ee373e
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Cells lining the retinal vasculature were marked by CD34, cadherin 5 (CDH5), Regulator Of G Protein Signaling 5 (RGS5), and the ADAM metallopeptidase with Thrombospondin Type 1 Motif 9 (ADAMTS9) (Fig. 1d, e ).

summary:
In Homo sapiens, vascular cells lining the retinal vasculature are marked by CD34, cadherin 5 (CDH5), regulator of G protein signaling 5 (RGS5), and ADAM metallopeptidase with thrombospondin type 1 motif 9 (ADAMTS9).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:7fb37ae151656cf6af8a
claim_id: claim:7fb37ae151656cf6af8a
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
The first subtype (FOS-expressing) was enriched with markers known to be expressed in astrocytes including intermediate-filament glial fibrillary acidic protein (GFAP) and the sparc-like protein (SPARCL1) 5 , 23 .

summary:
In Homo sapiens, the FOS-expressing macroglial subtype in the retina is enriched with markers known to be expressed in astrocytes, including glial fibrillary acidic protein (GFAP) and sparc-like protein (SPARCL1).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:aafa1a89b0a29a7707c8
claim_id: claim:aafa1a89b0a29a7707c8
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Within this subtype, the immediate-early response genes FOS, FOSB, JUN, and EGR1 24 were also detected (Fig. 3c ).

summary:
In Homo sapiens, the FOS-expressing macroglial subtype in the retina expresses the immediate-early response genes FOS, FOSB, JUN, and EGR1.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:c0e10ddb18b090494137
claim_id: claim:c0e10ddb18b090494137
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
The second subtype displayed increased expression of multiple genes associated with AMD including COL4A3, vascular endothelial growth factor (VEGFA), and HTRA1, and was found to be significantly enriched in the macula compared to the periphery (Fig. 3h–k ).

summary:
In Homo sapiens, the COL4A3-expressing macroglial subtype in the retina displays increased expression of COL4A3, vascular endothelial growth factor A (VEGFA), and HTRA1.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:3fb42982c51cf50cdd9e
claim_id: claim:3fb42982c51cf50cdd9e
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Furthermore, significant upregulation of genes associated with metabolism including the glucose transporter (SLC2A1/GLUT1), the glutamate transporter (SLC1A3/GLAST1), and Serine Hydroxymethyltransferase 2 (SHMT2), which is involved in de novo serine synthesis 30 , 31 was observed in this subset of Müller glia.

summary:
In Homo sapiens, the COL4A3-expressing Müller glia subtype in the retina shows significant upregulation of the glucose transporter SLC2A1, the glutamate transporter SLC1A3, and serine hydroxymethyltransferase 2 (SHMT2).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:5e5c72951a2952deb3c4
claim_id: claim:5e5c72951a2952deb3c4
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
The third subtype expressed higher levels of ferritin heavy chain (FTH1) and ferritin light chain (FTL) (Fig. 3c ).

summary:
In Homo sapiens, the FTL-expressing macroglial subtype in the retina expresses higher levels of ferritin heavy chain (FTH1) and ferritin light chain (FTL).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:c75c8390a9a38cb7a8b1
claim_id: claim:c75c8390a9a38cb7a8b1
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
In addition, this macroglial subset also expresses diazepam-binding inhibitor (DBI), which regulates activation of microglia by limiting the magnitude of inflammatory responses upon initiation and facilitating a return to baseline homeostasis 36 .

summary:
In Homo sapiens, the FTL-expressing macroglial subtype in the retina also expresses diazepam-binding inhibitor (DBI).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:670a1238c0459c18769a
claim_id: claim:670a1238c0459c18769a
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Three subtype-specific markers, FOS, FTL, and COL4A3, had significantly higher expression within their corresponding subpopulation (adjusted p -value < 0.001, one-sided Wilcoxon rank-sum test) (Fig. 3d ), which we verified using fluorescent in situ hybridization.

summary:
In Homo sapiens, three macroglial subtype-specific markers FOS, FTL, and COL4A3 had significantly higher expression within their corresponding macroglial subpopulation in the retina.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:0957a36fcb34a8a8fdba
claim_id: claim:0957a36fcb34a8a8fdba
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
We validated that TIMP3 is expressed in Müller glia through co-localization with APOE, and in vascular cells through co-localization with TM4SF1 (Fig. 4d, e ), in addition to its previously reported expression in the retinal pigment epithelium 39 .

summary:
In Homo sapiens, tissue inhibitor of metalloproteinase 3 (TIMP3) is expressed in Müller glia, validated through co-localization with APOE in the retina.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:59257fe558233cf0517f
claim_id: claim:59257fe558233cf0517f
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
We validated that TIMP3 is expressed in Müller glia through co-localization with APOE, and in vascular cells through co-localization with TM4SF1 (Fig. 4d, e ), in addition to its previously reported expression in the retinal pigment epithelium 39 .

summary:
In Homo sapiens, tissue inhibitor of metalloproteinase 3 (TIMP3) is expressed in vascular cells, validated through co-localization with TM4SF1 in the retina.


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:e877780f73bc757cc1b0
claim_id: claim:e877780f73bc757cc1b0
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
summary: In Homo sapiens, complement factor I (CFI) co-localizes with APOE in Müller glia in the retina.
span_literal:
This complement factor co-localized with APOE in Müller glia, among other retinal cell types (Fig. 4c ).


claim_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a:claim:1bf308afbb84e3676cbe
claim_id: claim:1bf308afbb84e3676cbe
paper_key: hca:0423_10.1038_s41467-019-12780-8_0da964452a
span_literal:
Of note, GLUT1 and VEGFA are target genes of hypoxia-inducible factor HIF1A 32 , which was also found to be upregulated in this subset Fig. 3b, c ).

summary:
In Homo sapiens, hypoxia-inducible factor HIF1A is upregulated in the COL4A3-expressing Müller glia subtype in the retina.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:ddb017eb6f194690b1e2
claim_id: claim:ddb017eb6f194690b1e2
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
We identified 12 transcripts (11 genes - INS , HADH , SEC11C , PFKB2 , MAP1B , SCD , RNR2 , OLMALINC , DNAJC3 , UCHL1 and G6PC2 ) to be highly expressed in β-cells

summary:
In Homo sapiens, INS, HADH, SEC11C, PFKFB2, MAP1B, SCD, RNR2, OLMALINC, DNAJC3, UCHL1, and G6PC2 are highly expressed in pancreatic beta cells compared to alpha cells.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:2f40b9daef7d583a2611
claim_id: claim:2f40b9daef7d583a2611
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
17 transcripts (17 genes - GCG , TTR , ALDH1A1 , CLU , TMEM176B , GC , BEX3 , HIGD1A , ELL2 , MYL6 , CYSTM1 , H3F3B , LDHA , NAA20 , FABP5 , STMN1 , RBX1 ) to be highly expressed among α-cells

summary:
In Homo sapiens, GCG, TTR, ALDH1A1, CLU, TMEM176B, GC, BEX3, HIGD1A, ELL2, MYL6, CYSTM1, H3F3B, LDHA, NAA20, FABP5, STMN1, and RBX1 are highly expressed in pancreatic alpha cells compared to beta cells.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:acb3367e082b7f93f3f4
claim_id: claim:acb3367e082b7f93f3f4
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
Validation of human non-diabetic islet gene expression 8 – 11 showed concordantly high expression of transcripts in sixteen genes among our α-cells ( GCG , TTR , GC , TMEM176B , HIGD1A , GPX3 , TM4SF4 , FABP5 , LDHA , NAA20 , CRYBA2 , SERPINA1 , PDK4 , HLA-E , PALLD and C10orf10 , adjusted P-value between 2.28 × 10 −97 and 0.01)

summary:
In Homo sapiens, GCG, TTR, GC, TMEM176B, HIGD1A, GPX3, TM4SF4, FABP5, LDHA, NAA20, CRYBA2, SERPINA1, PDK4, HLA-E, PALLD, and C10orf10 show concordantly high expression in pancreatic alpha cells.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:f300207840dd04fff1c4
claim_id: claim:f300207840dd04fff1c4
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
and 14 genes among our β-cells ( INS , HADH , PFKB2 , G6PC2 , RPL3 , EIF4A2 , RRAGD , HNRNPC , IAPP , CANX , FAM162A , ACAT1 , TVP23B and SERINC1 , adjusted P-value between 2.81 × 10 −81 and 0.04)

summary:
In Homo sapiens, INS, HADH, PFKFB2, G6PC2, RPL3, EIF4A2, RRAGD, HNRNPC, IAPP, CANX, FAM162A, ACAT1, TVP23B, and SERINC1 show concordantly high expression in pancreatic beta cells.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:fd31308c0c7a9e8a5c70
claim_id: claim:fd31308c0c7a9e8a5c70
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
Nine α-cell genes ( ALDHA1, CLU, BEX3, ELL2, MYL6, CYSTM1, H3F3B, STMN1 and RBX1 ) and seven β-cell genes ( OLMALINC, RNR2, SCD, MAP1B, DNAJC3, SEC11C and UCHL1) were significantly expressed in our East-Asian data (Table 1 ) but not reported as unique non-diabetic upregulated human α- or β-cell genes 8 – 11 .

summary:
In Homo sapiens, ALDH1A1, CLU, BEX3, ELL2, MYL6, CYSTM1, H3F3B, STMN1, and RBX1 are significantly expressed in pancreatic alpha cells in East-Asian subjects.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:22f7a91b43927d45cd4a
claim_id: claim:22f7a91b43927d45cd4a
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
Nine α-cell genes ( ALDHA1, CLU, BEX3, ELL2, MYL6, CYSTM1, H3F3B, STMN1 and RBX1 ) and seven β-cell genes ( OLMALINC, RNR2, SCD, MAP1B, DNAJC3, SEC11C and UCHL1) were significantly expressed in our East-Asian data (Table 1 ) but not reported as unique non-diabetic upregulated human α- or β-cell genes 8 – 11 .

summary:
In Homo sapiens, OLMALINC, RNR2, SCD, MAP1B, DNAJC3, SEC11C, and UCHL1 are significantly expressed in pancreatic beta cells in East-Asian subjects.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:47d7d1f11bb475703c83
claim_id: claim:47d7d1f11bb475703c83
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
summary: In Homo sapiens, REG1A is highly expressed in exocrine cells of the pancreas.
span_literal:
We excluded 47 exocrine cells (with high REG1A expression) and 18 doublet cells and performed additional hierarchical clustering and PCA analyses based on INS , GCG and SST transcript expression levels


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:7bbaa83f93e9625c8dd0
claim_id: claim:7bbaa83f93e9625c8dd0
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
For three hits (DNAJC3, UCHL1 and PFKB2) that showed higher expression levels in our β-cells (as compared to α-cells) we further performed immunohistochemistry validations on islet sections of the three subjects used in the study.

summary:
In Homo sapiens, DNAJC3, UCHL1, and PFKFB2 show higher expression levels in pancreatic beta cells as compared to pancreatic alpha cells.


claim_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0:claim:4c6261059108477c08ef
claim_id: claim:4c6261059108477c08ef
paper_key: hca:0425_10.1038_s41598-017-05266-4_54c44ec7e0
span_literal:
FAM46A that was reported to be upregulated in mouse β-cells 7 however showed higher expression in our human α-cells (adjusted P-value = 4.21 × 10 −4 ).

summary:
In Homo sapiens, FAM46A shows higher expression in pancreatic alpha cells compared to pancreatic beta cells.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:0d0184cc9d8f998584a5
claim_id: claim:0d0184cc9d8f998584a5
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
summary: In Homo sapiens, naive or central memory T cells express CCR7, SELL, and TCF7.
span_literal:
CD4 + T cells comprised 6–7 clusters: resting cells expressing CCR7 , SELL and TCF7 , (corresponding to naive or TCM cells)


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:d80793e3cfa0aeead812
claim_id: claim:d80793e3cfa0aeead812
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
summary: In Homo sapiens, regulatory T cells express the defining genes FOXP3, IL2RA, and CTLA4.
span_literal:
a distinct regulatory T cell (Treg) cluster expressing Treg-defining genes FOXP3 , IL2RA , and CTLA4


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:c2f3a54fa9433e76b88f
claim_id: claim:c2f3a54fa9433e76b88f
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
two TEM/TRM-like clusters expressing CCL5 , cytotoxicity-associated genes ( GZMB, GZMK ), and TRM markers ( CXCR6 , ITGA1 )

summary:
In Homo sapiens, effector memory/tissue resident memory CD8+ T cells express CCL5, GZMB, GZMK, CXCR6, and ITGA1.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:d46d903dc5b0a4f28286
claim_id: claim:d46d903dc5b0a4f28286
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal: an activated TRM/TEM cluster expressing IFNG, CCL4, CCL3
summary:
In Homo sapiens, activated tissue resident memory/effector memory T cells express IFNG, CCL4, and CCL3.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:7928357c6623cf549882
claim_id: claim:7928357c6623cf549882
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
clusters representing terminally differentiated effector cells (TEMRA) expressing cytotoxic markers PRF1 and NKG7

summary:
In Homo sapiens, terminally differentiated effector cells express the cytotoxic markers PRF1 and NKG7.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:e56c37413333719620ab
claim_id: claim:e56c37413333719620ab
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
summary: In Homo sapiens, resting CD4+ naive/central memory T cells are defined by SELL, KLF2, and LEF1.
span_literal:
a putative resting CD4 + Naive/Central memory (NV/CM) module enriched in CD4 + T cells and defined by genes associated with lymphoid homing, egress and quiescence ( SELL , KLF2 , LEF1 , respectively)


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:e4f6bd873e31ded468dd
claim_id: claim:e4f6bd873e31ded468dd
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
summary: In Homo sapiens, resting CD4+/CD8+ T cells are distinguished by expression of IL7R and AQP3.
span_literal:
a CD4 + /CD8 + Resting module, distinguished by expression of IL7R , a receptor required for T cell survival 40 , 41 , and AQP3 , which encodes a water channel protein of unclear function in lymphocytes 42


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:541818ef0e2c1d09185d
claim_id: claim:541818ef0e2c1d09185d
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
A Proliferation module expressed by activated CD4 + and CD8 + lineages included genes associated with T cell activation/proliferation ( IL2, LIF ) and cell division ( CENPV , G0S2 , ORC6 )

summary:
In Homo sapiens, the proliferation module of activated CD4+ and CD8+ T cells includes IL2, LIF, CENPV, G0S2, and ORC6.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:7f6a68f189d50511f7e7
claim_id: claim:7f6a68f189d50511f7e7
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
summary: In Homo sapiens, the proliferation module of activated T cells is marked by expression of NME1.
span_literal:
This module was also marked by expression of NME1 , a metastasis suppressor/endonuclease-encoding gene 43 not previously associated with T cells


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:2c1064ff8cb578a708c5
claim_id: claim:2c1064ff8cb578a708c5
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
An Interferon (IFN) Response module enriched among activated CD4 + T cells included multiple gene families associated with canonical IFN responses 44 – 46 ( IFIT3 , IFIT2 , STAT1 , MX1 , IRF7 , and JAK2 )

summary:
In Homo sapiens, the interferon response module enriched among activated CD4+ T cells includes IFIT3, IFIT2, STAT1, MX1, IRF7, and JAK2.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:e5f3d503236af31374a2
claim_id: claim:e5f3d503236af31374a2
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
CD8 + T cell-enriched modules included a Cytotoxic module, containing genes associated with cytotoxicity ( GNLY , GZMK ) and transcription factors associated with effector/memory differentiation ( ZEB2 , EOMES, ZNF683)

summary:
In Homo sapiens, the cytotoxic module enriched in CD8+ T cells contains GNLY, GZMK, ZEB2, EOMES, and ZNF683.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:cfd9a45087d91d0864ce
claim_id: claim:cfd9a45087d91d0864ce
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
a Cytokine module with genes encoding chemokines and cytokines ( CCL3 , CCL4 , CCL20 , IFNG , IL10 , TNF ), inhibitory molecules ( LAG3 , CD226 (TIGIT), HAVCR2 (TIM3)), and the widely expressed homeobox protein HOPX

summary:
In Homo sapiens, the cytokine module enriched in CD8+ T cells includes CCL3, CCL4, CCL20, IFNG, IL10, TNF, LAG3, CD226, HAVCR2, and HOPX.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:1f95f06fb18e2e96da47
claim_id: claim:1f95f06fb18e2e96da47
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
FOXP3 (Treg marker), CXCR6 (TRM marker), IFIT3 (IFN response marker), NME1 (activation marker), PRF1 (cytotoxic marker)

summary:
In Homo sapiens, FOXP3 is a marker of regulatory T cells, CXCR6 is a marker of tissue resident memory T cells, IFIT3 is an interferon response marker, NME1 is an activation marker, and PRF1 is a cytotoxic marker.


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:4f16775800024eeb7d6e
claim_id: claim:4f16775800024eeb7d6e
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
summary: In Homo sapiens, CCL5 is a marker of CD8+ effector memory T cells.
span_literal:
Resting memory T cells in tissues and blood express high levels of CCL5 (Supplementary Fig. 5 ), a marker of CD8 + TEM cells 35


claim_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d:claim:bcbb7fa726c465c3c19b
claim_id: claim:bcbb7fa726c465c3c19b
paper_key: hca:0426_10.1038_s41467-019-12464-3_0f8440336d
span_literal:
These results establish NME1 expression as a marker of T cell activation, coupled to the extent of proliferation.

summary:
In Homo sapiens, NME1 expression is established as a marker of activated T cells, coupled to the extent of proliferation.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:6368780abffd2c2400ce
claim_id: claim:6368780abffd2c2400ce
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
Besides SPARCL1, 81% of endothelial cells expressed PLVAP however, only 2% of the other cells expressed PLVAP.

summary:
In Homo sapiens, endothelial cells are marked by PLVAP expression, with 81% of endothelial cells expressing PLVAP compared to only 2% of other cells.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:2885ef1a08e1e6687c26
claim_id: claim:2885ef1a08e1e6687c26
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
Similarly, S100A2, KRT14, KRT17, and KRT6A were overwhelmingly expressed in cancer cells and their expression values were significantly higher than the other cells (log 10 FC > 3 and P < 0.001; Table S3 ).

summary:
In Homo sapiens, cancer cells are marked by overwhelmingly high expression of S100A2, KRT14, KRT17, and KRT6A compared to other cells.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:6d9c6407f0fbac2f1b45
claim_id: claim:6d9c6407f0fbac2f1b45
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
In addition, CTRB2, REG3A, and REG1A were highly expressed in more than 90% of acinar cells, and CTRB2 was the most different gene compared with the other cells (log 10 FC = 4.67; Table S3 ).

summary:
In Homo sapiens, acinar cells are marked by high expression of CTRB2, REG3A, and REG1A in more than 90% of acinar cells.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:051be026a22d08cd2240
claim_id: claim:051be026a22d08cd2240
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
Thus, we identified S100A2, PLVAP, and CTRB2 as novel markers for PASC, endothelial, and acinar cells, respectively (Figure 3 B).

summary:
In Homo sapiens, S100A2 is a novel marker for pancreatic adenosquamous carcinoma cells, PLVAP is a novel marker for endothelial cells, and CTRB2 is a novel marker for acinar cells.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:d63ff7555e50afa81c2b
claim_id: claim:d63ff7555e50afa81c2b
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
We identified 559 cancer cells according to epithelial and cancer markers including KRT19, KRT7, EPCAM, SOX9, and KRT23.

summary:
In Homo sapiens, cancer cells are identified by epithelial and cancer markers including KRT19, KRT7, EPCAM, SOX9, and KRT23.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:06d36ee108b69cba78f3
claim_id: claim:06d36ee108b69cba78f3
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
Notably, we observed that UBE2C, ASPM, CENPF, and TOP2A were significantly overexpressed in C1 compared to the other clusters.

summary:
In Homo sapiens, cancer cell cluster 1 is marked by significant overexpression of UBE2C, ASPM, CENPF, and TOP2A compared to other cancer cell clusters.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:602d2f7164ddf8e7fe09
claim_id: claim:602d2f7164ddf8e7fe09
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal: Furthermore, NUSAP1 and TPX2, as C1 marker genes, contribute to spindle organization.
summary:
In Homo sapiens, NUSAP1 and TPX2 are marker genes of cancer cell cluster 1, contributing to spindle organization.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:7c7820ae0399c101b0b7
claim_id: claim:7c7820ae0399c101b0b7
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
summary: In Homo sapiens, cancer cell cluster 2 expresses the transcription factors MXD1, ELF3, and LMO7.
span_literal:
We also observed that C2 expressed several transcription factors, including MXD1, ELF3, and LMO7 ( Table S9 ).


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:fdfaa55c7864bad0b57b
claim_id: claim:fdfaa55c7864bad0b57b
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
We discovered the overexpression of laminins (LAMA3, LAMC2, and LAMB3), MMP1, and SERPINE1 in C3 ( Table S10 ), suggesting that this cell type participates in microenvironmental reconstruction.

summary:
In Homo sapiens, cancer cell cluster 3 is marked by overexpression of LAMA3, LAMC2, LAMB3, MMP1, and SERPINE1, suggesting participation in microenvironmental reconstruction.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:f9ce50178b380be60193
claim_id: claim:f9ce50178b380be60193
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
Since the pathological tumor tissue was adenosquamous carcinoma, we observed several keratins, including KRT1, KRT6B, KRTDAP, and KRT10, in C5 ( Table S12 ).

summary:
In Homo sapiens, cancer cell cluster 5 expresses several keratins including KRT1, KRT6B, KRTDAP, and KRT10.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:967dd225ec663e8f8983
claim_id: claim:967dd225ec663e8f8983
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal: Notably, cluster 1 exhibited stem-like phenotypes expressing UBE2C, ASPM, and TOP2A.
summary:
In Homo sapiens, cancer cell cluster 1 exhibits stem-like phenotypes expressing UBE2C, ASPM, and TOP2A.


claim_key: hca:0427_10.7150_ijbs.58886_44183be8e8:claim:67775bbf09b4fa6cd745
claim_id: claim:67775bbf09b4fa6cd745
paper_key: hca:0427_10.7150_ijbs.58886_44183be8e8
span_literal:
The expression of EREG, FCGR2A, CCL4L2, and CTSC increased in myeloid cells from the normal pancreas to PASC.

summary:
In Homo sapiens, the expression of EREG, FCGR2A, CCL4L2, and CTSC increased in myeloid cells from the normal pancreas to pancreatic adenosquamous carcinoma.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:71b3833d6ae95dc09c75
claim_id: claim:71b3833d6ae95dc09c75
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
The cells in clusters 1 and 2 are interpreted as Schwann cells, with high expression of the proteolipid protein gene ( PLP1 ), which encodes the most abundant protein in myelin ( Fig. 1 C ).

summary:
In Homo sapiens, Schwann cells are characterized by high expression of proteolipid protein 1 (PLP1) in the choroid.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:b80c41d1918dab47e3d9
claim_id: claim:b80c41d1918dab47e3d9
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens choroid, melanocytes specifically express MLANA, PMEL, TYRP1, and DCT.
span_literal:
Cluster 3 is interpreted as being derived from melanocytes, which are responsible for choroidal pigmentation but have a largely unknown function within the choroid ( 6 ). Cells in this cluster demonstrate specific expression of the melanocyte-specific trafficking protein MLANA ( Fig. 1 C ), as well as melanocyte protein ( PMEL ), tyrosinase-associated protein-1 ( TYRP1 ), and dopachrome tautomerase ( DCT ) ( SI Appendix , Fig. S1 ).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:466d99d9647f7c110c25
claim_id: claim:466d99d9647f7c110c25
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, endothelial cells show high expression of VWF, CD34, and ICAM2.
span_literal:
Cluster 4 is proposed to consist of endothelial cells, with high expression of VWF ( Fig. 1 C ), CD34 , and ICAM2 ( SI Appendix , Fig. S1 ).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:52a6cf3d4a93ae6ecc30
claim_id: claim:52a6cf3d4a93ae6ecc30
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, smooth muscle cells are characterized by high expression of ACTA2 and RGS5.
span_literal:
Cells with smooth muscle expression patterns constituted cluster 5, with high expression of smooth muscle α-actin ( ACTA2 ) ( Fig. 1 C ) and RGS5 ( SI Appendix , Fig. S1 ).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:49de0138c0de4450edc5
claim_id: claim:49de0138c0de4450edc5
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
Clusters 8 to 11 are interpreted as circulating and resident leukocytes, with high expression of PTPRC (which encodes the cell surface gene product CD45, or leukocyte common antigen, expressed on all classes of leukocytes) ( Fig. 1 C ).

summary:
In Homo sapiens, leukocytes are characterized by high expression of PTPRC (encoding CD45, leukocyte common antigen).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:f1f7700b1daeb2ab8a75
claim_id: claim:f1f7700b1daeb2ab8a75
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, B cells express CD79A and T cells/natural killer cells express CD2.
span_literal:
Lymphocytes segregated into clusters 8 and 9, with CD79A -expressing B cells forming cluster 8 while CD2 -expressing T cells/NK cells formed cluster 9.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:85de3567d26b48aacca3
claim_id: claim:85de3567d26b48aacca3
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, monocytes and/or macrophages are characterized by high expression of AIF1.
span_literal:
Cluster 10 consists of monocytes and/or macrophages, with high expression of the activated macrophage inflammatory cytokine AIF1 .


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:f233b0275fae0e982e17
claim_id: claim:f233b0275fae0e982e17
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, Schwann cells express the canonical Schwann cell genes PLP1 and SOX10.
span_literal:
Both Schwann cell clusters express the canonical Schwann cell genes PLP1 and transcription factor SOX10 .


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:a3e4066a9a2f509ee19f
claim_id: claim:a3e4066a9a2f509ee19f
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, myelinating Schwann cells are characterized by high expression of MPZ and MBP.
span_literal:
The 2 most up-regulated genes in Schwann cell cluster 1 were myelin protein zero ( MPZ ) and myelin basic protein ( MBP ), both of which encode proteins found in myelinating Schwann cells.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:b028c8bd167dd125c8e3
claim_id: claim:b028c8bd167dd125c8e3
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, nonmyelinating Schwann cells express SCN7A, NGFR, NCAM1, and L1CAM.
span_literal:
In contrast, nonmyelinating Schwann cells express SCN7A , NGFR , NCAM1 , and L1CAM , all of which were enriched in cluster 2.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:e6a8431ae5707f10e656
claim_id: claim:e6a8431ae5707f10e656
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
Retinal endothelial cells were enriched in expression of regulators of barrier permeability, such as CLDN5 , which regulates endothelial cell permeability, and SLC2A1 , which encodes the major glucose transporter in the blood–brain barrier ( 33 ).

summary:
In Homo sapiens, retinal endothelial cells are enriched in expression of CLDN5 and SLC2A1 compared to choroidal endothelial cells.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:841948bd203937b14bb4
claim_id: claim:841948bd203937b14bb4
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
In contrast, choroidal endothelial cells were enriched in several genes involved in leukocyte recruitment and adhesion, including VCAM1 , CCL2 , SELP , and ICAM1 .

summary:
In Homo sapiens, choroidal endothelial cells are enriched in VCAM1, CCL2, SELP, and ICAM1 compared to retinal endothelial cells.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:d1999995516ec720624c
claim_id: claim:d1999995516ec720624c
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
Choroidal endothelial cells also demonstrated higher expression of CLU , a negative regulator of complement activation ( 34 ).

summary:
In Homo sapiens, choroidal endothelial cells demonstrate higher expression of CLU compared to retinal endothelial cells.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:1135df13b743bdbd0291
claim_id: claim:1135df13b743bdbd0291
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, venous endothelial cells are characterized by high expression of DARC and MMRN1.
span_literal:
Clusters 5 and 6 were interpreted as endothelial cells derived from venules and/or veins, with high expression of the chemokine receptor DARC ( 35 ) and adhesion protein MMRN1 ( 36 ), both of which have been reported to be vein specific.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:02442d952b57d17a42f8
claim_id: claim:02442d952b57d17a42f8
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
Cluster 7 consists of 1,013 cells classified as choriocapillaris endothelial cells, with high expression of membrane-associated carbonic anhydrase CA4 ( 11 ) and PLVAP , which localizes to endothelial fenestrae ( 37 ).

summary:
In Homo sapiens, choriocapillaris endothelial cells are characterized by high expression of CA4 and PLVAP.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:00eba4c390f03a79de31
claim_id: claim:00eba4c390f03a79de31
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
Cluster 8 consists of endothelial cells of arterial origin, with high expression of artery-enriched genes FBLN2 and SEMA3G ( 36 ).

summary:
In Homo sapiens, arterial endothelial cells are characterized by high expression of FBLN2 and SEMA3G.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:3d7d88cefd1b5a270455
claim_id: claim:3d7d88cefd1b5a270455
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, arterial endothelial cells demonstrate strong expression of GJA4, GJA5, and HEY1.
span_literal:
Arterial-derived cells demonstrate strong expression of gap-junction proteins GJA4 and GJA5 as well as Notch signaling protein HEY1, all of which regulate arteriogenesis ( 38 , 39 ).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:aeba59080f0b4d87f184
claim_id: claim:aeba59080f0b4d87f184
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, venous endothelial cells highly express DARC, SELE, VCAM1, and CCL23.
span_literal:
In contrast, veins highly express many genes associated with leukocyte recruitment, including DARC , SELE , VCAM1 , and CCL23 .


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:2c13cbd5f17067c24f03
claim_id: claim:2c13cbd5f17067c24f03
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
In addition to canonical choriocapillaris genes CA4 and PLVAP , the choriocapillaris demonstrates specific expression of genes important in regulating barrier function ( SIPR3 , SPARC ) ( 40 , 41 ) and cellular adhesion ( PCDH12 ) ( 42 ).

summary:
In Homo sapiens, choriocapillaris endothelial cells specifically express CA4, PLVAP, SIPR3, SPARC, and PCDH12.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:bd09fc07656fbbb45f2f
claim_id: claim:bd09fc07656fbbb45f2f
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
RGCC , a gene that responds to complement and has been shown to induce endothelial apoptosis, was specifically expressed in choriocapillaris endothelial cells.

summary:
In Homo sapiens, RGCC (regulator of cell cycle gene) is specifically expressed in choriocapillaris endothelial cells.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:6ce7947da319f6502a22
claim_id: claim:6ce7947da319f6502a22
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
We found that the choriocapillaris highly and specifically expresses the regulator of cell cycle gene ( RGCC ), a gene that responds to complement activation and induces apoptosis in endothelial cells.

summary:
In Homo sapiens, the choriocapillaris endothelial cell highly and specifically expresses the regulator of cell cycle gene (RGCC).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:daa39a7c1ba24547fe14
claim_id: claim:daa39a7c1ba24547fe14
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
Functionally, the choriocapillaris highly expresses HLA class I self-peptides ( 9 ), ICAM-1 ( 10 ), and carbonic anhydrase 4 (CA4) ( 11 ), which help regulate the metabolic and inflammatory environment within the choroid and the tissues it supports.

summary:
In Homo sapiens, the choriocapillaris endothelial cell highly expresses ICAM-1 and carbonic anhydrase 4 (CA4).


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:7ec075ae06a4df8d6ae5
claim_id: claim:7ec075ae06a4df8d6ae5
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
span_literal:
They express high levels of ICAM1 at resting states (although this constitutive ICAM1 expression increases during inflammatory challenge) ( 53 – 55 ), PLVAP ( 37 ) (a constituent of their fenestrae diaphragms), MHC class I antigens ( 56 ), and carbonic anhydrase IV ( CA4 ) ( 11 ) in contrast to other ocular endothelial cells.

summary:
In Homo sapiens, choriocapillaris endothelial cells express high levels of ICAM1, PLVAP, and CA4 in contrast to other ocular endothelial cells.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:0f35967410d3d191d60b
claim_id: claim:0f35967410d3d191d60b
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, S1PR3 expression is highly specific to choriocapillaris endothelial cells.
span_literal:
For example, S1PR3 expression, which has been implicated in VEGF and MMP-2 production ( 59 ), was highly specific within the choriocapillaris.


claim_key: hca:0428_10.1073_pnas.1914143116_42027a0378:claim:426a2f90e1b32b6feada
claim_id: claim:426a2f90e1b32b6feada
paper_key: hca:0428_10.1073_pnas.1914143116_42027a0378
summary: In Homo sapiens, RGCC is among the most enriched genes in choriocapillaris endothelial cells.
span_literal:
One gene of particular interest in this study was RGCC , the sixth-most enriched gene in choriocapillaris endothelial cells.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:2a833a2979100470e111
claim_id: claim:2a833a2979100470e111
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
We identified two populations of macrophages including a subset that expressed tissue resident markers (MRC1, SIGLEC1, CD163, LYVE1, F13A1).

summary:
In Homo sapiens, tissue resident macrophages are marked by positive expression of MRC1, SIGLEC1, CD163, LYVE1, and F13A1.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:3898de201dfbe30b0896
claim_id: claim:3898de201dfbe30b0896
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
summary: In Homo sapiens, arterial endothelial cells are marked by CLIC3 expression.
span_literal:
Utilizing RNA in situ hybridization, we visualized expression of arterial (CLIC3), venous (ACKR1), capillary (BTNL9), and lymphatic (CCL21) markers identified from Seurat differential expression analysis


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:5f354db5f684ce07a262
claim_id: claim:5f354db5f684ce07a262
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
summary: In Homo sapiens, classical monocytes are marked by CD14 expression.
span_literal:
Unsupervised clustering revealed the presence of discrete monocyte (CD14+, CD16+, intermediate), macrophages (CCL3, TREM2, KLF2, LYVE1) and dendritic cell populations


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:4a059d37ccaa6b6b25e7
claim_id: claim:4a059d37ccaa6b6b25e7
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
Donor samples contained classical (CD14+) and non-classical (CD16+) monocytes as well as 2 populations of LYVE1+ resident macrophages that differed based on the expression of FOLR2, MRC1, SIGLEC1, and HSPH1.

summary:
In Homo sapiens, LYVE1-positive resident macrophages are marked by LYVE1 expression and differ based on expression of FOLR2, MRC1, SIGLEC1, and HSPH1.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:04ff65aeaadb3f16ba34
claim_id: claim:04ff65aeaadb3f16ba34
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
RNA in situ hybridization confirmed reduction in CD163+ cells DCM samples and compared to donor controls ([Fig. 4H](451312v1_fig4.tif)).

summary:
In Homo sapiens, CD163 is a positive marker of tissue resident macrophages, and CD163-positive cells are reduced in dilated cardiomyopathy samples compared to donor controls.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:bd3bc8781f92587c2770
claim_id: claim:bd3bc8781f92587c2770
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
Donor hearts contained 7 cardiomyocyte states marked by MYH6, MYL7, GRIK2, NPPA/NPPB, ADGRL3, and ACTA1 expression.

summary:
In Homo sapiens, donor cardiomyocyte states are marked by MYH6, MYL7, GRIK2, NPPA, NPPB, ADGRL3, and ACTA1 expression.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:b34d448f77fbd9b333ad
claim_id: claim:b34d448f77fbd9b333ad
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
summary: In Homo sapiens, fibroblasts are marked by DCN expression in the heart.
span_literal:
We validated shifts in fibroblast composition between donor controls and DCM hearts using RNA in situ hybridization. The overall numbers of fibroblasts (marked by DCN expression) remained similar between donor control and DCM hearts.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:4475d515f5fc2d55a06d
claim_id: claim:4475d515f5fc2d55a06d
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
Fibroblasts marked by POSTN, CCL2, and PCOLCE2 were enriched in DCM, while GPX3 and PLA2G2A macrophages were enriched in donor controls.

summary:
In Homo sapiens, fibroblast subpopulations are marked by POSTN, CCL2, and PCOLCE2 expression and are enriched in dilated cardiomyopathy.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:3ddec254f81c8bc461ae
claim_id: claim:3ddec254f81c8bc461ae
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
In addition, we identified an activation signature that included FAP, CTGF, LUM, ACTB, COL1A1, BGN, and MGP that was selectively expressed in fibroblasts from DCM hearts.

summary:
In Homo sapiens, activated fibroblasts from dilated cardiomyopathy hearts express FAP, CTGF, LUM, ACTB, COL1A1, BGN, and MGP.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:aff614e6bb31f15ed62d
claim_id: claim:aff614e6bb31f15ed62d
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
Donor endocardial cells expressed NRG3. Endocardial cells from DCM samples display strong upregulation of NRG1 and reduced NRG3 expression

summary:
In Homo sapiens, donor endocardial cells express NRG3, while endocardial cells from dilated cardiomyopathy samples display upregulation of NRG1 and reduced NRG3 expression.


claim_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20:claim:25b734e4f335dce3f51b
claim_id: claim:25b734e4f335dce3f51b
paper_key: hca:0430_10.1101_2021.07.06.451312_11ba989c20
span_literal:
Classical and intermediate monocytes and macrophages marked by CCL3, TREM2, and KLF2 expressed robust levels of inflammatory mediators including IL1A, IL1B, TNF, AREG, EREG, and multiple chemokines

summary:
In Homo sapiens, classical and intermediate monocytes and macrophages marked by CCL3, TREM2, and KLF2 express inflammatory mediators including IL1A, IL1B, TNF, AREG, and EREG.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:4919c799ce3b2934bbb8
claim_id: claim:4919c799ce3b2934bbb8
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
span_literal:
We identified two populations of macrophages, including a subset that expressed tissue-resident markers (Mac1: MRC1 , SIGLEC1 , CD163 , LYVE1 and F13A1 )

summary:
In Homo sapiens, tissue-resident macrophage (Mac1) is marked by positive expression of MRC1, SIGLEC1, CD163, LYVE1, and F13A1.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:32387c85a0d39f78f80b
claim_id: claim:32387c85a0d39f78f80b
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
span_literal: and a subset that expressed chemokines and cytokines (Mac2: CCL3 , CCL4 , CXCL3 , CXCL8 and IL1β )
summary:
In Homo sapiens, inflammatory macrophage (Mac2) is marked by positive expression of CCL3, CCL4, CXCL3, CXCL8, and IL1B.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:047c1b3865c4463d2a82
claim_id: claim:047c1b3865c4463d2a82
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
summary: In Homo sapiens, cardiomyocyte state 1 (Cm1) is marked by positive expression of MYH6.
span_literal:
Unsupervised clustering identified seven cardiomyocyte states with differing gene expression signatures ( Fig. 3c , d and Extended Data Fig. 6 ). Cardiomyocytes from donor samples existed in all seven states marked by MYH6 (Cm1), ACTA1 (Cm2), MYL7 (Cm3), ADGRL3 (Cm4), GRIK2 (Cm5), NPPA/NPPB (Cm6) and BMPR1B (Cm7) expression.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:5f53bc3a1248badaed79
claim_id: claim:5f53bc3a1248badaed79
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
summary: In Homo sapiens, nonclassical monocyte (Mono1) is marked by positive expression of FCGR3A.
span_literal:
Unsupervised clustering revealed the presence of discrete monocytes (Mono1, nonclassical- FCGR3A ; Mono2, classical- CD14 ; Mono3, intermediate- OLR1 ), macrophages (Mac1, TREM2 ; Mac2, FOLR2/LYVE1 ; Mac3, LYVE1/HSPH1; Mac4, CCL3 ; Mac5, KLF2 ) and dendritic cells ( CD1C )


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:03ef0138624e2faa0444
claim_id: claim:03ef0138624e2faa0444
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
span_literal:
We identified two fibroblast subpopulations primarily present in donor controls that expressed GPX3 (Fb3) and PLA2G2A (Fb4), respectively.

summary:
In Homo sapiens, fibroblast subpopulation Fb3 is marked by positive expression of GPX3, and fibroblast subpopulation Fb4 is marked by positive expression of PLA2G2A.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:c76f2c02797c44f00fbe
claim_id: claim:c76f2c02797c44f00fbe
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
summary: In Homo sapiens, fibroblast subpopulation Fb5 is marked by positive expression of ELN.
span_literal:
We observed additional minor fibroblast subpopulations characterized by the expression of ELN (Fb5), TNC (Fb6), CCL2 (Fb7), THBS4 (Fb8) and SERPINE1 (Fb9).


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:93f9e08f7ceb9c3e975d
claim_id: claim:93f9e08f7ceb9c3e975d
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
span_literal:
Utilizing RNA in situ hybridization, we visualized expression of recognized venous ( ACKR1 ), capillary ( BTNL9 ) and lymphatic ( CCL21 ) markers identified from Seurat differential expression analysis

summary:
In Homo sapiens, ACKR1 is a marker of venous endothelial cell, BTNL9 is a marker of capillary endothelial cell, and CCL21 is a marker of lymphatic endothelial cell.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:19251d04aaa62356ee83
claim_id: claim:19251d04aaa62356ee83
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
span_literal:
Endocardial cells from DCM samples (Edc2) displayed strong upregulation of NRG1 and reduced NRG3 expression

summary:
In Homo sapiens, dilated cardiomyopathy endocardial cell (Edc2) is marked by positive expression of NRG1 and negative expression of NRG3.


claim_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f:claim:d9704931785c248a467c
claim_id: claim:d9704931785c248a467c
paper_key: hca:0431_10.1038_s44161-022-00028-6_b4c8c1227f
summary: In Homo sapiens, fibroblast is marked by positive expression of DCN.
span_literal:
The overall numbers of fibroblasts (marked by DCN expression) remained similar between donor control and DCM hearts.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:7fd8a13d2ab2c214e40a
claim_id: claim:7fd8a13d2ab2c214e40a
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
summary: In Homo sapiens, natural killer cells are marked by positive expression of KLRB1 and TYROBP.
span_literal:
Among these, we broadly identified populations of CD4 + T cells, CD8 + T cells, and NK cells (marked by KLRB1 and TYROBP expression)


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:a80e128ec33f39b75bd0
claim_id: claim:a80e128ec33f39b75bd0
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal: Tregs associated with cluster 4 were found to have stronger expression of CTLA4 , TIGIT , and ICOS
summary:
In Homo sapiens, regulatory T cells in cluster 4 have stronger expression of CTLA4, TIGIT, and ICOS, while regulatory T cells in cluster 10 are marked by higher expression of CD27.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:25857f045a368fe172d4
claim_id: claim:25857f045a368fe172d4
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
Tfh and/or Tph cells, defined by the absence of FOXP3 and the expression of markers such as CXCL13 , PDCD1 , ICOS , and MAF

summary:
In Homo sapiens, T follicular helper and/or T peripheral helper cells are defined by the absence of FOXP3 and the expression of CXCL13, PDCD1, ICOS, and MAF.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:a73f85d148dce73d140e
claim_id: claim:a73f85d148dce73d140e
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
tissue-resident memory CD8 + resident memory T cells (Trm), identified by expression of markers such as ZNF683 and XCL1 , formed 2 clusters (clusters 2 and 8).

summary:
In Homo sapiens, CD8-positive tissue-resident memory T cells are identified by expression of ZNF683 and XCL1.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:cee3dacefce940ee734d
claim_id: claim:cee3dacefce940ee734d
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
A population of CD8 + T cells marked by the strong expression of GZMK but relative absence of GZMB was identified (cluster 3), consistent with a phenotype previously recognized in LN kidneys and rheumatoid arthritis synovium

summary:
In Homo sapiens, a population of CD8-positive T cells (cluster 3) is marked by strong expression of GZMK but relative absence of GZMB.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:b876e9841d9855317168
claim_id: claim:b876e9841d9855317168
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
In contrast, cluster 7 expressed higher levels of GZMB compared with cluster 3, suggesting a cytotoxic T lymphocyte (CTL) phenotype.

summary:
In Homo sapiens, cytotoxic T lymphocyte cluster 7 expresses higher levels of GZMB compared with cluster 3.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:e871c96600d16675cc01
claim_id: claim:e871c96600d16675cc01
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
Clusters 3 and 7, though, were both found to similarly express the cytokine IFNG and chemokines CCL4 and CCL5

summary:
In Homo sapiens, CD8-positive T cell clusters 3 and 7 express the cytokine IFNG and chemokines CCL4 and CCL5.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:8cfe2abf5496d84caf2a
claim_id: claim:8cfe2abf5496d84caf2a
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
While both share a similar core transcriptional program composed of markers such as KLRB1 , TYROBP , and NKG7 , the NK cells of cluster 9 are largely differentiated by stronger expression of XCL1 , suggestive of a CD56 bright NK cell population, while those of cluster 11 overexpress PRF1 , multiple granzyme genes, and CCL5 , likely representing a CD56 dim population

summary:
In Homo sapiens, natural killer cells share expression of KLRB1, TYROBP, and NKG7; CD56-bright natural killer cells (cluster 9) are differentiated by stronger expression of XCL1, while CD56-dim natural killer cells (cluster 11) overexpress PRF1 and CCL5.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:041c706e3be13189ecd2
claim_id: claim:041c706e3be13189ecd2
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
While both share a similar core transcriptional program composed of markers such as KLRB1 , TYROBP , and NKG7 , the NK cells of cluster 9 are largely differentiated by stronger expression of XCL1 , suggestive of a CD56 bright NK cell population, while those of cluster 11 overexpress PRF1 , multiple granzyme genes, and CCL5 , likely representing a CD56 dim population

summary:
In Homo sapiens, CD56-dim natural killer cells (cluster 11) overexpress PRF1 and CCL5, and share expression of KLRB1, TYROBP, and NKG7.


claim_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf:claim:d7273613152dc9f71c3c
claim_id: claim:d7273613152dc9f71c3c
paper_key: hca:0432_10.1172_jci.insight.156341_02dc39adcf
span_literal:
In addition, a cluster marked by the expression of IFN-stimulated genes (ISGs) such as IFIT1 , IFIT3 , IFI44 , OAS1 , and LY6E , among others, was identified.

summary:
In Homo sapiens, an interferon-stimulated gene-high T cell cluster is marked by expression of IFIT1, IFIT3, IFI44, OAS1, and LY6E.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:046669358f371333d7bc
claim_id: claim:046669358f371333d7bc
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
the islets of Langerhans are composed of endocrine cells expressing glucagon (alpha cells), insulin (beta cells), somatostatin (delta cells), pancreatic polypeptide (PP cells), and ghrelin (epsilon cells)

summary:
In Homo sapiens, alpha cells express glucagon (GCG), beta cells express insulin (INS), delta cells express somatostatin (SST), pancreatic polypeptide cells express pancreatic polypeptide (PPY), and epsilon cells express ghrelin (GHRL) in the islets of Langerhans.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:31467188a677d0604721
claim_id: claim:31467188a677d0604721
paper_key: hca:0433_10.15252_embr.201540946_1830154973
summary:
In Homo sapiens, pancreatic polypeptide cells express pancreatic polypeptide (PPY) in the islets of Langerhans.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:0b7a27c4006f36695adf
claim_id: claim:0b7a27c4006f36695adf
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
PCA on the full dataset separates a group of 18 cells based on high glucagon (GCG) and transthyretin (TTR) expression and a group of 9 cells expressing pancreatic polypeptide (PPY) from a heterogeneous group of 37 cells

summary:
In Homo sapiens, alpha cells are characterized by high glucagon (GCG) and transthyretin (TTR) expression in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:e317e85b2fb1f80e82b5
claim_id: claim:e317e85b2fb1f80e82b5
paper_key: hca:0433_10.15252_embr.201540946_1830154973
summary: In Homo sapiens, beta cells are identified by high insulin (INS) expression in pancreatic islets.
span_literal:
we identified a group of 12 cells with high insulin (INS) expression, a group of 11 cells characterized by PRSS2 , CTRB2 , REG3A , REG1A , and REG1B and a group of two somatostatin (SST) ‐expressing cells


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:d9e97a9d08615debfc7b
claim_id: claim:d9e97a9d08615debfc7b
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
we identified a group of 12 cells with high insulin (INS) expression, a group of 11 cells characterized by PRSS2 , CTRB2 , REG3A , REG1A , and REG1B and a group of two somatostatin (SST) ‐expressing cells

summary:
In Homo sapiens, acinar cells are characterized by PRSS2, CTRB2, REG3A, REG1A, and REG1B expression in the pancreas.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:62aab20b0e9dda92daa7
claim_id: claim:62aab20b0e9dda92daa7
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal: a group of 8 cells was characterized by keratin18 (KRT18) and keratin8 (KRT8)
summary:
In Homo sapiens, ductal cells are characterized by keratin 18 (KRT18) and keratin 8 (KRT8) expression in the pancreas.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:27c6302693a49d720217
claim_id: claim:27c6302693a49d720217
paper_key: hca:0433_10.15252_embr.201540946_1830154973
summary: In Homo sapiens, PDX1 shows beta cell-specific expression in pancreatic islets.
span_literal:
The genome browser tracks illustrate the beta cell‐specific expression of PDX1 , a master regulatory transcription factor directly controlling insulin expression.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:ea2694569ce2200c8e00
claim_id: claim:ea2694569ce2200c8e00
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal: In contrast, the alpha lineage‐defining factor ARX is expressed in both alpha and some PP cells
summary:
In Homo sapiens, the alpha lineage-defining transcription factor ARX is expressed in alpha cells in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:5abe5563d3402a6fb141
claim_id: claim:5abe5563d3402a6fb141
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal: In contrast, the alpha lineage‐defining factor ARX is expressed in both alpha and some PP cells
summary:
In Homo sapiens, the alpha lineage-defining transcription factor ARX is expressed in pancreatic polypeptide cells in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:09f98f382243db073cfc
claim_id: claim:09f98f382243db073cfc
paper_key: hca:0433_10.15252_embr.201540946_1830154973
summary: In Homo sapiens, PAX6 shows pan-endocrine expression in mature human pancreatic islets.
span_literal:
Other transcription factors that are important for pancreas development have different degrees of cell type‐specific expression in mature human islets, including pan‐endocrine ( PAX6 ), beta cell‐specific ( PAX4 ), and duct/delta ( HHEX ) patterns


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:5a9c4562fe30bdf3c69e
claim_id: claim:5a9c4562fe30bdf3c69e
paper_key: hca:0433_10.15252_embr.201540946_1830154973
summary: In Homo sapiens, MAFB is robustly expressed in alpha cells in pancreatic islets.
span_literal:
While MAFA is transcribed in beta cells specifically, we observed robust MAFB expression in alpha, beta, and delta cells.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:e7d1ae8aedfac77655b8
claim_id: claim:e7d1ae8aedfac77655b8
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
For example, MORF4L1 shows a similar pan‐endocrine pattern to the canonical islet cell marker NEUROD1

summary:
In Homo sapiens, MORF4L1 shows a pan-endocrine expression pattern similar to the canonical islet cell marker NEUROD1 in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:3f4c5503b4d7a6be7398
claim_id: claim:3f4c5503b4d7a6be7398
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal: some beta cells show high expression of polycomb ring finger oncogene (BMI1)
summary:
In Homo sapiens, some beta cells show high expression of polycomb ring finger oncogene (BMI1) in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:7170a43c012f87fe29fc
claim_id: claim:7170a43c012f87fe29fc
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal: PP cells can be characterized by the transcription factors ETV1 and MEIS1
summary:
In Homo sapiens, pancreatic polypeptide cells can be characterized by the transcription factors ETV1 and MEIS1 in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:eb6bf54312ddeabe104c
claim_id: claim:eb6bf54312ddeabe104c
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
While several highly correlated genes could be identified for INS and SST (e.g., zinc transporter SLC39A4 and Notch pathway component DLK1 for INS and transcription factors NKX6‐3 , ZNF430 for SST )

summary:
In Homo sapiens, the zinc transporter SLC39A4 and the Notch pathway component DLK1 are highly correlated with INS expression in beta cells, and the transcription factors NKX6-3 and ZNF430 are highly correlated with SST expression in delta cells.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:0734cb8b663b5ad8c806
claim_id: claim:0734cb8b663b5ad8c806
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
While several highly correlated genes could be identified for INS and SST (e.g., zinc transporter SLC39A4 and Notch pathway component DLK1 for INS and transcription factors NKX6‐3 , ZNF430 for SST )

summary:
In Homo sapiens, the transcription factors NKX6-3 and ZNF430 are highly correlated with SST expression in delta cells in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:37e25e8874d32a488f44
claim_id: claim:37e25e8874d32a488f44
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
In line with the target gene expression pattern, REST is specifically expressed in ductal and acinar cells

summary:
In Homo sapiens, the transcriptional repressor REST is specifically expressed in ductal cells and acinar cells in the pancreas.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:8bbfbd7288bc96e9fcc7
claim_id: claim:8bbfbd7288bc96e9fcc7
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
In line with the target gene expression pattern, REST is specifically expressed in ductal and acinar cells

summary:
In Homo sapiens, the transcriptional repressor REST is specifically expressed in acinar cells in the pancreas.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:277d66a200976d37469f
claim_id: claim:277d66a200976d37469f
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
We found that the human alpha cell‐specific gene group‐specific component (vitamin D binding protein) GC and the human beta cell‐specific gene DLK1 (Fig 3 D) displayed opposite expression patterns as to what had been reported in mouse islet cells.

summary:
In Homo sapiens, the group-specific component (vitamin D binding protein) GC is an alpha cell-specific gene, and DLK1 is a beta cell-specific gene in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:3c5719ae468af674850b
claim_id: claim:3c5719ae468af674850b
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal: In human islets, DLK1 was specifically expressed only in insulin‐positive cells
summary:
In Homo sapiens, DLK1 is specifically expressed only in insulin-positive beta cells in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:4ee3190a5d41ddeb3f2a
claim_id: claim:4ee3190a5d41ddeb3f2a
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
These include the pan‐endocrine marker MORF4L1 , alpha cell‐specific IRX2 , beta cell‐specific BMI1 , and PP cell‐specific MEIS1 and ETV1 .

summary:
In Homo sapiens, MORF4L1 is a pan-endocrine marker, IRX2 is alpha cell-specific, BMI1 is beta cell-specific, and MEIS1 and ETV1 are pancreatic polypeptide cell-specific in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:ed7000bc7df937585dd9
claim_id: claim:ed7000bc7df937585dd9
paper_key: hca:0433_10.15252_embr.201540946_1830154973
summary:
In Homo sapiens, MEIS1 and ETV1 are pancreatic polypeptide cell-specific transcription factors in pancreatic islets.


claim_key: hca:0433_10.15252_embr.201540946_1830154973:claim:e1254981d16ea767b5f4
claim_id: claim:e1254981d16ea767b5f4
paper_key: hca:0433_10.15252_embr.201540946_1830154973
span_literal:
Furthermore, key MODY (Mature Onset of Diabetes in Young) 21 genes PDX1, PAX4, INS, HNF1A, GCK are predominantly specific to beta cells

summary:
In Homo sapiens, key Mature Onset of Diabetes in Young genes PDX1, PAX4, INS, HNF1A, and GCK are predominantly specific to beta cells in pancreatic islets.


claim_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4:claim:0383c15933a8f529e979
claim_id: claim:0383c15933a8f529e979
paper_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4
span_literal: GABRB3 and GABRG2 were strongly upregulated in artemether-treated α cells
summary:
In Homo sapiens, GABRB3 and GABRG2 are upregulated in artemether-treated alpha cells, indicating these GABA A receptor subunit genes mark alpha cells responding to artemether treatment.


claim_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4:claim:6a63fec577e11b2c450c
claim_id: claim:6a63fec577e11b2c450c
paper_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4
span_literal:
In α cells, we observed a strong and significant downregulation of α cell-specific genes, including EIF4A1 , CRYBA2 , PDK4 , and MUC13 following artemether treatment

summary:
In Homo sapiens, alpha cell-specific genes EIF4A1, CRYBA2, PDK4, and MUC13 are downregulated in alpha cells following artemether treatment, indicating these genes are markers of alpha cell identity.


claim_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4:claim:a5cef52365e96ba6dea5
claim_id: claim:a5cef52365e96ba6dea5
paper_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4
span_literal:
Key β cell-specific genes were upregulated in α cells following artemether treatment, including GNAS and ABCC8 , the gene coding for the sulfonylurea receptor

summary:
In Homo sapiens, key beta cell-specific genes GNAS and ABCC8 (the gene coding for the sulfonylurea receptor) were upregulated in alpha cells following artemether treatment, indicating these genes are positive markers of beta cells.


claim_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4:claim:5cdee8d225d3865e20b0
claim_id: claim:5cdee8d225d3865e20b0
paper_key: hca:0434_10.1016_j.cell.2016.11.010_b880f4a6e4
span_literal:
GABA is primarily produced by β cells, whereas several GABA A -receptor subunits are specifically expressed on α cells

summary:
In Homo sapiens, GABA A receptor subunits are specifically expressed on alpha cells, while GABA is primarily produced by beta cells.


claim_key: hca:0435_10.1038_nm.4336_19432336d2:claim:f80826d9ea1cfc009a70
claim_id: claim:f80826d9ea1cfc009a70
paper_key: hca:0435_10.1038_nm.4336_19432336d2
span_literal:
Remission group-A BCR-ABL + SCs, also showed overexpression of Wnt/β-catenin-pathway-associated genes ( GAS2 and CTNNB1 ), the TGF-β-pathway gene SKIL , regulators of NF-κB ( NFKB1A and SQSTM (also known as p62 )), the hypoxia factors HIF1A and the Wilms tumor protein (WT1) partner WTAP , as well as downregulation of the chemokine receptor CXCR4 and the transcription factor FOS , in comparison with normal HSCs

summary:
In Homo sapiens, group-A remission BCR-ABL-positive chronic myeloid leukemia stem cells show overexpression of GAS2, CTNNB1, SKIL, NFKB1A, SQSTM1, HIF1A, and WTAP, and downregulation of CXCR4 and FOS, in comparison with normal hematopoietic stem cells.


claim_key: hca:0435_10.1038_nm.4336_19432336d2:claim:f65e6320404e52104ccc
claim_id: claim:f65e6320404e52104ccc
paper_key: hca:0435_10.1038_nm.4336_19432336d2
span_literal:
Comparison of gene expression of the BC and CP BCR-ABL + SC clusters revealed 1,166 differentially expressed genes ( Fig. 6b and Supplementary Table 11 ), including overexpression of HGF 36 and reduced expression of the Wnt pathway negative-regulator EAF2 (ref. 37 ).

summary:
In Homo sapiens, blast crisis BCR-ABL-positive chronic myeloid leukemia stem cells show overexpression of HGF and reduced expression of EAF2 compared to chronic phase BCR-ABL-positive chronic myeloid leukemia stem cells.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:0ee3cba8d6b238b3f878
claim_id: claim:0ee3cba8d6b238b3f878
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
The clustering result was annotated by the known markers including KRT12 , KRT3 and GJA1 for differentiated cell; KRT14 , KRT15 and KRT19 for progenitor; MKI67 , BIRC5 and RRM2 for amplifying cell; TCF4 , POSTN and A2M for LSC; TYR , TYRP1 and MLANA for melanocyte; and KRT4 , KRT7 and KRT13 for conjunctival cells

summary:
In Homo sapiens, keratin 12, keratin 3, and gap junction protein alpha 1 are markers of differentiated cells in the limbal basal epithelium of the cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:b633d9feb3c236599e86
claim_id: claim:b633d9feb3c236599e86
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
The clustering result was annotated by the known markers including KRT12 , KRT3 and GJA1 for differentiated cell; KRT14 , KRT15 and KRT19 for progenitor; MKI67 , BIRC5 and RRM2 for amplifying cell; TCF4 , POSTN and A2M for LSC; TYR , TYRP1 and MLANA for melanocyte; and KRT4 , KRT7 and KRT13 for conjunctival cells

summary:
In Homo sapiens, keratin 14, keratin 15, and keratin 19 are markers of progenitor cells in the limbal basal epithelium of the cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:dd604e59447be2f40dd5
claim_id: claim:dd604e59447be2f40dd5
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
The clustering result was annotated by the known markers including KRT12 , KRT3 and GJA1 for differentiated cell; KRT14 , KRT15 and KRT19 for progenitor; MKI67 , BIRC5 and RRM2 for amplifying cell; TCF4 , POSTN and A2M for LSC; TYR , TYRP1 and MLANA for melanocyte; and KRT4 , KRT7 and KRT13 for conjunctival cells

summary:
In Homo sapiens, MKI67, BIRC5, and RRM2 are markers of transiently amplifying cells in the limbal basal epithelium of the cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:d743e05efc0f94e726f1
claim_id: claim:d743e05efc0f94e726f1
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
summary:
In Homo sapiens, TCF4, POSTN (periostin), and A2M (alpha-2-macroglobulin) are markers of limbal stem cells in the cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:de8a7e838ae560521d74
claim_id: claim:de8a7e838ae560521d74
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
summary:
In Homo sapiens, TYR (tyrosinase), TYRP1 (tyrosinase-related protein 1), and MLANA (melan-A) are markers of melanocytes in the limbal basal epithelium of the cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:5bee286ce9d9789d7611
claim_id: claim:5bee286ce9d9789d7611
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
C0/2 were terminally differentiated cells (TDCs) as they expressed the highest levels of differentiation markers including corneal epithelial specific differentiation markers, cytokeratin 3 ( KRT3 ) and KRT12 , and keratinocyte cornification markers SPRR2A , SPRR1B and IVL , but did not express the proliferation and epithelial SC makers

summary:
In Homo sapiens, terminally differentiated cells in the limbal basal epithelium express the highest levels of KRT3, KRT12, SPRR2A, SPRR1B, and IVL (involucrin).


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:500eaf87e89c85305a00
claim_id: claim:500eaf87e89c85305a00
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
Among 4 clusters expressing a low level of differentiation markers, C8 was the only cluster highly expressing major proliferation markers, including BIRC5 , RRM2 , TOP2A , MKI67 and PLK1

summary:
In Homo sapiens, transiently amplifying cells (C8) in the limbal basal epithelium highly express the proliferation markers BIRC5, RRM2, TOP2A, MKI67, and PLK1.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:33b760bdcf8ff3dbc86a
claim_id: claim:33b760bdcf8ff3dbc86a
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
C5 and C6 expressed some putative SC markers, such as SLC2A3 , ITM2A , POSTN , and TCF4 , at a middle level

summary:
In Homo sapiens, limbal progenitor cells (C5 and C6) express the putative stem cell markers SLC2A3, ITM2A, POSTN (periostin), and TCF4 at a middle level.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:ed3790d81444612986c3
claim_id: claim:ed3790d81444612986c3
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
C10 is identified as the putative LSC because it has the lowest levels of differentiation markers and the highest expression of putative SC markers, including ITM2A , TCF4 , POSTN , A2M , ABCG2 and ITGA9

summary:
In Homo sapiens, limbal stem cells (C10) have the highest expression of putative stem cell markers ITM2A, TCF4, POSTN (periostin), A2M (alpha-2-macroglobulin), ABCG2, and ITGA9.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:482bc08deb641c146bf9
claim_id: claim:482bc08deb641c146bf9
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
For LSC (C10), exclusively expressed markers, such as TSPAN7 , SOX17 , SELE , ECSCR , RAMP 3, AC011526.1 , RNASE1 , NPDC1, C10orf10 , IGFBP4 , SLC2A3 , NNMT , KLF2 , and PDK4 , were revealed

summary:
In Homo sapiens, limbal stem cells (C10) exclusively express TSPAN7, SOX17, SELE, ECSCR, RAMP3, AC011526.1, RNASE1, NPDC1, C10orf10, IGFBP4, SLC2A3, NNMT, KLF2, and PDK4.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:5c0c21c85cd646a13fb3
claim_id: claim:5c0c21c85cd646a13fb3
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
Unlike the marker genes in LSC, the marker genes in LPC (C5 and C6), such as DCN , PLIN2 DEGS1 , MMP10 , IFITM3 , SLC6A6 , LTB4R , and SLPI , do not show exclusive expression pattern but rather have a higher expression level in C5/6 compared with other clusters

summary:
In Homo sapiens, limbal progenitor cells (C5 and C6) have higher expression of DCN (decorin), PLIN2, DEGS1, MMP10, IFITM3, SLC6A6, LTB4R, and SLPI compared with other clusters.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:d04ae4020891ba43233e
claim_id: claim:d04ae4020891ba43233e
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
Marker genes specifically expressed in each cell type were selected as such: TSPAN7 and SOX17 for LSC, DCN and PLIN2 for LPC, TK1 for TAC, HTRA1 for PMC, and TYR and MLANA for MC, with known marker KRT3 for TDC as control

summary:
In Homo sapiens, TSPAN7 and SOX17 are markers for limbal stem cells, DCN (decorin) and PLIN2 for limbal progenitor cells, TK1 for transiently amplifying cells, HTRA1 for post-mitotic cells, TYR and MLANA for melanocytes, and KRT3 for terminally differentiated cells in the corneal limbus.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:d2ef49285c6b942871ac
claim_id: claim:d2ef49285c6b942871ac
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
Marker genes specifically expressed in each cell type were selected as such: TSPAN7 and SOX17 for LSC, DCN and PLIN2 for LPC, TK1 for TAC, HTRA1 for PMC, and TYR and MLANA for MC, with known marker KRT3 for TDC as control

summary:
In Homo sapiens, DCN (decorin) and PLIN2 are markers for limbal progenitor cells in the corneal limbus.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:be6d22717675b45d3003
claim_id: claim:be6d22717675b45d3003
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
TSPAN7 + and SOX17 + cells were sparsely distributed at the limbal basal epithelial layer, but not at the corneal epithelium, which is consistent with the idea that these cells are LSCs.

summary:
In Homo sapiens, TSPAN7-positive and SOX17-positive cells are sparsely distributed at the limbal basal epithelial layer, consistent with their identity as limbal stem cells.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:8dd08756c5878994c037
claim_id: claim:8dd08756c5878994c037
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
DCN + and PLIN2 + cells were identified at the same basal layer and likely represent limbal progenitor cells in agreement with their features and locations within the tissue.

summary:
In Homo sapiens, DCN-positive and PLIN2-positive cells at the limbal basal layer likely represent limbal progenitor cells.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:efb6b5e47257caed4c34
claim_id: claim:efb6b5e47257caed4c34
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
Moreover, we observed that TK1+ cells, which we identified as TACs, were sparsely distributed at the basal epithelium of peripheral cornea

summary:
In Homo sapiens, TK1-positive cells, identified as transiently amplifying cells, are sparsely distributed at the basal epithelium of the peripheral cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:7f09602dbf0561c9e0cf
claim_id: claim:7f09602dbf0561c9e0cf
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
HTRA1 + cells, which indicate PMCs, were dominantly distributed at suprabasal epithelial layers, while KRT3 + cells, indicating TDCs, were enriched at superficial layers of the central cornea

summary:
In Homo sapiens, HTRA1-positive cells indicate post-mitotic cells distributed at suprabasal epithelial layers of the cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:49efb96c228483c9282b
claim_id: claim:49efb96c228483c9282b
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
HTRA1 + cells, which indicate PMCs, were dominantly distributed at suprabasal epithelial layers, while KRT3 + cells, indicating TDCs, were enriched at superficial layers of the central cornea

summary:
In Homo sapiens, KRT3-positive cells indicate terminally differentiated cells enriched at superficial layers of the central cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:397b22624b40c593571b
claim_id: claim:397b22624b40c593571b
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
Interestingly, MLANA + and TYR + melanocytes were sparsely located at the limbal basal layer where LSC resides

summary:
In Homo sapiens, MLANA-positive and TYR-positive melanocytes are sparsely located at the limbal basal layer.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:341d0bea330e90a562ff
claim_id: claim:341d0bea330e90a562ff
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
To validate LSC (C10), TSPAN7 and SOX17 proteins were observed to be exclusively localized at the limbal basal layer while the suprabasal and superficial limbal cells and full layers of the peripheral and central corneal epithelium were totally negative

summary:
In Homo sapiens, TSPAN7 and SOX17 proteins are exclusively localized at the limbal basal layer, validating them as markers for limbal stem cells.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:5429a6dcbed049665d86
claim_id: claim:5429a6dcbed049665d86
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
TK1, a new marker related to cell proliferation for C8 was sparsely located on the basal layer of limbus and peripheral cornea

summary:
In Homo sapiens, TK1 is a new marker related to cell proliferation for transiently amplifying cells (C8), sparsely located on the basal layer of the limbus and peripheral cornea.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:b08d9abc7443ec811275
claim_id: claim:b08d9abc7443ec811275
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
C9/11 were validated as melanocytes sparsely located in the limbal basal epithelium by MLANA antibody

summary:
In Homo sapiens, melanocytes (C9/11) in the limbal basal epithelium were validated by MLANA antibody staining.


claim_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4:claim:fa105ef5af5061d8eaa5
claim_id: claim:fa105ef5af5061d8eaa5
paper_key: hca:0436_10.1016_j.jtos.2020.12.004_24ddeb29a4
span_literal:
TSPAN7 and SOX17 are discovered and validated as new LSC markers based on their exclusive expression pattern and spatial localization in limbal basal epithelium by RNAscope and immunostaining, and functional role in cell growth and tissue regeneration models with RNA interference in cultures.

summary:
In Homo sapiens, TSPAN7 and SOX17 are discovered and validated as new limbal stem cell markers based on their exclusive expression pattern and spatial localization in the limbal basal epithelium.


claim_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939:claim:f8afd0aeae0d2d9ec316
claim_id: claim:f8afd0aeae0d2d9ec316
paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
span_literal:
Among recognized fiber type markers 34,35, *MYH1* (fast type 2X), *MYH2* (fast type 2A), *MYH7* (slow type I fibers) and *MYH7B* (slow type I fibers) were present in our dataset, and *MYH2* expression significantly declined with age, consistent with type II fiber atrophy 36.

summary:
In Homo sapiens skeletal muscle, MYH1 is a marker of fast type 2X fiber, MYH2 is a marker of fast type 2A fiber, MYH7 is a marker of slow type I fiber, and MYH7B is a marker of slow type I fiber.


claim_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939:claim:8e3852edef324fc0027a
claim_id: claim:8e3852edef324fc0027a
paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
span_literal:
Among recognized fiber type markers 34,35, *MYH1* (fast type 2X), *MYH2* (fast type 2A), *MYH7* (slow type I fibers) and *MYH7B* (slow type I fibers) were present in our dataset, and *MYH2* expression significantly declined with age, consistent with type II fiber atrophy 36.

summary:
In Homo sapiens skeletal muscle, MYH7 is a marker of slow type I fiber. In Homo sapiens skeletal muscle, MYH7B is a marker of slow type I fiber.


claim_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939:claim:52fb23d9f87e6ddade66
claim_id: claim:52fb23d9f87e6ddade66
paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
span_literal: FAP subtypes – one expressed the muscle contraction gene Tryadin (*TRDN
summary:
In Homo sapiens skeletal muscle, one fibro-adipogenic progenitor cell subtype expresses TRDN, while the other fibro-adipogenic progenitor cell subtype expresses RYR1.


claim_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939:claim:410641fd64d923c16dd5
claim_id: claim:410641fd64d923c16dd5
paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
summary: In Homo sapiens skeletal muscle, one fibro-adipogenic progenitor cell subtype expresses RYR1.
span_literal:
FAP subtypes – one expressed the muscle contraction gene Tryadin (*TRDN*), while the other expressed the skeletal muscle ryanodine receptor (*RYR1


claim_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939:claim:35518e4f7accf78059d7
claim_id: claim:35518e4f7accf78059d7
paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
summary: In Homo sapiens skeletal muscle, satellite cells are positive for PAX7.
span_literal:
However, within SCs, which were Pax7+, we observed several distinct subclusters, possibly defining functional subgroups for this cell type.


claim_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939:claim:5387e5db0626e3674c40
claim_id: claim:5387e5db0626e3674c40
paper_key: hca:0437_10.1101_2021.01.22.21250336_e963bc0939
span_literal:
This unique cluster contained *CDKN1A/MYH8/COL19A1/LRRK2*+ cells, and was present only in samples from older adults

summary:
In Homo sapiens aged skeletal muscle, a unique cluster of fast skeletal muscle fiber nuclei expresses CDKN1A, MYH8, COL19A1, and LRRK2.


claim_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16:claim:621f19b4d8263b357d27
claim_id: claim:621f19b4d8263b357d27
paper_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16
summary: In Homo sapiens, CCL21 is a marker gene for lymphatic endothelial cells in the left ventricle.
span_literal:
Using the EC-lymphatic marker gene CCL21 (logFC = 5.2, p = 4.0 × 10 −22 ) we observed increased numbers of EC-lymphatic cells in the ICM samples that were clustered in fibrotic regions in the tissue


claim_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16:claim:387cd06b58c9642f8316
claim_id: claim:387cd06b58c9642f8316
paper_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16
span_literal:
To validate the EC-angiogenic cells, we co-stained with the endothelial cell marker PECAM1 and EC-angiogenic cell-specific marker MYO1B (logFC = 2.15, p = 1.7 × 10 −14 ).

summary:
In Homo sapiens, PECAM1 is a marker for endothelial cells and MYO1B is a specific marker for angiogenic endothelial cells in the left ventricle.


claim_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16:claim:3f7c47d03a8faf250e61
claim_id: claim:3f7c47d03a8faf250e61
paper_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16
summary: In Homo sapiens, MMRN1 is a marker gene for lymphatic endothelial cells in the left ventricle.
span_literal:
Within the EC-lymphatic subcluster, MMRN1 , was decreased in ICM compared with NF. MMRN1 is an ECM protein that is a marker gene for lymphatic endothelial cells and binds to collagens I, II, and III, which leads to enhanced activated platelet adhesion and thrombus formation after injury.


claim_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16:claim:ee79c16d081bbb5d0c22
claim_id: claim:ee79c16d081bbb5d0c22
paper_key: hca:0438_10.1016_j.celrep.2023.112086_4947038a16
span_literal:
ABCA9 is an important gene in monocyte to macrophage differentiation 23 and CD163L1 expression in macrophages is associated with tissue resident anti-inflammatory macrophages in cancer.

summary:
In Homo sapiens, ABCA9 is a positive marker of macrophages associated with monocyte to macrophage differentiation, and CD163L1 expression is associated with tissue resident anti-inflammatory macrophages.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:626d3a44c537e6a594d8
claim_id: claim:626d3a44c537e6a594d8
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
span_literal:
Neuronal subtype markers included excitatory neuron marker SCL17A7 , upper layer marker CUX2 , layer 4 marker RORB , deep layer marker TLE4 , as well as interneuron (IN) marker GAD2 and subtype markers PVALB , SST , VIP and SV2C .

summary:
In Homo sapiens, excitatory neurons are marked by SLC17A7, upper cortical layer excitatory neurons are marked by CUX2, layer 4 excitatory neurons are marked by RORB, deep layer excitatory neurons are marked by TLE4, interneurons are marked by GAD2, and interneuron subtypes are marked by PVALB, SST, VIP, and SV2C.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:b86038d4cff364d6cdd4
claim_id: claim:b86038d4cff364d6cdd4
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
span_literal:
marker genes for microglia reactivity ( CD68 , CD74 , FTL , MSR1 ) colocalized with the lineage microglia marker RUNX1 , and mapped such activated cells to chronic active boundaries of subcortical MS lesions.

summary:
In Homo sapiens, reactive microglia are marked by CD68, CD74, FTL, and MSR1, and the microglia lineage is marked by RUNX1.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:a69f2325523102eabc05
claim_id: claim:a69f2325523102eabc05
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
span_literal:
RFX4 expression was specific to the astrocyte lineage and captured all SLC1A2 -positive GM and CD44 -expressing WM astrocytes

summary:
In Homo sapiens, RFX4 expression is specific to the astrocyte lineage, SLC1A2 marks gray matter astrocytes, and CD44 marks white matter astrocytes.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:4761b0e1582b0a3a143f
claim_id: claim:4761b0e1582b0a3a143f
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
span_literal:
we found that snRNA-seq can distinguish phagocytosing cells in MS based on their transport of ingested myelin transcripts into peri-nuclear structures or the nucleus itself.

summary:
In Homo sapiens, phagocytosing microglia and/or macrophages can be identified by single-nucleus RNA sequencing based on their ingestion of myelin transcripts.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:b89002dc24ff7d5845ae
claim_id: claim:b89002dc24ff7d5845ae
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
span_literal: Myelinating OLs characterized by myelin gene expression and the transcription factor ST18
summary:
In Homo sapiens, myelinating oligodendrocytes are characterized by expression of the transcription factor ST18.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:9123b9e98cd3c110d7b0
claim_id: claim:9123b9e98cd3c110d7b0
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
span_literal:
meningeal infiltration of IGHG1 / MZB1 -expressing plasma cells (that predominated over SKAP1 + T cells) was a common finding in sulci with underlying upper cortical layer demyelination and loss of CUX2 -expressing neurons

summary:
In Homo sapiens, plasma cells in meningeal infiltrates express IGHG1 and MZB1, while T cells express SKAP1.


claim_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c:claim:5208e0d389c7569d6870
claim_id: claim:5208e0d389c7569d6870
paper_key: hca:0439_10.1038_s41586-019-1404-z_d7516e129c
summary: In Homo sapiens, pyramidal cells are characterized by high expression of THY1 and NRGN.
span_literal:
numbers of intermediate (EN-L4) and deep-layer (EN-L5-6) excitatory neurons, THY1/NRGN -high-expressing pyramidal cells, VIP -expressing, somatostatin ( SST ) - and parvalbumin ( PVALB )-expressing INs were similar between MS samples and controls


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:2169370656b93a42e767
claim_id: claim:2169370656b93a42e767
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
the top four differentially and selectively expressed genes in human islet endocrine cells in vitro and in vivo are not the canonical genes but a new set of non-canonical gene markers including ZNF385D , TRPM3 , LRFN2 , PLUT (β-cells); PTPRT , FAP , PDK4 , LOXL4 (α-cells); LRFN5 , ADARB2 , ERBB4 , KCNT2 (δ-cells); and CACNA2D3 , THSD7A , CNTNAP5 , RBFOX3 (γ-cells).

summary:
In Homo sapiens pancreatic islets, ZNF385D, TRPM3, LRFN2, and PLUT are non-canonical marker genes for beta cells identified by single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:1f68a52a29276ffa50f9
claim_id: claim:1f68a52a29276ffa50f9
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
the top four differentially and selectively expressed genes in human islet endocrine cells in vitro and in vivo are not the canonical genes but a new set of non-canonical gene markers including ZNF385D , TRPM3 , LRFN2 , PLUT (β-cells); PTPRT , FAP , PDK4 , LOXL4 (α-cells); LRFN5 , ADARB2 , ERBB4 , KCNT2 (δ-cells); and CACNA2D3 , THSD7A , CNTNAP5 , RBFOX3 (γ-cells).

summary:
In Homo sapiens pancreatic islets, PTPRT, FAP, PDK4, and LOXL4 are non-canonical marker genes for alpha cells identified by single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:57e6e261855f36f52566
claim_id: claim:57e6e261855f36f52566
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
the top four differentially and selectively expressed genes in human islet endocrine cells in vitro and in vivo are not the canonical genes but a new set of non-canonical gene markers including ZNF385D , TRPM3 , LRFN2 , PLUT (β-cells); PTPRT , FAP , PDK4 , LOXL4 (α-cells); LRFN5 , ADARB2 , ERBB4 , KCNT2 (δ-cells); and CACNA2D3 , THSD7A , CNTNAP5 , RBFOX3 (γ-cells).

summary:
In Homo sapiens pancreatic islets, LRFN5, ADARB2, ERBB4, and KCNT2 are non-canonical marker genes for delta cells identified by single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:27ae550c50cac6655fa4
claim_id: claim:27ae550c50cac6655fa4
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
summary:
In Homo sapiens pancreatic islets, CACNA2D3, THSD7A, CNTNAP5, and RBFOX3 are non-canonical marker genes for gamma cells identified by single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:8a8da28b5dccc76213e3
claim_id: claim:8a8da28b5dccc76213e3
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
A strong correlation was observed between established canonical gene cell markers ( GCG , INS , SST , and PPY ) along with several other known selective markers with α-, β-, δ-, and γ-cells in scRNA-seq.

summary:
In Homo sapiens pancreatic islets, GCG is a canonical marker gene for alpha cells as confirmed by single-cell RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:24de44fbfa56c2de2124
claim_id: claim:24de44fbfa56c2de2124
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
A strong correlation was observed between established canonical gene cell markers ( GCG , INS , SST , and PPY ) along with several other known selective markers with α-, β-, δ-, and γ-cells in scRNA-seq.

summary:
In Homo sapiens pancreatic islets, INS is a canonical marker gene for beta cells as confirmed by single-cell RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:147caca714d0e0b240de
claim_id: claim:147caca714d0e0b240de
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
A strong correlation was observed between established canonical gene cell markers ( GCG , INS , SST , and PPY ) along with several other known selective markers with α-, β-, δ-, and γ-cells in scRNA-seq.

summary:
In Homo sapiens pancreatic islets, SST is a canonical marker gene for delta cells as confirmed by single-cell RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:71b922fe53515d5ce121
claim_id: claim:71b922fe53515d5ce121
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
summary:
In Homo sapiens pancreatic islets, PPY is a canonical marker gene for gamma cells as confirmed by single-cell RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:58b4f0639664b6febe1c
claim_id: claim:58b4f0639664b6febe1c
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
In particular, top endocrine cell gene markers ( PTPRT , ZNF385D , LRFN5 , and CNTNAP5 for α-, β-, δ-, and γ-cells, respectively) displayed a more distinctive localization pattern than their corresponding canonical single-cell clustering gene markers ( GCG , INS , SST , and PPY ) for α-, β-, δ-, and γ-cells, respectively, in the snRNA-seq data objects

summary:
In Homo sapiens pancreatic islets, PTPRT is a top single-nucleus RNA sequencing marker gene for alpha cells, displaying a more distinctive localization pattern than the canonical marker GCG.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:a252b399255747df9868
claim_id: claim:a252b399255747df9868
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
In particular, top endocrine cell gene markers ( PTPRT , ZNF385D , LRFN5 , and CNTNAP5 for α-, β-, δ-, and γ-cells, respectively) displayed a more distinctive localization pattern than their corresponding canonical single-cell clustering gene markers ( GCG , INS , SST , and PPY ) for α-, β-, δ-, and γ-cells, respectively, in the snRNA-seq data objects

summary:
In Homo sapiens pancreatic islets, ZNF385D is a top single-nucleus RNA sequencing marker gene for beta cells, displaying a more distinctive localization pattern than the canonical marker INS.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:310804f86d65264bc268
claim_id: claim:310804f86d65264bc268
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
In particular, top endocrine cell gene markers ( PTPRT , ZNF385D , LRFN5 , and CNTNAP5 for α-, β-, δ-, and γ-cells, respectively) displayed a more distinctive localization pattern than their corresponding canonical single-cell clustering gene markers ( GCG , INS , SST , and PPY ) for α-, β-, δ-, and γ-cells, respectively, in the snRNA-seq data objects

summary:
In Homo sapiens pancreatic islets, LRFN5 is a top single-nucleus RNA sequencing marker gene for delta cells, displaying a more distinctive localization pattern than the canonical marker SST.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:d64ad6d660965ce5ffdc
claim_id: claim:d64ad6d660965ce5ffdc
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
summary:
In Homo sapiens pancreatic islets, CNTNAP5 is a top single-nucleus RNA sequencing marker gene for gamma cells, displaying a more distinctive localization pattern than the canonical marker PPY.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:fbc6736e915d3bc4119d
claim_id: claim:fbc6736e915d3bc4119d
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
the top differentially expressed genes in the snRNA-seq analysis in non-endocrine cells contained the canonical gene markers that define these cell types in scRNA-seq ( REG1A , CFTR , FLT1 , COL1A1 , and PRKG1 for acinar, ductal, endothelial, activated stellate, quiescent stellate cell, respectively).

summary:
In Homo sapiens pancreatic islets, REG1A is a top differentially expressed marker gene for acinar cells in single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:d2e322527097f573b788
claim_id: claim:d2e322527097f573b788
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
the top differentially expressed genes in the snRNA-seq analysis in non-endocrine cells contained the canonical gene markers that define these cell types in scRNA-seq ( REG1A , CFTR , FLT1 , COL1A1 , and PRKG1 for acinar, ductal, endothelial, activated stellate, quiescent stellate cell, respectively).

summary:
In Homo sapiens pancreatic islets, CFTR is a top differentially expressed marker gene for ductal cells in single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:bbdd9e49b8e1b31e5750
claim_id: claim:bbdd9e49b8e1b31e5750
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
the top differentially expressed genes in the snRNA-seq analysis in non-endocrine cells contained the canonical gene markers that define these cell types in scRNA-seq ( REG1A , CFTR , FLT1 , COL1A1 , and PRKG1 for acinar, ductal, endothelial, activated stellate, quiescent stellate cell, respectively).

summary:
In Homo sapiens pancreatic islets, FLT1 is a top differentially expressed marker gene for endothelial cells in single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:bd1d7d56bd17adeccd74
claim_id: claim:bd1d7d56bd17adeccd74
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
summary:
In Homo sapiens pancreatic islets, COL1A1 is a top differentially expressed marker gene for activated stellate cells in single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:f8e58a049f851f5ad028
claim_id: claim:f8e58a049f851f5ad028
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
summary:
In Homo sapiens pancreatic islets, PRKG1 is a top differentially expressed marker gene for quiescent stellate cells in single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:affdde363ae9b5ec812e
claim_id: claim:affdde363ae9b5ec812e
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
Projection of the four top gene makers for exocrine cells from the snRNA-seq data on UMAP: REG1A (acinar cells), CFTR (ductal cells), FLT1 (endothelial cells), COL1A1 (activated stellate cells), PRR16 (quiescent stellate cells).

summary:
In Homo sapiens pancreatic islets, PRR16 is a top marker gene for quiescent stellate cells in single-nucleus RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:c89cd1565e717ffe7b70
claim_id: claim:c89cd1565e717ffe7b70
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
These include ZNF385D , TRPM3 , LRFN2 and PLUT (for β-cells); PTPRT , FAP , PDK4 , and LOXL4 (for α-cells); LRFN5 , ADARB2 , ERBB4 , and KCNT2 (for δ-cells); and CACNA2D3 , THSD7A , CNTNAP5 , and RBFOX3 (for γ-cells).

summary:
In Homo sapiens pancreatic islets, ZNF385D, TRPM3, LRFN2, and PLUT are newly identified single-nucleus RNA sequencing gene markers for beta cells.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:733d220ad30246af743b
claim_id: claim:733d220ad30246af743b
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
These include ZNF385D , TRPM3 , LRFN2 and PLUT (for β-cells); PTPRT , FAP , PDK4 , and LOXL4 (for α-cells); LRFN5 , ADARB2 , ERBB4 , and KCNT2 (for δ-cells); and CACNA2D3 , THSD7A , CNTNAP5 , and RBFOX3 (for γ-cells).

summary:
In Homo sapiens pancreatic islets, PTPRT, FAP, PDK4, and LOXL4 are newly identified single-nucleus RNA sequencing gene markers for alpha cells.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:76728086a411866743d9
claim_id: claim:76728086a411866743d9
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
These include ZNF385D , TRPM3 , LRFN2 and PLUT (for β-cells); PTPRT , FAP , PDK4 , and LOXL4 (for α-cells); LRFN5 , ADARB2 , ERBB4 , and KCNT2 (for δ-cells); and CACNA2D3 , THSD7A , CNTNAP5 , and RBFOX3 (for γ-cells).

summary:
In Homo sapiens pancreatic islets, LRFN5, ADARB2, ERBB4, and KCNT2 are newly identified single-nucleus RNA sequencing gene markers for delta cells.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:e5798a321531a7c9b60e
claim_id: claim:e5798a321531a7c9b60e
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
summary:
In Homo sapiens pancreatic islets, CACNA2D3, THSD7A, CNTNAP5, and RBFOX3 are newly identified single-nucleus RNA sequencing gene markers for gamma cells.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:74235afbd2ad2587bccc
claim_id: claim:74235afbd2ad2587bccc
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
For example, in β-cells, INS and IAPP are the top differentially expressed genes, whereas they are not the top differentially expressed genes in the snRNA-seq datasets.

summary:
In Homo sapiens pancreatic islets, INS and IAPP are the top differentially expressed genes in beta cells in single-cell RNA sequencing.


claim_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7:claim:b7c582acce75412ac912
claim_id: claim:b7c582acce75412ac912
paper_key: hca:0440_10.1186_s13073-023-01179-2_de903e74e7
span_literal:
we looked at the expression of the INS mRNA-binding protein HNRNPA2B1 , an RNA-binding protein that regulates INS mRNA stability and translation

summary:
In Homo sapiens pancreatic islets, HNRNPA2B1 is an INS mRNA-binding protein expressed in beta cells that regulates INS mRNA stability and translation.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:735a83b07268a3050ed2
claim_id: claim:735a83b07268a3050ed2
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal:
OPCs express a characteristic set of markers, such as PDGFRA and PCDH15 , which decline as these cells mature into oligodendrocytes (designated as ‘Oligos’), whereas other lineage markers, such as OLIG2 or SOX10 , are present in both mature and immature cells.

summary:
In Homo sapiens, oligodendrocyte precursor cells express PDGFRA and PCDH15 as characteristic markers, while OLIG2 and SOX10 are present in both oligodendrocyte precursor cells and mature oligodendrocytes.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:2957734c77451ddb4c77
claim_id: claim:2957734c77451ddb4c77
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: For example, clusters Ex1, Ex4 and Ex7–9 had high expression of TLE4 (specific for layer VI).
summary:
In Homo sapiens, excitatory neuron clusters Ex1, Ex4, and Ex7–9 in the dorsolateral prefrontal cortex had high expression of TLE4, a marker specific for cortical layer VI.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:e08b4ea26a1dccc4baef
claim_id: claim:e08b4ea26a1dccc4baef
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: Ex1, Ex8 and Ex9 showed concurrent expression of layer V/VI markers such as TOX
summary:
In Homo sapiens, excitatory neuron clusters Ex1, Ex8, and Ex9 showed expression of TOX, a layer V/VI marker.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:78ceb38a9409c481845c
claim_id: claim:78ceb38a9409c481845c
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: Ex6 and Ex7 additionally showed expression of the layer-IV-specific gene RORB
summary:
In Homo sapiens, excitatory neuron clusters Ex6 and Ex7 showed expression of RORB, a layer IV-specific gene.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:a1ce6099282288ab98d5
claim_id: claim:a1ce6099282288ab98d5
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: HTR2C , which is specific to a subset of layer V neurons, was prominent in Ex1
summary:
In Homo sapiens, HTR2C, specific to a subset of layer V neurons, was prominently expressed in excitatory neuron cluster Ex1.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:9e9d7231ceea216691ac
claim_id: claim:9e9d7231ceea216691ac
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: PCP4 , which is also specific to layer V, was present in Ex1–3, Ex7 and Ex9
summary:
In Homo sapiens, PCP4, a layer V-specific marker, was present in excitatory neuron clusters Ex1–3, Ex7, and Ex9.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:a7c26b56ce38f293da45
claim_id: claim:a7c26b56ce38f293da45
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal:
Superficial layer (I–III) markers such as CUX2 and RASGRF2 were mainly seen in the large cluster Ex10.

summary:
In Homo sapiens, superficial cortical layer markers CUX2 and RASGRF2 were mainly expressed in excitatory neuron cluster Ex10.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:5caef210331366fcf008
claim_id: claim:5caef210331366fcf008
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal:
Inhib_7 was classified as inhibitory parvalbumin (PVALB) because it expressed GAD1 and PVALB and lacked VIP and SST

summary:
In Homo sapiens, inhibitory parvalbumin neuron cluster Inhib_7 expressed GAD1 and PVALB and lacked VIP and SST.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:c9ff6fe3881fd8572395
claim_id: claim:c9ff6fe3881fd8572395
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal:
based on the higher percentage of GFAP expression in Astros_3 (38%) compared to Astros_2 (21%), we suspect that Astros_3 is more likely to represent reactive astrocytes

summary:
In Homo sapiens, astrocyte cluster Astros_3 had higher GFAP expression compared to astrocyte cluster Astros_2, suggesting Astros_3 represents reactive astrocytes.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:cd8e32b66dbb987026b8
claim_id: claim:cd8e32b66dbb987026b8
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: macrophage/microglia: SPI1 , MRC1 , TMEM119 and CX3CR1
summary:
In Homo sapiens, macrophage/microglia were marked by SPI1, MRC1, TMEM119, and CX3CR1; endothelial cells by CLDN5 and VTN; astrocytes by GLUL, SOX9, AQP4, GJA1, NDRG2, GFAP, ALDH1A1, ALDH1L1, and VIM; oligodendrocyte precursor cells by PTGDS, PDGFRA, PCDH15, OLIG2, and OLIG1; oligodendrocytes by PLP1, MAG, MOG, MOBP, and MBP; excitatory neurons by SATB2, SLC17A7, and SLC17A6; inhibitory neurons by GAD1, GAD2, and SLC32A1; neurons by SNAP25, STMN2, and RBFOX3.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:cb5138e03714c45ec63a
claim_id: claim:cb5138e03714c45ec63a
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: endothelial: CLDN5 and VTN
summary:
In Homo sapiens, endothelial cells were marked by CLDN5 and VTN in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:5611e0c10ba68006aa32
claim_id: claim:5611e0c10ba68006aa32
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: astrocytes: GLUL , SOX9 , AQP4 , GJA1 , NDRG2 , GFAP , ALDH1A1 , ALDH1L1 and VIM
summary:
In Homo sapiens, astrocytes were marked by GLUL, SOX9, AQP4, GJA1, NDRG2, GFAP, ALDH1A1, ALDH1L1, and VIM in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:48a12dd25d29079e5970
claim_id: claim:48a12dd25d29079e5970
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: OPCs : PTGDS , PDGFRA , PCDH15 , OLIG2 and OLIG1
summary:
In Homo sapiens, oligodendrocyte precursor cells were marked by PTGDS, PDGFRA, PCDH15, OLIG2, and OLIG1 in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:4fbec6199dbec16bb159
claim_id: claim:4fbec6199dbec16bb159
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: oligodendrocytes: PLP1 , MAG , MOG , MOBP and MBP
summary:
In Homo sapiens, oligodendrocytes were marked by PLP1, MAG, MOG, MOBP, and MBP in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:fc47ad3ad36dec42e184
claim_id: claim:fc47ad3ad36dec42e184
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: excitatory neurons: SATB2 , SLC17A7 and SLC17A6
summary:
In Homo sapiens, excitatory neurons were marked by SATB2, SLC17A7, and SLC17A6 in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:3136d6511bbdc91e61c3
claim_id: claim:3136d6511bbdc91e61c3
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: inhibitory neurons: GAD1 , GAD2 and SLC32A1
summary:
In Homo sapiens, inhibitory neurons were marked by GAD1, GAD2, and SLC32A1 in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:80c74a4f5f85d1c42162
claim_id: claim:80c74a4f5f85d1c42162
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal: neurons: SNAP25 , STMN2 and RBFOX3
summary:
In Homo sapiens, neurons were marked by SNAP25, STMN2, and RBFOX3 in the dorsolateral prefrontal cortex.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:289b72129f5ad603511a
claim_id: claim:289b72129f5ad603511a
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal:
The neuronal cluster with the most change was Ex7, a deep layer cluster characterized primarily by DPP10 expression.

summary:
In Homo sapiens, excitatory neuron cluster Ex7, a deep layer cluster, was characterized primarily by DPP10 expression.


claim_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60:claim:16593f62896d64f61ac6
claim_id: claim:16593f62896d64f61ac6
paper_key: hca:0441_10.1038_s41593-020-0621-y_a3edefca60
span_literal:
SLC17A7 (which encodes VGLUT) was used as a marker for excitatory cells, and RXFP1 was used to identify deep layer neurons.

summary:
In Homo sapiens, SLC17A7 was used as a marker for excitatory neurons, and RXFP1 was used to identify deep layer neurons.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:ccc331646ec551f3888b
claim_id: claim:ccc331646ec551f3888b
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
In addition to the known cell identity genes FOXA1 (luminal hormone sensing), EHF and ELF5 (LASP), TP63 and KRT14 (basal-myoepithelial), epithelial subtypes displayed several uncharacterized markers and inferred gene regulatory networks.

summary:
In Homo sapiens breast tissue, FOXA1 is a known cell identity gene of luminal hormone sensing cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:1d1f39f8216a59171b0c
claim_id: claim:1d1f39f8216a59171b0c
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
In addition to the known cell identity genes FOXA1 (luminal hormone sensing), EHF and ELF5 (LASP), TP63 and KRT14 (basal-myoepithelial), epithelial subtypes displayed several uncharacterized markers and inferred gene regulatory networks.

summary:
In Homo sapiens breast tissue, EHF and ELF5 are known cell identity genes of luminal adaptive secretory precursor cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:35f064eb1d3075555b8b
claim_id: claim:35f064eb1d3075555b8b
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
In addition to the known cell identity genes FOXA1 (luminal hormone sensing), EHF and ELF5 (LASP), TP63 and KRT14 (basal-myoepithelial), epithelial subtypes displayed several uncharacterized markers and inferred gene regulatory networks.

summary:
In Homo sapiens breast tissue, TP63 and KRT14 are known cell identity genes of basal-myoepithelial cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:e1d56410e6321b5363ee
claim_id: claim:e1d56410e6321b5363ee
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Comparison between the genes enriched in cell types based on our multiome analysis with data reported by others showed substantial overlap for the markers of individual cell types: ERBB4 , ANKRD30A , AFF3 , TTC6 , MYBPC1 and THSD4 in LHS cells; KRT15 , ELF5 , CCL28 and KIT in LASP cells; KLHL29 in BM cells; LAMA2 and SLIT2 in fibroblasts; MECOM , LDB2 , ST6GALNAC3 , STNL9 , AL357507.1 , PKHD1L1 and MMRN1 in endothelial cells; PTPRC , SKAP1 , ARHGAP15 and THEMIS in T cells 12 ; KLHL13 in basal-alpha (BAα) cells; ELF5 in LASP_alveolar progenitor (AP) cells; ESR1 in LHS_hormone sensing α (HSα) cells; CD96 in T cells; RUNX1T1 in fibroblasts; ALCAM in macrophages; and MECOM in endothelial cells 13 .

summary:
In Homo sapiens breast tissue, ERBB4, ANKRD30A, AFF3, TTC6, MYBPC1 and THSD4 are markers enriched in luminal hormone sensing cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:304b8f2220bcf702d223
claim_id: claim:304b8f2220bcf702d223
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Comparison between the genes enriched in cell types based on our multiome analysis with data reported by others showed substantial overlap for the markers of individual cell types: ERBB4 , ANKRD30A , AFF3 , TTC6 , MYBPC1 and THSD4 in LHS cells; KRT15 , ELF5 , CCL28 and KIT in LASP cells; KLHL29 in BM cells; LAMA2 and SLIT2 in fibroblasts; MECOM , LDB2 , ST6GALNAC3 , STNL9 , AL357507.1 , PKHD1L1 and MMRN1 in endothelial cells; PTPRC , SKAP1 , ARHGAP15 and THEMIS in T cells 12 ; KLHL13 in basal-alpha (BAα) cells; ELF5 in LASP_alveolar progenitor (AP) cells; ESR1 in LHS_hormone sensing α (HSα) cells; CD96 in T cells; RUNX1T1 in fibroblasts; ALCAM in macrophages; and MECOM in endothelial cells 13 .

summary:
In Homo sapiens breast tissue, KRT15, ELF5, CCL28 and KIT are markers enriched in luminal adaptive secretory precursor cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:82f61d235ae08c3d4dca
claim_id: claim:82f61d235ae08c3d4dca
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary:
In Homo sapiens breast tissue, LAMA2 and SLIT2 are markers enriched in fibroblasts. In Homo sapiens breast tissue, RUNX1T1 is a marker enriched in fibroblasts.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:fa0c14996a3305d8574a
claim_id: claim:fa0c14996a3305d8574a
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary:
In Homo sapiens breast tissue, MECOM, LDB2, ST6GALNAC3, STNL9, AL357507.1, PKHD1L1 and MMRN1 are markers enriched in endothelial cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:685846b9fe14884ef697
claim_id: claim:685846b9fe14884ef697
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary:
In Homo sapiens breast tissue, PTPRC, SKAP1, ARHGAP15 and THEMIS are markers enriched in T cells. In Homo sapiens breast tissue, CD96 is a marker enriched in T cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:9d276ac093b4b0ddeac0
claim_id: claim:9d276ac093b4b0ddeac0
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary:
In Homo sapiens breast tissue, ELF5 is a marker enriched in luminal adaptive secretory precursor alveolar progenitor cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:443bb8cfff5303ca3d6d
claim_id: claim:443bb8cfff5303ca3d6d
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary:
In Homo sapiens breast tissue, ESR1 is a marker enriched in luminal hormone sensing hormone sensing alpha cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:fbed9c93227bbade35ee
claim_id: claim:fbed9c93227bbade35ee
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary: In Homo sapiens breast tissue, FHOD3 is enriched in basal-myoepithelial cells.
span_literal:
These include BM cell-enriched FHOD3 , LASP cell-enriched BARX2 and NCALD , and LHS cell-enriched CTNND2 , DACH1 , INPP4B and NEK10 .


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:1b0702e684dd7df971e2
claim_id: claim:1b0702e684dd7df971e2
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
These include BM cell-enriched FHOD3 , LASP cell-enriched BARX2 and NCALD , and LHS cell-enriched CTNND2 , DACH1 , INPP4B and NEK10 .

summary:
In Homo sapiens breast tissue, BARX2 and NCALD are enriched in luminal adaptive secretory precursor cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:e696d1ae86ee1a62912a
claim_id: claim:e696d1ae86ee1a62912a
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
These include BM cell-enriched FHOD3 , LASP cell-enriched BARX2 and NCALD , and LHS cell-enriched CTNND2 , DACH1 , INPP4B and NEK10 .

summary:
In Homo sapiens breast tissue, CTNND2, DACH1, INPP4B and NEK10 are enriched in luminal hormone sensing cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:c1cdcf2736fe03171b08
claim_id: claim:c1cdcf2736fe03171b08
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal: ESR1 expression was generally limited to LHS cells (Fig. 2a ).
summary:
In Homo sapiens breast tissue, ESR1 expression is generally limited to luminal hormone sensing cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:b27cfa1a75e02c774232
claim_id: claim:b27cfa1a75e02c774232
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal: FOXA1 expression was mostly restricted to LHS cells (Fig. 2d ).
summary:
In Homo sapiens breast tissue, FOXA1 expression is mostly restricted to luminal hormone sensing cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:149b60c928ca9d243011
claim_id: claim:149b60c928ca9d243011
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Therefore, based on expression and chromatin accessibility, FOXA1, not ESR1 and GATA3, is the appropriate marker of LHS cells.

summary:
In Homo sapiens breast tissue, based on expression and chromatin accessibility, FOXA1 is the appropriate marker of luminal hormone sensing cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:bbbec5f8ea4adaf3ef0c
claim_id: claim:bbbec5f8ea4adaf3ef0c
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal: EHF expression was enriched in the LASP cells compared to other cell types (Fig. 2j ).
summary:
In Homo sapiens breast tissue, EHF expression is enriched in luminal adaptive secretory precursor cells compared to other cell types.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:ddbde3d162a0604f1e1a
claim_id: claim:ddbde3d162a0604f1e1a
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Despite enrichment of KIT expression in LASP cells, its promoter regions showed similar accessibility across all three cell types (Fig. 2p,q ).

summary:
In Homo sapiens breast tissue, KIT expression is enriched in luminal adaptive secretory precursor cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:d209ba8deb58f99e04fa
claim_id: claim:d209ba8deb58f99e04fa
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
The BM cell marker TP63 showed enriched expression and chromatin accessibility in BM cells (Fig. 2r,s ).

summary:
In Homo sapiens breast tissue, TP63 is a marker of basal-myoepithelial cells showing enriched expression and chromatin accessibility.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:a66e3b1a999ad012dcd6
claim_id: claim:a66e3b1a999ad012dcd6
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary: In Homo sapiens breast tissue, KRT14 expression is restricted to basal-myoepithelial cells.
span_literal:
Similarly, KRT14 expression was restricted to BM cells (Fig. 2u ); its promoter showed a distinct accessibility pattern in BM cells (Fig. 2v ).


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:f424d1f25d5085b39237
claim_id: claim:f424d1f25d5085b39237
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
CD4 + T cell-enriched IL7R and CD8 + T cell-enriched IFNγ showed T cell-specific expression and chromatin accessibility (Fig. 6a ).

summary:
In Homo sapiens breast tissue, IL7R shows T cell-specific expression and is enriched in CD4-positive T cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:d359e6d45d2c00b1b629
claim_id: claim:d359e6d45d2c00b1b629
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
CD4 + T cell-enriched IL7R and CD8 + T cell-enriched IFNγ showed T cell-specific expression and chromatin accessibility (Fig. 6a ).

summary:
In Homo sapiens breast tissue, IFNγ shows T cell-specific expression and is enriched in CD8-positive T cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:25ab0942c14eec3619c2
claim_id: claim:25ab0942c14eec3619c2
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Similarly, the expression and chromatin accessibility of CD8 + T cell-enriched GZMK was restricted to T cells (Fig. 6b ).

summary:
In Homo sapiens breast tissue, GZMK expression and chromatin accessibility are restricted to T cells, enriched in CD8-positive T cells.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:edd917604dbb64ba882b
claim_id: claim:edd917604dbb64ba882b
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal: The chromatin accessibility of macrophage-enriched FCGR3A was restricted to macrophages (Fig. 6c ).
summary:
In Homo sapiens breast tissue, FCGR3A is enriched in macrophages with chromatin accessibility restricted to macrophages.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:b1d6dc5755fffb2cd331
claim_id: claim:b1d6dc5755fffb2cd331
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Among endothelial cells, the lymphatic endothelial cell marker LYVE1 was expressed in the endothelial cell 2 subcluster and in the macrophage subpopulation, but the chromatin accessibility patterns in these two cell types were not similar (Fig. 6d ).

summary:
In Homo sapiens breast tissue, the lymphatic endothelial cell marker LYVE1 is expressed in the endothelial cell 2 subcluster.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:bf10e1545e2ebdd86ee6
claim_id: claim:bf10e1545e2ebdd86ee6
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Similarly, the endothelial stalk-like subtype marker ACKR1 was expressed in a subset of the endothelial cell 1 subcluster but the chromatin in the regulatory regions of this gene was accessible in all cell types (Fig. 6e ).

summary:
In Homo sapiens breast tissue, ACKR1 is a marker of the endothelial stalk-like subtype, expressed in a subset of the endothelial cell 1 subcluster.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:635b738d9584ccb71c2b
claim_id: claim:635b738d9584ccb71c2b
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
Myofibroblasts are enriched for COL1A1 and PDPN , whereas inflammatory fibroblasts express higher levels of CD34 and CXCL12 .

summary:
In Homo sapiens breast tissue, myofibroblasts are enriched for COL1A1 and PDPN, whereas inflammatory fibroblasts express higher levels of CD34 and CXCL12.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:d5a4dc40689e0abdba30
claim_id: claim:d5a4dc40689e0abdba30
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
summary: In Homo sapiens breast tissue, MYH11 and MYLK are enriched in differentiated pericytes.
span_literal:
MYH11 and MYLK are enriched in differentiated pericytes, whereas CD36 and RGS5 are enriched in immature pericytes.


claim_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c:claim:8f65ccdb08685200087f
claim_id: claim:8f65ccdb08685200087f
paper_key: hca:0442_10.1038_s41591-024-03011-9_e42f5ec07c
span_literal:
FOXA1 expression was restricted to LHS cells and ESR1 expression was higher in LHS cells compared to LASP cells in both groups.

summary:
In Homo sapiens breast tissue, FOXA1 expression is restricted to luminal hormone sensing cells and ESR1 expression is higher in luminal hormone sensing cells compared to luminal adaptive secretory precursor cells.


claim_key: hca:0443_10.1101_2021.07.19.452954_47077e842d:claim:26e9594acfcf360fba93
claim_id: claim:26e9594acfcf360fba93
paper_key: hca:0443_10.1101_2021.07.19.452954_47077e842d
span_literal:
These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease.

summary:
In Homo sapiens, macrophages show a cross-tissue conserved dichotomy between LYVE1-expressing and HLA class II-expressing populations, and lipid-associated macrophage-like macrophages are broadly present across healthy tissues.


claim_key: hca:0443_10.1101_2021.07.19.452954_47077e842d:claim:3220bb350df186e97994
claim_id: claim:3220bb350df186e97994
paper_key: hca:0443_10.1101_2021.07.19.452954_47077e842d
span_literal:
These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease.

summary:
In Homo sapiens, HLA class II-expressing macrophages represent one side of a cross-tissue conserved dichotomy among macrophages.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:004542f3bcbb6acdc36a
claim_id: claim:004542f3bcbb6acdc36a
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, CD16-positive monocytes are marked by positive expression of CD16 (FCGR3B).
span_literal:
These included CD16 + monocytes, CD14 + monocytes, two transitional Mo/MΦ FCGR3A low and Mo/MΦ FCGR3A high populations with coexpression of both monocyte and macrophage markers (see next section), DC1s, DC2s ( 49 ), mature DCs, and Langerhans cells ( Fig. 3B ).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:c457322ca8bc74467eb6
claim_id: claim:c457322ca8bc74467eb6
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
Although most myeloid subsets were present in multiple tissues, notable exceptions included PPARG high lung macrophages, which were present only in lung, and CD207 /Langerin + Langerhans cells, which were present only (97%) in skin and esophagus mucosa, consistent with their role in antigen sampling within stratified epithelia ( 52 , 53 ) ( Fig. 3C and fig. S15, F and I ).

summary:
In Homo sapiens, lung macrophages are marked by high expression of PPARG, and Langerhans cells are marked by positive expression of CD207 (Langerin) in skin and esophagus mucosa.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:f962cea5c6bc21344eee
claim_id: claim:f962cea5c6bc21344eee
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
Although most myeloid subsets were present in multiple tissues, notable exceptions included PPARG high lung macrophages, which were present only in lung, and CD207 /Langerin + Langerhans cells, which were present only (97%) in skin and esophagus mucosa, consistent with their role in antigen sampling within stratified epithelia ( 52 , 53 ) ( Fig. 3C and fig. S15, F and I ).

summary:
In Homo sapiens, Langerhans cells are marked by positive expression of CD207 (Langerin) in skin and esophagus mucosa.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:285e3181861b59949d09
claim_id: claim:285e3181861b59949d09
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
Two expression states of LYVE1 high and HLA II high macrophage populations were dichotomous—either LYVE1 high HLA II low or LYVE1 low HLA II high —and represented the end points of two alternative branches.

summary:
In Homo sapiens, LYVE1 high macrophages are marked by high expression of LYVE1 and low expression of HLA class II genes, while HLA class II high macrophages are marked by low expression of LYVE1 and high expression of HLA class II genes.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:f8af3cd822352b4588ad
claim_id: claim:f8af3cd822352b4588ad
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, HLA class II high macrophages express higher levels of APOE, C1QA, C1QB, and C1QC.
span_literal:
HLA II high cells were enriched for immune-related processes and expressed higher levels of complement components APOE and C1QA , C1QB , and C1QC ( Fig. 3B and fig. S16, C and D ).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:3abf87d908e1dbc096c0
claim_id: claim:3abf87d908e1dbc096c0
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
Select lipid pathway genes, including fatty-acid binding protein FABP4 , lipoprotein lipase LPL , and phagocytic lipid receptor CD36 , were highly expressed in LAMs from tissues with high adipose content, including adipose, atherosclerotic lesions, and intestine creeping fat samples, possibly reflecting increased lipid-induced transcriptional stimulation of these target genes under these conditions ( 85 ).

summary:
In Homo sapiens, lipid-associated macrophages from tissues with high adipose content highly express fatty-acid binding protein FABP4, lipoprotein lipase LPL, and phagocytic lipid receptor CD36.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:e86d98ea82c61d04dba9
claim_id: claim:e86d98ea82c61d04dba9
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
The cardiac fibroblast signature genes included TFs involved in cardiac development (e.g., GATA4 and GATA6 ), revealing that expression of these developmental TFs is retained in the adult cardiac fibroblast compartment ( 89 - 92 ).

summary:
In Homo sapiens, cardiac fibroblasts are marked by expression of the transcription factors GATA4 and GATA6 in the heart.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:451005c6f64450b497dd
claim_id: claim:451005c6f64450b497dd
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
The skeletal muscle signature showed increased expression of the CXCL14 and CXCL12 chemokines and of components of the renin-angiotensin-aldosterone system ( AGTR1 and MME ), which regulate skeletal muscle mass ( 93 , 94 ) [reminiscent of the expression of the same components by WNT2B + fibroblasts in a local renin-angiotensin system in the colon ( 16 )].

summary:
In Homo sapiens, skeletal muscle fibroblasts show increased expression of CXCL14, CXCL12, AGTR1, and MME.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:bfc5c2e50dd60dc7995e
claim_id: claim:bfc5c2e50dd60dc7995e
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, alveolar fibroblasts specifically express FGFR4 in the lung.
span_literal:
Alveolar fibroblasts also specifically expressed FGFR4 ( Fig. 4B ), which is essential for alveologenesis in mice ( 109 ) and is genetically linked with bronchopulmonary dysplasia that affects alveoli in humans ( 110 ).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:d09656f3c1f1794c09bc
claim_id: claim:d09656f3c1f1794c09bc
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
Of all tissue fibroblasts, lung alveolar fibroblasts distinctively expressed a calcium signaling and actomyosin contractility program ( Fig. 4, E and F , and fig. S18D ), including the mechanosensitive calcium ion channel PIEZO2 ( Fig. 4G ), which has been proposed to sense pulmonary stretch ( 111 , 112 ); multiple calcium channels and adrenergic and purinergic receptors, which have been implicated in stimulating calcium release from intracellular stores ( CACNA1D, TRPC6, MCOLN2/TRPML2 ); and myosin light chain kinase ( MYLK ), which is involved in mediating calcium-induced actomyosin contraction ( 113 ).

summary:
In Homo sapiens, lung alveolar fibroblasts distinctively express the mechanosensitive calcium ion channel PIEZO2, calcium channels CACNA1D, TRPC6, MCOLN2, and myosin light chain kinase MYLK.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:69656c8b4a055fb9514d
claim_id: claim:69656c8b4a055fb9514d
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
These included acetylcholine receptor subunits ( CHRNE , CHRNA1 , CHRND ), the NMJ-organizing receptor tyrosine kinase MUSK , and NMJ-enriched ECM components ( COL13A1 , LAMA2 ).

summary:
In Homo sapiens, neuromuscular junction-localized myonuclei specifically express acetylcholine receptor subunits CHRNE, CHRNA1, CHRND, the receptor tyrosine kinase MUSK, and extracellular matrix components COL13A1 and LAMA2.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:2c72c990fc51f8ef9270
claim_id: claim:2c72c990fc51f8ef9270
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
the congenital muscular dystrophies genes COL6A1 , COL6A2 , and COL6A3 are expressed in fibroblasts, consistent with joint laxity and progressive contractures along with muscle weakness ( 126 )

summary:
In Homo sapiens, fibroblasts express the congenital muscular dystrophy genes COL6A1, COL6A2, and COL6A3.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:69dd2fb46f2c2a5c1912
claim_id: claim:69dd2fb46f2c2a5c1912
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, immune cells express the recessive limb girdle muscular dystrophy gene DYSF.
span_literal:
and the recessive limb girdle muscular dystrophies gene DYSF is expressed in immune cells, consistent with the role of more aggressive monocytes in disease progression ( 127 ).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:ec6592ba57403d63ae62
claim_id: claim:ec6592ba57403d63ae62
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, slow myocytes preferentially express the disease genes MYH7 and PPARGC1A.
span_literal:
As expected, slow myocytes preferentially expressed type 1 fiber markers ( 36 , 128 ) and disease genes MYH7 (FDR < 10 −15 in cytoplasmic myonuclei) and PPARGC1A (FDR < 10 −15 in regular myonuclei).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:b12194965130906c4a95
claim_id: claim:b12194965130906c4a95
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, fast myocytes specifically express the type 2 fiber marker MYH2.
span_literal:
Fast myocytes specifically expressed the type 2 fiber marker MYH2 (FDR < 10 −15 in cytoplasmic myonuclei), in line with respective clinical myosinopathy phenotypes ( 129 ).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:0c3c89892a4bd6607d4d
claim_id: claim:0c3c89892a4bd6607d4d
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
The myotonic dystrophy (MD) type 2 gene CNBP , was enriched in regular myonuclei from fast myocytes [FDR < 10 −12 ; ( 28 ); fig. S9, E and F ], which are preferentially affected in MD type 2 ( 130 , 131 ).

summary:
In Homo sapiens, the myotonic dystrophy type 2 gene CNBP is enriched in regular myonuclei from fast myocytes.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:b8b0ec82f81dd98792da
claim_id: claim:b8b0ec82f81dd98792da
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
By contrast, MD type 1 disease gene DMPK was preferentially expressed in cytoplasmic myonuclei from slow myocytes ( P < 0.036, Welch’s t test), which are perturbed in MD type 1 ( 132 ).

summary:
In Homo sapiens, the myotonic dystrophy type 1 disease gene DMPK is preferentially expressed in cytoplasmic myonuclei from slow myocytes.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:5c13abf6c1277caca0a6
claim_id: claim:5c13abf6c1277caca0a6
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, regular myonuclei subsets from slow myocytes are enriched in TPM3.
span_literal:
Regular myonuclei subsets from slow myocytes were also enriched in TPM3 [FDR < 10 −15 ; ( 28 ); fig. S9, E and F ], which has been linked to congenital fiber type disproportion, a condition characterized by smaller slow myocyte fibers ( 133 ).


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:780c89fe97cb9e9e9c4a
claim_id: claim:780c89fe97cb9e9e9c4a
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
summary: In Homo sapiens, adipocytes in all muscle types express high levels of DMD.
span_literal:
In humans, high levels of DMD expression (comparable to that in myonuclei) were observed in adipocytes in all muscle types; pericytes and Schwann cells in skeletal muscle and esophagus muscularis; and enteric neurons in esophagus muscularis [mean expression log(TP10K+1) > 2.0; Fig. 5C ].


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:6688c250ad8b2fd8c91b
claim_id: claim:6688c250ad8b2fd8c91b
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
In humans, high levels of DMD expression (comparable to that in myonuclei) were observed in adipocytes in all muscle types; pericytes and Schwann cells in skeletal muscle and esophagus muscularis; and enteric neurons in esophagus muscularis [mean expression log(TP10K+1) > 2.0; Fig. 5C ].

summary:
In Homo sapiens, Schwann cells in skeletal muscle and esophagus muscularis express high levels of DMD.


claim_key: hca:0444_10.1126_science.abl4290_bce423dc46:claim:adf863682d77dedcea8f
claim_id: claim:adf863682d77dedcea8f
paper_key: hca:0444_10.1126_science.abl4290_bce423dc46
span_literal:
CASQ2 , which encodes a cardiac muscle member of the calsequestrin family, and the myosin heavy chain 6 and 7 genes ( MYH6 and MYH7 ) were the top myonuclei-specific genes driving the enrichment signal for atrial fibrillation in all three studies ( table S19 ).

summary:
In Homo sapiens, cardiac myonuclei are marked by expression of CASQ2, MYH6, and MYH7 as top myonuclei-specific genes associated with atrial fibrillation.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:71e04454077f6a621917
claim_id: claim:71e04454077f6a621917
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
This population showed elevated expression of known activated fibroblast markers such as POSTN , NOX4 , FAP , and COL1A1/COL1A2

summary:
In Homo sapiens, activated fibroblasts show elevated expression of known markers POSTN, NOX4, FAP, COL1A1, and COL1A2 in the left ventricle.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:baaa6805576310af8024
claim_id: claim:baaa6805576310af8024
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
as well as previously unreported genes such as Family With Sequence Similarity 155 Member A ( FAM155A ) and Teashirt Zinc Finger Homeobox 2 ( TSHZ2 )

summary:
In Homo sapiens, activated fibroblasts show elevated expression of previously unreported marker genes Family With Sequence Similarity 155 Member A (FAM155A) and Teashirt Zinc Finger Homeobox 2 (TSHZ2).


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:b753599f6030d7214bfd
claim_id: claim:b753599f6030d7214bfd
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
An additional activated fibroblast marker, Thrombospondin-4 ( THBS4 ), has been shown to be up-regulated in matrifibrocytes

summary:
In Homo sapiens, Thrombospondin-4 (THBS4) is a marker of activated fibroblasts and has been shown to be up-regulated in matrifibrocytes.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:05c876036f8dfbc87555
claim_id: claim:05c876036f8dfbc87555
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
we performed RNA in-situ hybridization using the highly specific activated fibroblast marker COL22A1 (log fold change=8.14; adjusted P =3.96×10 −112 ) and the general fibroblast marker DCN

summary:
In Homo sapiens, COL22A1 is a highly specific marker of activated fibroblasts, while DCN is a general fibroblast marker in the left ventricle.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:2bcf5c9e11edb619643e
claim_id: claim:2bcf5c9e11edb619643e
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
This endothelial sub-population displayed increased expression of previously reported angiogenic endothelial markers, including KIT , NRP2 , COL15A1 , PCDH17 , and ITGA6

summary:
In Homo sapiens, the endothelial sub-population EC-TMEM163 displays increased expression of angiogenic endothelial cell markers KIT, NRP2, COL15A1, PCDH17, and ITGA6.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:dbd86e13916388abdc10
claim_id: claim:dbd86e13916388abdc10
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
Compared to other lymphocytes, LC- LINGO2 showed increased expression of several known natural killer (NK) cell markers including KLRF1 , GNLY , CD244 , and PRF1

summary:
In Homo sapiens, the lymphocyte sub-population LC-LINGO2 showed increased expression of known natural killer cell markers KLRF1, GNLY, CD244, and PRF1 compared to other lymphocytes.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:3672a435e1461e63827a
claim_id: claim:3672a435e1461e63827a
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
Immunofluorescence staining of the macrophage marker CD163 and cell cycle marker MKI67 confirmed the enrichment of these proliferating macrophages in NF patients

summary:
In Homo sapiens, CD163 is a macrophage marker and MKI67 is a cell cycle marker used to identify proliferating macrophages in the left ventricle.


claim_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162:claim:e338ad1be5efd9f317d4
claim_id: claim:e338ad1be5efd9f317d4
paper_key: hca:0445_10.1038_s41586-022-04817-8_327bf47162
span_literal:
Immunofluorescence staining of the macrophage marker CD163 and cell cycle marker MKI67 confirmed the enrichment of these proliferating macrophages in NF patients

summary:
In Homo sapiens, MKI67 is a cell cycle marker used to identify proliferating macrophages in the left ventricle.


claim_key: hca:0446_10.1186_s13073-021-00933-8_a1bc5f6475:claim:4fc59b8c73b00fce02e1
claim_id: claim:4fc59b8c73b00fce02e1
paper_key: hca:0446_10.1186_s13073-021-00933-8_a1bc5f6475
summary: In Homo sapiens, CD68 is a marker for monocytes/macrophages in the choroid plexus.
span_literal:
We next sought to confirm the presence of increased numbers of Mo/MP in the ChP by staining with an antibody against CD68, which is a marker for Mo/MP cells.


claim_key: hca:0446_10.1186_s13073-021-00933-8_a1bc5f6475:claim:672d3d0bc2086010eb4d
claim_id: claim:672d3d0bc2086010eb4d
paper_key: hca:0446_10.1186_s13073-021-00933-8_a1bc5f6475
span_literal:
Compared to Mo/MP-2, the Mo/MP-1 subcluster expresses LYVE1, which is a marker that is highly expressed in a subset of macrophages in the meninges

summary:
In Homo sapiens, the monocyte/macrophage subcluster 1 expresses LYVE1, which is a marker highly expressed in a subset of macrophages in the meninges.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:54a1f19e6e071bb9aabd
claim_id: claim:54a1f19e6e071bb9aabd
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
summary: In Homo sapiens, satellite glial cells in the dorsal root ganglion are marked by FABP7 and APOE.
span_literal:
SGCs (10.7% of total nuclei) were labeled with the representative markers FABP7 and APOE and formed Cluster 2


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:1573a6e7f85b37ad3012
claim_id: claim:1573a6e7f85b37ad3012
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
Astrocytes (9.6% of total nuclei) were identified with the representative markers ATP1A2 , AQP4 , GJA1 , and SLC1A2 as Cluster 2

summary:
In Homo sapiens, astrocytes in the spinal cord are identified by the markers ATP1A2, AQP4, GJA1, and SLC1A2.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:2178ba1959c2d8dfa30c
claim_id: claim:2178ba1959c2d8dfa30c
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
oligodendrocytes (52.4% of total nuclei) were identified as Cluster 0 with MBP , MOBP , MOG , and PLP1

summary:
In Homo sapiens, oligodendrocytes in the spinal cord are identified by the markers MBP, MOBP, MOG, and PLP1.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:4174229a635c9cf01329
claim_id: claim:4174229a635c9cf01329
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
HTR4 (5-hydroxytryptamine receptor 4, which modulates the release of various neurotransmitters in both PNS and CNS) showed significantly higher expression levels in Cluster 5 than in other clusters in human DRG SGCs

summary:
In Homo sapiens, HTR4 (5-hydroxytryptamine receptor 4) shows significantly higher expression in satellite glial cell cluster 5 compared to other clusters in the dorsal root ganglion.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:aa3b630bcef75464ad22
claim_id: claim:aa3b630bcef75464ad22
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
NGF/Ngf (nerve growth factor, involved in the regulation of growth and differentiation of sympathetic and certain sensory neurons) was highly expressed in human SGCs but slightly in mouse SGCs

summary:
In Homo sapiens, NGF (nerve growth factor) is highly expressed in satellite glial cells of the dorsal root ganglion.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:0c8bb9b8a6096ab6c699
claim_id: claim:0c8bb9b8a6096ab6c699
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
The inflammatory pain-related gene PRKCA (protein kinase C alpha, which modulates different cellular processes, such as cell adhesion and cell transformation) showed extremely high expression levels in human SGCs

summary:
In Homo sapiens, PRKCA (protein kinase C alpha) shows extremely high expression in satellite glial cells.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:35a69c3bc7890fa6fc06
claim_id: claim:35a69c3bc7890fa6fc06
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
These include FABP7 and APOE for SGCs; ATP1A2 , AQP4 , GJA1 , and SLC1A2 for Astrocytes; PTPRC , CTSS , and ITGAM for Microglia; MBP , MOBP , MOG , and PLP1 for oligodendrocytes.

summary:
In Homo sapiens, satellite glial cells are identified by FABP7 and APOE; astrocytes by ATP1A2, AQP4, GJA1, and SLC1A2; microglia by PTPRC, CTSS, and ITGAM; and oligodendrocytes by MBP, MOBP, MOG, and PLP1.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:cc77f2e2910d44fb3d8d
claim_id: claim:cc77f2e2910d44fb3d8d
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
neuropathic pain-related genes P2RX4/P2rx4 (purinergic receptor P2X 4, which functions as a ligand-gated ion channel with high calcium permeability), HMGB1/Hmgb1 , MAPK14/Mapk14 (mitogen-activated protein kinase 14), PIK3CB/Pik3cb (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta, associated with immune responses after injury or infection), and CRK/Crk (CRK proto-oncogene, which encodes a member of an adapter protein family that binds to several tyrosine-phosphorylated proteins) were highly expressed in humans, but slightly in mice

summary:
In Homo sapiens, the neuropathic pain-related genes P2RX4, HMGB1, MAPK14, PIK3CB, and CRK are highly expressed in microglia of the spinal cord.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:09fbd3e65853fece65cb
claim_id: claim:09fbd3e65853fece65cb
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
Neuropathic pain-related genes HMGB1/Hmgb1 and DPYSL2/Dpysl2 (dihydropyrimidinase-like 2, which regulates synaptic signaling through interactions with calcium channels) were highly expressed in human astrocytes, but slightly in mice

summary:
In Homo sapiens, the neuropathic pain-related genes HMGB1 and DPYSL2 (dihydropyrimidinase-like 2) are highly expressed in astrocytes of the spinal cord.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:7cd3ddb5c7ed71bbabbe
claim_id: claim:7cd3ddb5c7ed71bbabbe
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
RNF19A/Rnf19a (ring finger protein 19A, RBR E3 ubiquitin protein ligase, involved in amyotrophic lateral sclerosis [ALS] and Parkinson’s disease) were highly expressed in humans but not in mice

summary:
In Homo sapiens, RNF19A (ring finger protein 19A, RBR E3 ubiquitin protein ligase) is highly expressed in astrocytes of the spinal cord.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:f37010d2585c6c389d4f
claim_id: claim:f37010d2585c6c389d4f
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
GRAP2/Grap2 (GRB2 related adaptor protein 2, involved in leukocyte- specific protein-tyrosine kinase signaling) was highly expressed in human Cluster 5 but slightly in mice

summary:
In Homo sapiens, GRAP2 (GRB2 related adaptor protein 2) is highly expressed in oligodendrocyte cluster 5 of the spinal cord.


claim_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8:claim:e22cb80b23d5f9112be6
claim_id: claim:e22cb80b23d5f9112be6
paper_key: hca:0448_10.1101_2022.02.15.480622_6cb3eae5b8
span_literal:
AIMP2/Aimp2 (aminoacyl- tRNA synthetase complex interacting multifunctional protein 2, part of the aminoacyl-tRNA synthetase complex) was highly expressed in human Cluster 4 but slightly in mouse

summary:
In Homo sapiens, AIMP2 (aminoacyl-tRNA synthetase complex interacting multifunctional protein 2) is highly expressed in oligodendrocyte cluster 4 of the spinal cord.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:6c2c693eb66c156bf849
claim_id: claim:6c2c693eb66c156bf849
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal: cluster #1 corresponded to cDC1 ( XCR1 + C1orf54 + )
summary:
In Homo sapiens skin, classical dendritic cell type 1 is marked by positive expression of XCR1 and C1orf54.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:f65c732ea7ea076ec129
claim_id: claim:f65c732ea7ea076ec129
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
Cutaneous CD14 + DC3 expressed EREG , SLC2A3 , IL23A , and HSPA genes, which were not reported as being expressed by DC3 in the blood, likely indicating skin-specific CD14 + DC3 differentiation in response to local cues.

summary:
In Homo sapiens skin, CD14-positive type 3 dendritic cell expresses EREG, SLC2A3, IL23A, and HSPA genes.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:59152bbf798353d5dfc0
claim_id: claim:59152bbf798353d5dfc0
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
We also detected a cluster of cells highly expressing genes normally associated with mature DCs enriched in immunoregulatory molecules (mregDC, #4), including CD200 and CD274

summary:
In Homo sapiens, mature dendritic cells enriched in immunoregulatory molecules highly express CD200 and CD274.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:59266934ddd6c5a256b5
claim_id: claim:59266934ddd6c5a256b5
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
IRF2 was a highly active transcription factor in clusters #1 (cDC1), #2 and #3 (DC2), and #4 (mregDC); ATF3 in clusters #6 and #7 (CD14 + DC3); RELB in cluster #4 (mregDC); MAFB and MAFG in clusters #8 and #9 (macrophages); and XBP1, CEBPB, and HIF1A in CD14 + DC3s and macrophages

summary:
In Homo sapiens skin, IRF2 is a highly active transcription factor in classical dendritic cell type 1.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:bd68eff785d74e70f62c
claim_id: claim:bd68eff785d74e70f62c
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
IRF2 was a highly active transcription factor in clusters #1 (cDC1), #2 and #3 (DC2), and #4 (mregDC); ATF3 in clusters #6 and #7 (CD14 + DC3); RELB in cluster #4 (mregDC); MAFB and MAFG in clusters #8 and #9 (macrophages); and XBP1, CEBPB, and HIF1A in CD14 + DC3s and macrophages

summary:
In Homo sapiens skin, IRF2 and RELB are highly active transcription factors in mature dendritic cells enriched in immunoregulatory molecules.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:e0d0cc6f43c7df64d9b7
claim_id: claim:e0d0cc6f43c7df64d9b7
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
summary:
In Homo sapiens skin, ATF3, XBP1, CEBPB, and HIF1A are highly active transcription factors in CD14-positive type 3 dendritic cell.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:7f6fd9484b21dcb25647
claim_id: claim:7f6fd9484b21dcb25647
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
summary:
In Homo sapiens skin, MAFB, MAFG, XBP1, CEBPB, and HIF1A are highly active transcription factors in macrophages.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:41e59de7179eef240dec
claim_id: claim:41e59de7179eef240dec
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
summary: In Homo sapiens skin, MARCO-positive macrophages are marked by expression of MARCO and F13A1.
span_literal:
cells within the MIX population were positive for MARCO and F13A1 , which allowed us to annotate them as MARCO + macrophages.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:25c14399fb9adf9e0e1f
claim_id: claim:25c14399fb9adf9e0e1f
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
summary: In Homo sapiens skin, classical dendritic cell type 1 shows high expression of HLA-DQA1 and HLA-DR.
span_literal:
cDC1s and DC2s showed high expression of genes related to antigen presentation signaling and T cell differentiation such as HLA-DQA1 and HLA-DR , while CD14 + DC3s highly expressed genes related to IL-17 signaling and neutrophil activation such as IL23A and CXCL2 , and mregDCs highly expressed genes related to DC differentiation and lymphocyte migration such as IRF4 and CCL17


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:8968bdfaf9e3b6ea188a
claim_id: claim:8968bdfaf9e3b6ea188a
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
summary:
In Homo sapiens skin, mature dendritic cells enriched in immunoregulatory molecules highly express IRF4 and CCL17.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:7bd586a44e6039c1113d
claim_id: claim:7bd586a44e6039c1113d
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
we found that IL1B , CXCL8 , IL10 , and IL23A were abundantly expressed in CD14 + DC3s, while IL15 and IL32 were expressed in mregDCs

summary:
In Homo sapiens skin, CD14-positive type 3 dendritic cell abundantly expresses IL1B, CXCL8, IL10, and IL23A.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:aa58cd0cac792bb83aa5
claim_id: claim:aa58cd0cac792bb83aa5
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
we found that IL1B , CXCL8 , IL10 , and IL23A were abundantly expressed in CD14 + DC3s, while IL15 and IL32 were expressed in mregDCs

summary:
In Homo sapiens skin, mature dendritic cells enriched in immunoregulatory molecules express IL15 and IL32.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:d132c2eee854ac4398e6
claim_id: claim:d132c2eee854ac4398e6
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
summary: In Homo sapiens skin, CCR1-positive macrophages show high expression of CXCL8, CXCL2, and IL1B.
span_literal:
CCR1 + macrophages showed high expression of genes related to inflammatory cytokines and chemokines including CXCL8 , CXCL2 , and IL1B , while MARCO + macrophages expressed chemokine genes and genes involved in the complement cascade such as C1QB and C1QC , and TREM2 + macrophages expressed lipid-related genes such as LIPA


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:f5050633b6e110481fc2
claim_id: claim:f5050633b6e110481fc2
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal: Because BIRC3 is highly expressed in mregDCs ( Fig. 1 d ), we used it as a marker for mregDCs.
summary:
In Homo sapiens skin, BIRC3 is highly expressed in mature dendritic cells enriched in immunoregulatory molecules and is used as a marker for this cell type.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:cf2ddf0e2c6009b5861b
claim_id: claim:cf2ddf0e2c6009b5861b
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
CD83 , an activation marker for DCs ( Zhou and Tedder, 1995 ), AREG and EREG associated with fibrosis ( Zhang et al., 2021 ), and the receptors for glucose and lipids, OLR1 and SLC2A3

summary:
In Homo sapiens psoriatic skin, IL1B/IL23A-coexpressing CD14-positive type 3 dendritic cells are characterized by expression of CD83, AREG, EREG, OLR1, and SLC2A3.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:cb7a895871ae912f1a63
claim_id: claim:cb7a895871ae912f1a63
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
Maier et al. (2020) identified mregDCs with high expression of immunomodulatory genes ( CD274 , PDCD1LG2 , and CD200 ) and mature genes ( CD40 , CCR7 , and IL12B ) in human and mouse lungs.

summary:
In Homo sapiens, mature dendritic cells enriched in immunoregulatory molecules have high expression of CD274, PDCD1LG2, CD200, CD40, CCR7, and IL12B.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:40aa35cca3933c96d853
claim_id: claim:40aa35cca3933c96d853
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
CD14 + DC3s also expressed genes related to Th17 cell differentiation and activation, such as IL6 and IL23A .

summary:
In Homo sapiens skin, CD14-positive type 3 dendritic cell expresses IL6 and IL23A, genes related to T helper type 17 cell differentiation and activation.


claim_key: hca:0449_10.1084_jem.20202345_e99c99a876:claim:72504848000fc0a9de81
claim_id: claim:72504848000fc0a9de81
paper_key: hca:0449_10.1084_jem.20202345_e99c99a876
span_literal:
We found that DC3_2 had the highest expression of SLC2A3 , a gene coding for the membrane protein glucose transporter 3 (GLUT3), and immunostaining showed a higher percentage of GLUT3 positivity in CD14 + DC3s than in DC2s or macrophages

summary:
In Homo sapiens skin, CD14-positive type 3 dendritic cell subcluster DC3_2 has the highest expression of SLC2A3 (glucose transporter 3), and CD14-positive type 3 dendritic cells show a higher percentage of GLUT3 positivity than type 2 dendritic cells or macrophages.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:56154def97b1a8cdd256
claim_id: claim:56154def97b1a8cdd256
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
summary: In Homo sapiens developing cerebellum, CA8, ITPR1, DAB1, and RORA are markers of Purkinje cells.
span_literal:
we detected CA8, ITPR1, DAB1, and RORA in Purkinje cells, 5LIT2 in the rhombic lip, and RELN and RBFOX3 in granule neurons.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:bf00f52fe7df28bbb4e2
claim_id: claim:bf00f52fe7df28bbb4e2
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: WLS, 50×2, and CRYAB expression was restricted, which enabled us to identify the RLVZ
summary:
In Homo sapiens developing cerebellum, WLS, SOX2, and CRYAB expression is restricted to the rhombic lip ventricular zone.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:85dc7e6a6d4df40a0c04
claim_id: claim:85dc7e6a6d4df40a0c04
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
summary: In Homo sapiens developing cerebellum, MKI67, PAX6, and LMX1A are markers of rhombic lip cells.
span_literal:
MKI67, PAX6, and LMX1A were expressed throughout the subclusters, consistent with their known expression as RL markers.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:b2d5e83dc506d8c29eb4
claim_id: claim:b2d5e83dc506d8c29eb4
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
OLIG3, R5P03, and 5LFN13 were expressed throughout the RL while WNT2B, CALCB, ATP6V1C2, and CALCA were expressed in the RLVZ, and DPYD expression was enriched in the RLSVZ.

summary:
In Homo sapiens developing cerebellum, OLIG3, RSPO3, and SLFN13 are markers expressed throughout the rhombic lip.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:bb17e827ae7be28cd5ca
claim_id: claim:bb17e827ae7be28cd5ca
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
OLIG3, R5P03, and 5LFN13 were expressed throughout the RL while WNT2B, CALCB, ATP6V1C2, and CALCA were expressed in the RLVZ, and DPYD expression was enriched in the RLSVZ.

summary:
In Homo sapiens developing cerebellum, WNT2B, CALCB, ATP6V1C2, and CALCA are markers of the rhombic lip ventricular zone.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:cf7132a7e43e106cfc07
claim_id: claim:cf7132a7e43e106cfc07
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
OLIG3, R5P03, and 5LFN13 were expressed throughout the RL while WNT2B, CALCB, ATP6V1C2, and CALCA were expressed in the RLVZ, and DPYD expression was enriched in the RLSVZ.

summary:
In Homo sapiens developing cerebellum, DPYD expression is enriched in the rhombic lip subventricular zone.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:35907e2597b6d56a8705
claim_id: claim:35907e2597b6d56a8705
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: Consistent with their RL origin, eCN and UBC express the classic RL markers PAX6, LMX1A, and EOMES.
summary:
In Homo sapiens developing cerebellum, excitatory cerebellar nuclei neurons and unipolar brush cells express the rhombic lip markers PAX6, LMX1A, and EOMES.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:45b0429bb252bec385e4
claim_id: claim:45b0429bb252bec385e4
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
We identified eCN/UBC on the basis of these markers and the absence of MIK67 expression since eCN and UBC are non-proliferative at the ages sampled

summary:
In Homo sapiens developing cerebellum, excitatory cerebellar nuclei neurons/unipolar brush cells are identified by the absence of MKI67 expression as they are non-proliferative.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:f689105d1a2e9ccfa1ec
claim_id: claim:f689105d1a2e9ccfa1ec
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
MIK67 and DCC expression in GCP declines as GCP differentiate into GN concurrent with increased expression of RELN and RBFOX3.

summary:
In Homo sapiens developing cerebellum, MKI67 and DCC expression declines in granule cell progenitors as they differentiate into granule neurons, while RELN and RBFOX3 expression increases in granule neurons.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:aef3ffd8d9a5088911b4
claim_id: claim:aef3ffd8d9a5088911b4
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
MIK67 and DCC expression in GCP declines as GCP differentiate into GN concurrent with increased expression of RELN and RBFOX3.

summary:
In Homo sapiens developing cerebellum, RELN and RBFOX3 expression increases in granule neurons as granule cell progenitors differentiate into granule neurons.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:6976d9f2b79d9cbe5d76
claim_id: claim:6976d9f2b79d9cbe5d76
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
RORA was expressed throughout the Purkinje cell cluster, as were markers that in mouse display parasagittal banding patterns of alternating Purkinje cells,32 including PLCB4 and EBF2

summary:
In Homo sapiens developing cerebellum, RORA, PLCB4, and EBF2 are expressed throughout the Purkinje cell cluster.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:cfc32e542cb80f09b9ef
claim_id: claim:cfc32e542cb80f09b9ef
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: Few Purkinje cells expressed more mature markers, ALDOCand PCP2.
summary:
In Homo sapiens developing cerebellum, few Purkinje cells expressed the mature markers ALDOC and PCP2.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:59c4a5bd70354ea7f957
claim_id: claim:59c4a5bd70354ea7f957
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
CALB1 was expressed at higher levels in later samples, while SKOR2 expression declined with increasing sample age, consistent with its role in early Purkinje cell differentiation.

summary:
In Homo sapiens developing cerebellum, CALB1 is expressed at higher levels in later Purkinje cells, while SKOR2 expression declines with age, consistent with its role in early Purkinje cell differentiation.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:a1359c871cea32927702
claim_id: claim:a1359c871cea32927702
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: One subcluster expressed CA8, consistent with Purkinje cells originating from the intermediate zone
summary:
In Homo sapiens developing cerebellum, CA8 is expressed in a subcluster consistent with Purkinje cells originating from the intermediate zone.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:f705bce9d3b83a5ff5b2
claim_id: claim:f705bce9d3b83a5ff5b2
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: SCA genes were significantly enriched in Purkinje cells, driven by DAB1 and ITPR1 expression
summary:
In Homo sapiens cerebellum, spinocerebellar ataxia genes are significantly enriched in Purkinje cells, driven by DAB1 and ITPR1 expression.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:58e6f929547a8c4d1390
claim_id: claim:58e6f929547a8c4d1390
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: SCA genes were prominently expressed in inhibitory cerebellar neurons (KIF26B, MAPT, PLD3, NEFL)
summary:
In Homo sapiens developing cerebellum, spinocerebellar ataxia genes KIF26B, MAPT, PLD3, and NEFL are prominently expressed in inhibitory cerebellar nuclei neurons.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:4abcf72b5d1231fb59a4
claim_id: claim:4abcf72b5d1231fb59a4
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
Genes associated with these common cerebellar malformations were significantly enriched in Purkinje cells, with prominent expression of AUT52, BCL11A, EBF2, and EBF3

summary:
In Homo sapiens developing cerebellum, cerebellar malformation genes AUTS2, BCL11A, EBF2, and EBF3 are prominently expressed in Purkinje cells.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:5027cd376c468fbdee1f
claim_id: claim:5027cd376c468fbdee1f
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
ASD genes were most prominently expressed in Purkinje cells (5HANK2, SUV420H1, BCL11A, ASXL3) and eCN/UBC (CCSER1, NRXN1, DIP2C, FXBOll, NUAK1, UBN2, PCM1).

summary:
In Homo sapiens developing cerebellum, autism spectrum disorder genes SHANK2, SUV420H1, BCL11A, and ASXL3 are most prominently expressed in Purkinje cells.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:14da2d31fd836f757d97
claim_id: claim:14da2d31fd836f757d97
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
ASD genes were most prominently expressed in Purkinje cells (5HANK2, SUV420H1, BCL11A, ASXL3) and eCN/UBC (CCSER1, NRXN1, DIP2C, FXBOll, NUAK1, UBN2, PCM1).

summary:
In Homo sapiens developing cerebellum, autism spectrum disorder genes CCSER1, NRXN1, DIP2C, FBXO11, NUAK1, UBN2, and PCM1 are most prominently expressed in excitatory cerebellar nuclei neurons/unipolar brush cells.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:74c141a54ddbf7ede62b
claim_id: claim:74c141a54ddbf7ede62b
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: Purkinje cells (AUTS2, PRKG1, FOXP2, CHD3, GABRB2, BCL11A, EBF3, SOX4, TCF20, DCX, ASXL3
summary:
In Homo sapiens developing cerebellum, intellectual disability genes AUTS2, PRKG1, FOXP2, CHD3, GABRB2, BCL11A, EBF3, SOX4, TCF20, DCX, and ASXL3 are prominently expressed with significant enrichment in Purkinje cells.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:595d1a5f014923e0c1d9
claim_id: claim:595d1a5f014923e0c1d9
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: Proliferative human RLSVZ progenitors express both LMX1A and EOMES.
summary:
In Homo sapiens developing cerebellum, proliferative rhombic lip subventricular zone progenitors express both LMX1A and EOMES.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:57c814d10893e44f9093
claim_id: claim:57c814d10893e44f9093
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
We validated the enrichment of our LCM-isolation by comparing gene expression of established RL (LMX1A, BARHL1), EGL (ATOH1, PAX6), and PCL [CALB1, SKOR2) markers in the RNA-seq dataset from LCM-isolated samples and bulk-isolated cerebellum

summary:
In Homo sapiens developing cerebellum, LMX1A and BARHL1 are established markers of the rhombic lip, ATOH1 and PAX6 are established markers of the external granule cell layer, and CALB1 and SKOR2 are established markers of the Purkinje cell layer.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:5a12739d309caed004c6
claim_id: claim:5a12739d309caed004c6
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
We validated the enrichment of our LCM-isolation by comparing gene expression of established RL (LMX1A, BARHL1), EGL (ATOH1, PAX6), and PCL [CALB1, SKOR2) markers in the RNA-seq dataset from LCM-isolated samples and bulk-isolated cerebellum

summary:
In Homo sapiens developing cerebellum, ATOH1 and PAX6 are established markers of the external granule cell layer.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:1a18d7440558467a6f93
claim_id: claim:1a18d7440558467a6f93
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal:
We validated the enrichment of our LCM-isolation by comparing gene expression of established RL (LMX1A, BARHL1), EGL (ATOH1, PAX6), and PCL [CALB1, SKOR2) markers in the RNA-seq dataset from LCM-isolated samples and bulk-isolated cerebellum

summary:
In Homo sapiens developing cerebellum, CALB1 and SKOR2 are established markers of the Purkinje cell layer.


claim_key: hca:0450_10.1101_2020.06.30.174391_27363b5885:claim:7dfc5dfe4388ad5b9398
claim_id: claim:7dfc5dfe4388ad5b9398
paper_key: hca:0450_10.1101_2020.06.30.174391_27363b5885
span_literal: Canonical RL gene expression (MKI67, OTX2, LMX1A, EOMES) declines as differentiate into eCN/UBC.
summary:
In Homo sapiens developing cerebellum, canonical rhombic lip gene expression of MKI67, OTX2, LMX1A, and EOMES declines as cells differentiate into excitatory cerebellar nuclei neurons/unipolar brush cells.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:605720d53332732d96bd
claim_id: claim:605720d53332732d96bd
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
The only cell surface markers meeting these criteria were the known markers CD90 ( Saalbach et al., 1998 ) (although CD90 is also expressed in human embryonic stem cells), PDGFRα, and PDGFRβ ( Driskell and Watt, 2015 )

summary:
In Homo sapiens, CD90, PDGFRα, and PDGFRβ are pan-fibroblast cell surface markers expressed in dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:011145659a8b96c42c91
claim_id: claim:011145659a8b96c42c91
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
However, the analysis did identify the small leucine-rich proteoglycans LUM and DCN as secreted pan-fibroblast markers

summary:
In Homo sapiens, lumican (LUM) and decorin (DCN) are secreted pan-fibroblast markers of dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:473583280aa2aa72521d
claim_id: claim:473583280aa2aa72521d
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
One of the most highly enriched markers in papillary dermis was the α5 chain of collagen VI ( COL6A5 ) ( Fitzgerald et al., 2008 , Fitzgerald et al., 2013 , Gara et al., 2008 ).

summary:
In Homo sapiens, the alpha 5 chain of collagen VI (COL6A5) is one of the most highly enriched markers in papillary dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:fd64e099f71bd75c0087
claim_id: claim:fd64e099f71bd75c0087
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal: COL23A1 was also overexpressed in the papillary versus reticular dermis.
summary:
In Homo sapiens, COL23A1 is overexpressed in papillary dermal fibroblasts compared with reticular dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:3debebf5435ac91278eb
claim_id: claim:3debebf5435ac91278eb
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
There was also increased expression of components of the Wnt pathway ( WIF1 , APCDD1, RSP01, AXIN2 ) in papillary dermis, suggesting evolutionary conservation between mouse and human (cf. Figure 1 b).

summary:
In Homo sapiens, WIF1, APCDD1, RSPO1, and AXIN2 show increased expression in papillary dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:2b798a6def55b4a2aa17
claim_id: claim:2b798a6def55b4a2aa17
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
summary: In Homo sapiens, CD39 is a conserved marker of papillary dermal fibroblasts.
span_literal:
No conserved markers of reticular lineages were identified; however, CD39 was identified as a conserved marker of papillary dermal lineages in both mouse and humans.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:4ebb6846dda2c9edf963
claim_id: claim:4ebb6846dda2c9edf963
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
summary: In Homo sapiens, COL6A5 expression is restricted to papillary dermal fibroblasts.
span_literal:
We confirmed that COL6A5 expression was restricted to papillary dermal fibroblasts ( Figure 3 a and b) ( Martinelli-Boneschi et al., 2017 , Sabatelli et al., 2011 ).


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:f4aa6ed1d8c8a788cfe6
claim_id: claim:f4aa6ed1d8c8a788cfe6
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
Immunostaining for APCDD1 ( Figure 3 c and d), HSPB3 ( Figure 3 e and f), and WIF1 ( Figure 3 g and h) confirmed differential expression of these markers in papillary dermis ( Figure 2 b).

summary:
In Homo sapiens, APCDD1, HSPB3, and WIF1 are differentially expressed markers in papillary dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:f517dbda008c7e887b9d
claim_id: claim:f517dbda008c7e887b9d
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
Consistent with their expression in mouse fibroblast subpopulations ( Figure 1 g and h), CD36 was up-regulated in the lower reticular dermis and hypodermis ( Figure 3 i and j, data not shown), and CD39 was up-regulated in the papillary dermis ( Figure 3 k and l).

summary:
In Homo sapiens, CD36 is up-regulated in lower reticular dermal and hypodermal fibroblasts, and CD39 is up-regulated in papillary dermal fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:2f55e198e7fb64a0b992
claim_id: claim:2f55e198e7fb64a0b992
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
summary: In Homo sapiens, COL6A5, COL23A1, and HSPB3 are highly enriched in papillary fibroblasts (group 3).
span_literal:
COL6A5, COL23A1, and HSPB3, identified by spatial transcriptional profiling as localized to the papillary dermis ( Figure 2 b), were highly enriched in group 3, suggesting that this group represents papillary fibroblasts.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:c903f00d7c7600dcac68
claim_id: claim:c903f00d7c7600dcac68
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
summary: In Homo sapiens, CD74, HLA-DR4, and CLDN5 are markers of dermal fibroblast subpopulation group 5.
span_literal:
CD74 and HLA-DR4, both components of MHC class II ( Karakikes et al., 2012 ), and CLDN5, a component of tight junctions ( Findley and Koval, 2009 ), marked group 5.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:e9e0bac49e2e83c0474c
claim_id: claim:e9e0bac49e2e83c0474c
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
summary: In Homo sapiens, RGS5 is a well-characterized marker of pericytes in the dermis.
span_literal:
One of those, RGS5, is well characterized as a marker of pericytes ( Bondjers et al., 2003 ), and antibodies to RGS5 labeled blood vessel-associated pericytes throughout the dermis ( Figure 6 j).


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:567e95c377f6b89dbf42
claim_id: claim:567e95c377f6b89dbf42
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
By flow sorting papillary cells on the basis that they were CD39 + CD26 – ( Figure 6 k and l), we could enrich for expression of the papillary markers COL6A5, WNT5A, RSPO1, and LEF1 ( Figure 6 m–p).

summary:
In Homo sapiens, papillary dermal fibroblasts are enriched by CD39-positive and CD26-negative sorting and express the papillary markers COL6A5, WNT5A, RSPO1, and LEF1.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:53c5b3f8f3b6e7db0c0f
claim_id: claim:53c5b3f8f3b6e7db0c0f
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
The first, which has a cell surface phenotype of lin – CD90 + CD39 + CD26 – , is characterized by the expression of specific collagen chains such as COL6A5 and is localized to the upper dermis.

summary:
In Homo sapiens, the papillary dermal fibroblast subpopulation is CD90-positive, CD39-positive, CD26-negative, and expresses COL6A5, localized to the upper dermis.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:cf2f9d93117b046236f0
claim_id: claim:cf2f9d93117b046236f0
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
The second is lin – CD90 + CD36 + cells that are situated in the lower dermis and include pre-adipocytes.

summary:
In Homo sapiens, the lower dermal fibroblast subpopulation including pre-adipocytes is CD90-positive and CD36-positive.


claim_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e:claim:4cf9087ff9c121af9762
claim_id: claim:4cf9087ff9c121af9762
paper_key: hca:0451_10.1016_j.jid.2018.01.016_d2589a157e
span_literal:
The remaining three groups are located throughout the reticular dermis: lin – CD90 + CD39 – RGS5 + cells that correspond to pericytes ( Bondjers et al., 2003 ) and lin – CD90 + CD39 + CD26 + and lin – CD90 + CD39 – RGS5 – cells, which to our knowledge are as yet uncharacterized fibroblast subpopulations.

summary:
In Homo sapiens, pericytes in the reticular dermis are CD90-positive, CD39-negative, and RGS5-positive.


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:4adb7236c27fb6a45e9b
claim_id: claim:4adb7236c27fb6a45e9b
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, MEF2C shows transcription factor binding activity in cardiomyocytes.
span_literal:
This revealed footprinting-based binding activity of known transcription factors such as MEF2C (ref. 7 ) in cardiomyocytes, CEBPD) 8 in myeloid cells, FOS–JUNB 9 in fibroblasts and SRF 10 in vascular smooth muscle cells (vSMCs), which correlated with the expression of their predicted target genes in snRNA-seq data


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:c2020a2d8510b895c135
claim_id: claim:c2020a2d8510b895c135
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, RYR2 is a marker gene for cardiomyocytes.
span_literal:
RYR2 cardiomyocytes, PDGFRA fibroblasts, MKI67 cycling cells, ABCC9 pericytes, FASN adipocytes, VWF endothelial cells, IL7R myeloid cells, and MYH11 vSMCs


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:44faa1f80173f6368eec
claim_id: claim:44faa1f80173f6368eec
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, MYH11 is a cell-type marker gene for vascular smooth muscle cells.
span_literal:
The vSMC-enriched molecular niche 11 had a more distinct cell-type marker gene expression of vSMCs ( MYH11 ) compared with the cell-type defined niche 6


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:fa77d35b8dc9b6970298
claim_id: claim:fa77d35b8dc9b6970298
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, ANKRD1 is significantly upregulated in ventricular cardiomyocyte state 2.
span_literal:
Differential gene expression analysis revealed a significant upregulation of ANKRD1 in both vCM2 and vCM3, whereas NPPB showed a distinct upregulation and increased chromatin accessibility in vCM3


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:025220fc5f5a900e2ae1
claim_id: claim:025220fc5f5a900e2ae1
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
span_literal:
Differential gene expression analysis revealed a significant upregulation of ANKRD1 in both vCM2 and vCM3, whereas NPPB showed a distinct upregulation and increased chromatin accessibility in vCM3

summary:
In Homo sapiens, ANKRD1 is significantly upregulated in ventricular cardiomyocyte state 3. In Homo sapiens, NPPB shows distinct upregulation and increased chromatin accessibility in ventricular cardiomyocyte state 3.


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:a46f0da2fa8b4451ea50
claim_id: claim:a46f0da2fa8b4451ea50
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
span_literal:
vCM2 additionally showed enhanced expression of MYH7 (Extended Data Fig. 6b ), a cardiomyocyte-associated stress gene that encodes the β-myosin heavy chain 23

summary:
In Homo sapiens, ventricular cardiomyocyte state 2 shows enhanced expression of MYH7, encoding the beta-myosin heavy chain.


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:979e67126ba39e1b20d0
claim_id: claim:979e67126ba39e1b20d0
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
span_literal:
Our analysis suggested POSTN as a characteristic marker for endocardial endothelial cells, which we validated using smFISH

summary:
In Homo sapiens, POSTN is a characteristic marker for endocardial endothelial cells, validated using single-molecule fluorescence in situ hybridization.


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:79c85df009cb444f3b1b
claim_id: claim:79c85df009cb444f3b1b
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, fibroblast state 1 is marked by SCARA5, a marker for myofibroblast progenitors.
span_literal:
Fib1 was marked by SCARA5 , which we recently reported as a marker for myofibroblast progenitors in the human kidney 34


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:439e7d3bbf9d150bd235
claim_id: claim:439e7d3bbf9d150bd235
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, fibroblast state 2 (myofibroblast) is marked by POSTN, COL1A1, and FN1.
span_literal:
Fib2 was marked by POSTN , COL1A1 and FN1 , which, together with the fact that this population expresses most extracellular matrix (ECM)-related genes, suggests that Fib2 indeed comprises terminally differentiated myofibroblasts


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:a0ad7e30c9b0ccdf0b4e
claim_id: claim:a0ad7e30c9b0ccdf0b4e
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, fibroblast state 2 (myofibroblast) exhibits upregulation of RUNX1.
span_literal:
Notably, Fib2 also exhibited an upregulation of RUNX1 , which we recently reported as being involved in kidney myofibroblast differentiation 35


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:f5ff168121e9e3290e12
claim_id: claim:f5ff168121e9e3290e12
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, resident myeloid cells express LYVE1 and FOLR2 as markers.
span_literal:
We observed that two clusters showed expression of resident myeloid cell markers 42 ( LYVE - and FOLR -expressing myeloid clusters), as well as a CCL18 - and SPP1- expressing macrophage cluster and a monocyte and classical dendritic cell cluster


claim_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894:claim:c5808a382a9d29385e0e
claim_id: claim:c5808a382a9d29385e0e
paper_key: hca:0453_10.1038_s41586-022-05060-x_14fb298894
summary: In Homo sapiens, CD36 is upregulated in the SPP1-positive macrophage population.
span_literal:
We observed an upregulation of CD36 in the SPP1 + myeloid population; CD36 encodes a macrophage receptor known to be important for macrophage phagocytosis, binding to apoptotic and dead neutrophils and having a unique role in cardiac remodelling following myocardial infarction 46


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:12bd0432f44702b1a433
claim_id: claim:12bd0432f44702b1a433
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
VCT and VCT-proliferative (VCT-p) upregulate known stem and progenitor cell markers ( LGR5 , L1TD1 and TP63 ), Wnt signalling molecules ( WLS and TNIK ), the SEMA3F–NRP2 signalling complex and the VCT marker BCAM 18

summary:
In Homo sapiens, villous cytotrophoblast and villous cytotrophoblast-proliferative upregulate LGR5, L1TD1, TP63, WLS, TNIK, SEMA3F, NRP2, and the villous cytotrophoblast marker BCAM.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:a54c71eac465df2754e0
claim_id: claim:a54c71eac465df2754e0
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
VCT and VCT-proliferative (VCT-p) upregulate known stem and progenitor cell markers ( LGR5 , L1TD1 and TP63 ), Wnt signalling molecules ( WLS and TNIK ), the SEMA3F–NRP2 signalling complex and the VCT marker BCAM 18

summary:
In Homo sapiens, villous cytotrophoblast-proliferative upregulates LGR5, L1TD1, TP63, WLS, TNIK, SEMA3F, NRP2, and BCAM.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:3b8996bb6b1653fe4ad2
claim_id: claim:3b8996bb6b1653fe4ad2
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
As VCT commit into VCT-fusing, they downregulate Wnt ( WLS , TNIK and LGR5 ) and BMP signals ( BMP7 and upregulation of BMP antagonist GREM2 ), and upregulate the endogenous retroviral genes ( ERVW-1, ERVFRD-1, ERVV-1 ) known to mediate trophoblast fusion 20

summary:
In Homo sapiens, villous cytotrophoblast-fusing downregulates WLS, TNIK, LGR5, and BMP7, upregulates GREM2, and upregulates the endogenous retroviral genes ERVW-1, ERVFRD-1, and ERVV-1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:bae993d37116c4fa89fc
claim_id: claim:bae993d37116c4fa89fc
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
summary: In Homo sapiens, syncytiotrophoblast expresses CYP19A1 and MFSD2A.
span_literal:
Our strategy for isolation of nuclei enables the capture of mature multinucleated SCTs (expressing CYP19A1 and MFSD2A )


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:8cd47581014a26335e85
claim_id: claim:8cd47581014a26335e85
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
As they commit to become VCT-CCCs, they downregulate the Wnt pathway ( WLS , TNIK and LGR5 expression), upregulate NOTCH1 , undergo an integrin shift (upregulating ITGB6 and ITGA2 ), and upregulate markers characteristic of epithelial–mesenchymal transition 22 ( LPCAT1 )

summary:
In Homo sapiens, villous cytotrophoblast of the cytotrophoblast cell column downregulates WLS, TNIK, and LGR5, and upregulates NOTCH1, ITGB6, ITGA2, and LPCAT1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:6f2d2b974961eede00e2
claim_id: claim:6f2d2b974961eede00e2
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Expression of NOTCH1 and ITGA2 is characteristic of putative trophoblast progenitor cells located in a small niche in the CCC 23 , 24

summary:
In Homo sapiens, trophoblast progenitor cells in the cytotrophoblast cell column are characterized by expression of NOTCH1 and ITGA2.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:bbc9dfbe8c4462f5f58c
claim_id: claim:bbc9dfbe8c4462f5f58c
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
summary: In Homo sapiens, extravillous trophoblast 2 upregulates ADAMTS20 and ITGA1.
span_literal:
EVTs-1 are proliferative while EVTs-2 do not proliferate and upregulate the metalloprotease gene ADAMTS20 and the integrin subunit gene ITGA1


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:f1f62555098538498e85
claim_id: claim:f1f62555098538498e85
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
iEVTs upregulate PLAC8 28 and plasminogen activator inhibitor genes SERPINE1 and SERPINE2 , with concomitant downregulation of the plasminogen activator gene PLAU

summary:
In Homo sapiens, interstitial extravillous trophoblast upregulates PLAC8, SERPINE1, and SERPINE2, and downregulates PLAU.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:c1771a015623a5e0035c
claim_id: claim:c1771a015623a5e0035c
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Genes contributing strongly to these factors are MKI67 , CENPK (cell cycle, factor 2); CSF1R , ADAM8 and LAIR2 (early trophoblast invasion, factor 4); CALD1 and COL21A1 (late trophoblast invasion, factor 6).

summary:
In Homo sapiens, early invasive extravillous trophoblast is associated with CSF1R, ADAM8, and LAIR2, while late invasive extravillous trophoblast is associated with CALD1 and COL21A1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:35ded295bfadc2342947
claim_id: claim:35ded295bfadc2342947
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Factor 10 captured eEVTs; the main genes contributing to this factor include NCAM1 , JAG1 , ADORA1 , EPHA1 and HES4 .

summary:
In Homo sapiens, endovascular extravillous trophoblast is characterized by NCAM1, JAG1, ADORA1, EPHA1, and HES4.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:e8334034ba299e497b1a
claim_id: claim:e8334034ba299e497b1a
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
VCT-CCCs upregulate NF-κB pathway genes ( NFKB2 and BACH2 ) and modulate AP-1 signalling genes ( JDP2 and ATF3 ), which may result in epithelial–mesenchymal transition

summary:
In Homo sapiens, villous cytotrophoblast of the cytotrophoblast cell column upregulates NFKB2, BACH2, JDP2, and ATF3.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:5abac33b3ec21b29f1ab
claim_id: claim:5abac33b3ec21b29f1ab
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
summary: In Homo sapiens, interstitial extravillous trophoblast upregulates ASCL2, ELK3, GATA3, and GRHL1.
span_literal:
As they invade, iEVTs upregulate the transcription factor ASCL2 34 , other transcription factors involved in cancer invasion ( ELK3–GATA3 complex 35 ), as well as tumour suppressor genes ( GRHL1 )


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:0d22cf27028f8db112e2
claim_id: claim:0d22cf27028f8db112e2
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
summary: In Homo sapiens, placental bed giant cells upregulate IFNAR1, IFNAR2, and IFI27.
span_literal:
As iEVTs transition into GCs, they upregulate receptors of the type I interferon pathway ( IFNAR1 and IFNAR2 ) and its targets ( IFI27 )


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:de85dc9bf98a3fa08e1f
claim_id: claim:de85dc9bf98a3fa08e1f
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
eEVTs have a unique pattern of transcription factor genes, which include HMGA2 , PAX8 , PLAGL1 , MYCN and PBX3

summary:
In Homo sapiens, endovascular extravillous trophoblast has a unique pattern of transcription factor genes including HMGA2, PAX8, PLAGL1, MYCN, and PBX3.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:cdad3ecefe347f814410
claim_id: claim:cdad3ecefe347f814410
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
eEVTs upregulate Notch signalling ( HES4 and JAG1 ) and the expression of TGFβ signalling genes ( TGFB1 , TGFBR1 and TGFBR2 ) is lower than in iEVT

summary:
In Homo sapiens, endovascular extravillous trophoblast upregulates HES4 and JAG1, and has lower expression of TGFB1, TGFBR1, and TGFBR2 compared to interstitial extravillous trophoblast.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:0a4bd12bf7930ff6f175
claim_id: claim:0a4bd12bf7930ff6f175
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
We previously defined two perivascular cell states 13 , PV1 ( MCAM -high) and PV2 ( MMP11 -high) in the arterial media.

summary:
In Homo sapiens, perivascular cell state 1 is marked by high MCAM expression and perivascular cell state 2 is marked by high MMP11 expression in the arterial media.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:46482730f04a26f34f5a
claim_id: claim:46482730f04a26f34f5a
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
We previously defined two perivascular cell states 13 , PV1 ( MCAM -high) and PV2 ( MMP11 -high) in the arterial media.

summary:
In Homo sapiens, perivascular cell state 2 is marked by high MMP11 expression in the arterial media.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:88649aed91e8bafc4bf8
claim_id: claim:88649aed91e8bafc4bf8
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Here we combine scRNA-seq and smFISH to identify two cell states within PV1: PV1- AOC3 ( AOC3 -high, MYH11 -high, FNDC1 -high and NTRK2 -high ) and PV1- STEAP4 (STEAP4 -high, EPHB6 -high and LZTS1 -high )

summary:
In Homo sapiens, perivascular cell state 1-AOC3 is marked by high expression of AOC3, MYH11, FNDC1, and NTRK2, and perivascular cell state 1-STEAP4 is marked by high expression of STEAP4, EPHB6, and LZTS1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:e3cc66487ae7cbcefc39
claim_id: claim:e3cc66487ae7cbcefc39
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Here we combine scRNA-seq and smFISH to identify two cell states within PV1: PV1- AOC3 ( AOC3 -high, MYH11 -high, FNDC1 -high and NTRK2 -high ) and PV1- STEAP4 (STEAP4 -high, EPHB6 -high and LZTS1 -high )

summary:
In Homo sapiens, perivascular cell state 1-STEAP4 is marked by high expression of STEAP4, EPHB6, and LZTS1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:4373ecd9a62186654f86
claim_id: claim:4373ecd9a62186654f86
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
GCs form by the fusion of iEVTs and upregulate adhesion genes ( JAM2 , EFNB1 and SEMA4C ) whose cognate receptor genes are expressed by other iEVTs ( JAM3 , EPHB2 , EPHB3 and PLXNB2 ), providing potential mechanisms for fusion

summary:
In Homo sapiens, placental bed giant cells upregulate JAM2, EFNB1, and SEMA4C, while interstitial extravillous trophoblast expresses JAM3, EPHB2, EPHB3, and PLXNB2.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:6a1cf630e743eec669d5
claim_id: claim:6a1cf630e743eec669d5
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Maternal macrophages upregulate adhesion receptor genes, including CADM1 (expressed in dM1 and dM2) and SEMA4A (expressed in dM1), whose cognate receptors NECTIN3 and PLXND1 are expressed in EVTs

summary:
In Homo sapiens, decidual macrophage 1 upregulates CADM1 and SEMA4A, and decidual macrophage 2 upregulates CADM1, while extravillous trophoblast expresses NECTIN3 and PLXND1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:8d1667e2315ca76031d1
claim_id: claim:8d1667e2315ca76031d1
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
both dM1 and dM2 express the chemokine genes CXCL16 and CCL3 , and their receptor genes CXCR6 39 and CCR1 are upregulated in invading EVTs

summary:
In Homo sapiens, decidual macrophage 1 and decidual macrophage 2 express CXCL16 and CCL3, while invading extravillous trophoblast upregulates CXCR6 and CCR1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:e56e372f1b63bf9a3603
claim_id: claim:e56e372f1b63bf9a3603
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal: dM1 ( EREG + and IL1B
summary:
In Homo sapiens, decidual macrophage 1 is positive for EREG and IL1B, while decidual macrophage 2 is positive for FOLR2 and CD14.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:641e4db49714606ffcfa
claim_id: claim:641e4db49714606ffcfa
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
summary: In Homo sapiens, placental bed giant cells downregulate CXCR6, CSF1R, and PLXND1.
span_literal:
The receptors that are potentially involved in EVT invasion, including CXCR6 , CSF1R 38 and PLXND1 , are downregulated in GCs


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:bc2826a83546a960cf72
claim_id: claim:bc2826a83546a960cf72
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
eEVTs express both ITGB1 and ITGA2 (forming the integrin α2β1) and its cognate collagen ligands ( COL6A1 , COL19A1 , COL26A1 and COL21A1 )

summary:
In Homo sapiens, endovascular extravillous trophoblast expresses ITGB1, ITGA2, COL6A1, COL19A1, COL26A1, and COL21A1.


claim_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e:claim:9e7b055de15d3a4d9c1f
claim_id: claim:9e7b055de15d3a4d9c1f
paper_key: hca:0454_10.1038_s41586-023-05869-0_c19e7dab1e
span_literal:
Interactions of eEVTs in the vasculature (ME5) could be mediated by EPHA1 , CXCL12 , FLT4 and ANGPT4 , with endothelial cells expressing their interacting partners EFNA1 , EFNA5 , VEGFC and TEK

summary:
In Homo sapiens, endovascular extravillous trophoblast expresses EPHA1, CXCL12, FLT4, and ANGPT4, while endothelial cells express EFNA1, EFNA5, VEGFC, and TEK.


claim_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926:claim:e5b104aa7722358b4af6
claim_id: claim:e5b104aa7722358b4af6
paper_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926
span_literal:
Although not the case at mRNA level, VSIG4 was found to be the best human KC protein marker in the CITE-seq data, while FOLR2, CD163, and CD169 were also identified as useful markers of these cells for flow cytometry and confocal microscopy on frozen and paraffin sections

summary:
In Homo sapiens, VSIG4 is the best protein marker of Kupffer cells, while FOLR2, CD163, and CD169 are also useful markers of Kupffer cells for flow cytometry and confocal microscopy.


claim_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926:claim:59d1e99211aece8a1224
claim_id: claim:59d1e99211aece8a1224
paper_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926
span_literal: Cluster9 also expressed many of these genes but lacked TIMD4
summary:
In Homo sapiens, monocyte-derived Kupffer cells (cluster9) lack expression of TIMD4, distinguishing them from bona fide Kupffer cells in the liver.


claim_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926:claim:a334f9ccec62f90bb9eb
claim_id: claim:a334f9ccec62f90bb9eb
paper_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926
summary: In Homo sapiens, FOLR2 is expressed by Kupffer cells in the healthy liver.
span_literal:
Similarly, we find that FOLR2 expression is not specific to tumor-associated hepatic macs ( Sharma et al., 2020 ) but is expressed by KCs in the healthy mouse and human liver.


claim_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926:claim:d1a8c276dd57a13777de
claim_id: claim:d1a8c276dd57a13777de
paper_key: hca:0455_10.1016_j.cell.2021.12.018_c0dc3d5926
span_literal:
Feature plots showing expression of ALK1 ( Acvrl1 ) in human myeloid cells (left) and GDF2/BMP10 in CD45 − cells (right).

summary:
In Homo sapiens, ALK1 (ACVRL1) is expressed by myeloid cells in the liver, while GDF2 and BMP10 are expressed by CD45-negative cells.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:fdac3e72132ef15d8146
claim_id: claim:fdac3e72132ef15d8146
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
summary: In Homo sapiens liver, CD5L expression identifies resident macrophages located in the sinusoids.
span_literal:
CD5L expression was clustered in spaces between hepatocytes consistent with resident macrophages located in the sinusoids


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:f4ecd1cb92b6b1367ee5
claim_id: claim:f4ecd1cb92b6b1367ee5
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
PDGFRB expression was concentrated along the edges of ALDOB-expressing hepatocytes in a distribution expected for HSCs, which are located in the subendothelial space

summary:
In Homo sapiens liver, PDGFRB expression identifies hepatic stellate cells located in the subendothelial space.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:eefea9d7b4078c1db3c4
claim_id: claim:eefea9d7b4078c1db3c4
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
summary: In Homo sapiens liver, KRT7 and SOX9 are enriched in cholangiocytes in periportal areas.
span_literal:
KRT7 and SOX9 were enriched in periportal areas, often in larger clusters consistent with cholangiocytes


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:152e920233bb623af54a
claim_id: claim:152e920233bb623af54a
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
DNASE13 and INMT expression were scattered through the parenchyma consistent with the distribution of LSECs

summary:
In Homo sapiens liver, DNASE1L3 and INMT expression identifies liver sinusoidal endothelial cells distributed through the parenchyma.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:5ed4c7766e9404e898e7
claim_id: claim:5ed4c7766e9404e898e7
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
summary: In Homo sapiens liver, macrophage cluster 1 is identified by expression of CD74.
span_literal:
Both macrophage populations were identified by expression of CD74, while Mac 2 cells also expressed CD5L and MARCO


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:c1055e64ab36cfe6eca9
claim_id: claim:c1055e64ab36cfe6eca9
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
These two populations differed primarily in the levels of CD74 expression, while both populations expressed PDGFRB and LAMB

summary:
In Homo sapiens liver, hepatic stellate cell cluster 1 and hepatic stellate cell cluster 2 both express PDGFRB and LAMB1, and differ primarily in CD74 expression levels.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:d00634e16397b9ae72fb
claim_id: claim:d00634e16397b9ae72fb
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
summary: In Homo sapiens liver, liver sinusoidal endothelial cells express DNASE1L3.
span_literal:
LSECs, which line the sinusoids, were identified more diffusely through the liver, and expressed DNASE1L3


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:7afb60d56a5f864ae6d7
claim_id: claim:7afb60d56a5f864ae6d7
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
The fourth hepatocyte cluster, not seen with MERFISH, contained 290 cells (2.7% of hepatocytes) and was defined by expression of APOC1, APOC3, APOA1, and APOA2

summary:
In Homo sapiens liver, hepatocyte cluster 4 is defined by expression of APOC1, APOC3, APOA1, and APOA2.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:42d214801797d001ee1e
claim_id: claim:42d214801797d001ee1e
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
Mac 2 cells were identified as MARCO+, CD5L+, and CD68+ with increased expression of VISG4 compared to Mac 1 cells and were located more diffusely through the lobule.

summary:
In Homo sapiens liver, macrophage cluster 2 is identified as MARCO-positive, CD5L-positive, and CD68-positive with increased expression of VSIG4 compared to macrophage cluster 1.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:9fd8e2dbf1368b5fd807
claim_id: claim:9fd8e2dbf1368b5fd807
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal: Mac 1 cells were MARCO- and CD5L- with lower levels of CD68.
summary:
In Homo sapiens liver, macrophage cluster 1 is MARCO-negative and CD5L-negative with lower levels of CD68.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:e9d1b15c135ccb1c29a4
claim_id: claim:e9d1b15c135ccb1c29a4
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
Within the genes evaluated by the MERFISH probes, the MHC class II chaperone CD7437 showed the greatest differential expression between the two HSC populations, with highest expression observed in HSC 1 cells.

summary:
In Homo sapiens liver, hepatic stellate cell cluster 1 shows the highest expression of CD74 compared to hepatic stellate cell cluster 2.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:1a167c0370d372b85c73
claim_id: claim:1a167c0370d372b85c73
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
Fibrotic macrophages showed a loss of MARCO, CD5L, CD68 expression characteristic of Mac 2 (noninflammatory) macrophages and retained an expression pattern that more closely matched Mac 1 cells in normal liver

summary:
In Homo sapiens liver, macrophage cluster 2 (noninflammatory macrophage) is characterized by expression of MARCO, CD5L, and CD68.


claim_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898:claim:b8be04c213e399de7442
claim_id: claim:b8be04c213e399de7442
paper_key: hca:0457_10.1101_2024.02.02.578633_57d5a20898
span_literal:
Fibrotic Hep 2 cluster showed an increase in expression of several notable genes, including SCL7A2, CPS1, ATP9A, DTX1, POR and EXT1 compared to all other hepatocyte populations

summary:
In Homo sapiens liver, fibrotic hepatocyte cluster 2 shows increased expression of SLC7A2, CPS1, ATP9A, DTX1, POR, and EXT1 compared to all other hepatocyte populations.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:3370a152d84054d83aa2
claim_id: claim:3370a152d84054d83aa2
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
CD5L expression was clustered in spaces between hepatocytes consistent with resident macrophages located in sinusoids

summary:
In Homo sapiens liver, CD5L expression is consistent with resident macrophages located in sinusoids.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:001d510677cb8535ae2b
claim_id: claim:001d510677cb8535ae2b
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
PDGFRB expression was concentrated along the edges of ALDOB -expressing hepatocytes in a distribution expected for HSCs, which are located in the subendothelial space

summary:
In Homo sapiens liver, PDGFRB expression is expected for hepatic stellate cells, which are located in the subendothelial space.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:7bd48dac2a5a97c66696
claim_id: claim:7bd48dac2a5a97c66696
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
summary: In Homo sapiens liver, KRT7 and SOX9 are enriched in cholangiocytes in periportal areas.
span_literal:
KRT7 and SOX9 were enriched in periportal areas consistent with cholangiocytes and include clusters suggestive of longitudinal sections of small bile ducts


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:c64801ec9f8748518090
claim_id: claim:c64801ec9f8748518090
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
DNASE13 and INMT expression were scattered through the parenchyma consistent with the distribution of ECs

summary:
In Homo sapiens liver, DNASE13 and INMT expression is consistent with the distribution of endothelial cells.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:502b3878f7fe55339186
claim_id: claim:502b3878f7fe55339186
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
CYP2A6 and ASS1 were enriched in portal regions similar to SDS , while CYP1A2 and GLUL were enriched in central regions similar to CYP2E1

summary:
In Homo sapiens liver, CYP2A6 and ASS1 are enriched in zone 1 periportal hepatocytes, while CYP1A2 and GLUL are enriched in zone 3 pericentral hepatocytes.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:1b7dc7107067efc6af5a
claim_id: claim:1b7dc7107067efc6af5a
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
Both macrophage populations were identified by expression of CD74 , while Mac 2 cells also expressed CD5L and MARCO

summary:
In Homo sapiens liver, both macrophage populations are identified by expression of CD74, while macrophage 2 cells also express CD5L and MARCO.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:30b2881691f9cb98a01f
claim_id: claim:30b2881691f9cb98a01f
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
These two populations differed primarily in the levels of CD74 expression, while both populations expressed PDGFRB and LAMB1

summary:
In Homo sapiens liver, both hepatic stellate cell populations express PDGFRB and LAMB1, and differ primarily in CD74 expression levels.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:7e4dc0a2bc233a26b40a
claim_id: claim:7e4dc0a2bc233a26b40a
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
summary: In Homo sapiens liver, endothelial cells express DNASE1L3.
span_literal:
ECs, many of which line the sinusoids, were identified more diffusely through the liver, and expressed DNASE1L3


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:7676635769381763f470
claim_id: claim:7676635769381763f470
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
Mac 2 cells were identified as MARCO + , CD5L + , and CD68 + with increased expression of VISG4 compared to Mac 1 cells and were located more diffusely through the lobule, most consistent with Kupffer cells.

summary:
In Homo sapiens liver, macrophage 2 cells are identified as MARCO-positive, CD5L-positive, and CD68-positive with increased expression of VSIG4 compared to macrophage 1 cells, most consistent with Kupffer cells.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:ee97e3137f47cf8ca39f
claim_id: claim:ee97e3137f47cf8ca39f
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal: Mac 1 cells were MARCO - and CD5L - with lower levels of CD68 .
summary:
In Homo sapiens liver, macrophage 1 cells are MARCO-negative and CD5L-negative with lower levels of CD68.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:bc7b34690e8a74374055
claim_id: claim:bc7b34690e8a74374055
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
snRNA-seq confirmed these expression patterns along with increased CD163 , VCAM1 , and TMEM26 in Mac 2 cells (Supplementary Data 2 ), all of which are evolutionarily conserved markers of Kupffer cells

summary:
In Homo sapiens liver, macrophage 2 cells show increased CD163, VCAM1, and TMEM26, all of which are evolutionarily conserved markers of Kupffer cells.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:40ac6bc77f860adf9a2f
claim_id: claim:40ac6bc77f860adf9a2f
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
the MHC class II chaperone CD74 45 showed the greatest differential expression between the two HSC populations, with highest expression observed in HSC 1 cells

summary:
In Homo sapiens liver, the major histocompatibility complex class II chaperone CD74 shows the highest expression in hepatic stellate cell 1 compared to hepatic stellate cell 2.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:23270dcfae9fe0db03d9
claim_id: claim:23270dcfae9fe0db03d9
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
summary: In Homo sapiens fibrotic liver, macrophages show a loss of MARCO, CD5L, and CD68.
span_literal:
fibrotic macrophages showed a loss of MARCO , CD5L , CD68 and retained an expression pattern that more closely matched Mac 1 cells in normal liver


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:9d3381b9ebf4853378fe
claim_id: claim:9d3381b9ebf4853378fe
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
The Fibrotic Hep 1 cluster showed a general reduction in expression of genes enriched in hepatocytes, while the Fibrotic Hep 2 cluster showed an increase in expression of several notable genes, including SLC7A2 , CPS1, ATP9A, DTX1, POR and EXT1 compared to all other hepatocyte populations.

summary:
In Homo sapiens fibrotic liver, fibrotic hepatocyte 2 shows increased expression of SLC7A2, CPS1, ATP9A, DTX1, POR, and EXT1 compared to all other hepatocyte populations.


claim_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea:claim:e82d4f4c0b754f339122
claim_id: claim:e82d4f4c0b754f339122
paper_key: hca:0458_10.1038_s41467-024-55325-4_d40c28a5ea
span_literal:
Fibrotic Hep 1 cells showed enrichment in genes including PNPLA3, CPEB4 , and ASPG , which are linked to hepatic steatosis, steatohepatitis, and/or fibrosis

summary:
In Homo sapiens fibrotic liver, fibrotic hepatocyte 1 cells show enrichment in PNPLA3, CPEB4, and ASPG.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:0e6d1de0085674b953d3
claim_id: claim:0e6d1de0085674b953d3
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
summary: In Homo sapiens, CXCL13 has emerged as a marker of tumor-reactive CD8-positive T cells.
span_literal:
CXCL13 in T cells has been noted in other CRC and melanoma single cell studies ( Lee et al., 2020 ; Li et al., 2019 ; Zhang et al., 2018 ), and has recently emerged as a marker of human tumor-reactive CD8+ T cells and response to immunotherapy


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:f7742dc4156f06ad7f07
claim_id: claim:f7742dc4156f06ad7f07
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
summary: In Homo sapiens colorectal cancer, PLZF-positive T cells are marked by ZBTB16 expression.
span_literal:
Programs enriched in MMRd versus MMRp T cells ( Table S2E )included two programs (pTNI18 with CXCL13, PDCD1,TOX ; pTNI06 with MHCII, IFNG and LAG3 ) with high and moderate activity in TCR αβ and TCR γδ -like T cells respectively, and one cytotoxicity program (pTNI16) shared among CD8+, γδ -like, PLZF + ( ZBTB16 ) T cells and NK cells.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:6f2ef24558e0bd7ac077
claim_id: claim:6f2ef24558e0bd7ac077
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
Programs enriched in MMRd versus MMRp T cells ( Table S2E )included two programs (pTNI18 with CXCL13, PDCD1,TOX ; pTNI06 with MHCII, IFNG and LAG3 ) with high and moderate activity in TCR αβ and TCR γδ -like T cells respectively, and one cytotoxicity program (pTNI16) shared among CD8+, γδ -like, PLZF + ( ZBTB16 ) T cells and NK cells.

summary:
In Homo sapiens colorectal cancer, TCR alpha-beta T cells show high activity of a program including CXCL13, PDCD1, and TOX.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:9835de9ec6a399b3b74c
claim_id: claim:9835de9ec6a399b3b74c
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
Programs enriched in MMRd versus MMRp T cells ( Table S2E )included two programs (pTNI18 with CXCL13, PDCD1,TOX ; pTNI06 with MHCII, IFNG and LAG3 ) with high and moderate activity in TCR αβ and TCR γδ -like T cells respectively, and one cytotoxicity program (pTNI16) shared among CD8+, γδ -like, PLZF + ( ZBTB16 ) T cells and NK cells.

summary:
In Homo sapiens colorectal cancer, TCR gamma-delta-like T cells show moderate activity of a program including IFNG and LAG3.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:5a2bfa91f1e7bdd95c33
claim_id: claim:5a2bfa91f1e7bdd95c33
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
PLZF + T cells and NK/ILC3 cells were selectively marked by an innate T cell program (pTNI08) that was reduced in both MMRd and MMRp tumors compared to normal tissue

summary:
In Homo sapiens, PLZF-positive T cells and natural killer/innate lymphoid cell 3 cells are selectively marked by an innate T cell program (pTNI08).


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:f6f6f68d627e25e711cb
claim_id: claim:f6f6f68d627e25e711cb
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
Thus, in MMRd tumors, subsets of T and NK cells acquire cytolytic properties ( GNLY , GZMB , PRF1 ), and T cells acquire exhaustion markers associated with chronic stimulation (e.g. PDCD1, TOX, LAG3, HAVCR2 ).

summary:
In Homo sapiens mismatch repair-deficient colorectal tumors, subsets of T cells and natural killer cells acquire cytolytic properties marked by GNLY, GZMB, and PRF1, and T cells acquire exhaustion markers PDCD1, TOX, LAG3, and HAVCR2.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:612c1242f9ae1ba5b94b
claim_id: claim:612c1242f9ae1ba5b94b
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
Thus, in MMRd tumors, subsets of T and NK cells acquire cytolytic properties ( GNLY , GZMB , PRF1 ), and T cells acquire exhaustion markers associated with chronic stimulation (e.g. PDCD1, TOX, LAG3, HAVCR2 ).

summary:
In Homo sapiens mismatch repair-deficient colorectal tumors, subsets of natural killer cells acquire cytolytic properties marked by GNLY, GZMB, and PRF1.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:bd6a5952f1c9637fd5a4
claim_id: claim:bd6a5952f1c9637fd5a4
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
Analogous to the previously described myCAFs ( Dominguez et al., 2019 ; Elyada et al., 2019 ; Öhlund et al., 2017 ), 3 cancer-associated fibroblast subsets (cS26–28) (and tumor pericytes) expressed a contractile program (pS03) that included smooth muscle actin ( ACTA2 )

summary:
In Homo sapiens colorectal cancer, cancer-associated fibroblast subsets express a contractile program that includes ACTA2 (smooth muscle actin).


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:4b45b435420c050ef41b
claim_id: claim:4b45b435420c050ef41b
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
inflammatory CAFs (iCAFs) ( Dominguez et al., 2019 ; Elyada et al., 2019 ; Öhlund et al., 2017 ) and inflammatory fibroblasts in inflammatory bowel disease ( Elmentaite et al., 2020 ; Haberman et al., 2014 ; Huang et al., 2019 ; Olsen et al., 2009 ; Smillie et al., 2019 ), included tissue remodeling factors ( MMP2 , MMP3 ) and neutrophil-attracting chemokines ( CXCL8 , CXCL1

summary:
In Homo sapiens, inflammatory cancer-associated fibroblasts express tissue remodeling factors MMP2 and MMP3 and neutrophil-attracting chemokines CXCL8 and CXCL1.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:dfcda3b56ad80c8e610c
claim_id: claim:dfcda3b56ad80c8e610c
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal: The BMP-expressing CAFs were distinguished from other CAF subsets by CXCL14 expression
summary:
In Homo sapiens colorectal cancer, BMP-expressing cancer-associated fibroblasts are distinguished from other cancer-associated fibroblast subsets by CXCL14 expression.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:3639eb1a5380fce2f591
claim_id: claim:3639eb1a5380fce2f591
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
CAFs also contributed expression of stem cell niche factors, such as RSPO3 and GREM1 , which were broadly expressed throughout tumors

summary:
In Homo sapiens colorectal cancer, cancer-associated fibroblasts express stem cell niche factors RSPO3 and GREM1.


claim_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6:claim:e582318398f83ae22ee7
claim_id: claim:e582318398f83ae22ee7
paper_key: hca:0460_10.1016_j.cell.2021.08.003_652ffcecb6
span_literal:
Monocytes and macrophages upregulated tumor-specific NMF-derived transcriptional programs ( Figure 2B , C ), characterized by genes that can amplify inflammation ( MMP12 and MMP9 in pM02), recruit myeloid cells (chemokines CCL2 and CCL7 in pM10), stimulate growth (growth factors VEGFA and EREG in pM14), and resolve inflammation ( APOE in pM06).

summary:
In Homo sapiens colorectal cancer, monocytes and macrophages upregulate programs characterized by MMP12, MMP9, CCL2, CCL7, VEGFA, EREG, and APOE.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:f5ea267efe307caaeb3e
claim_id: claim:f5ea267efe307caaeb3e
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
P cells (SAN_P_cell) that expressed canonical pacemaker-associated channel genes ( HCN1 , HCN4 and CACNA1D ) and the transcription factor (TF) TBX3

summary:
In Homo sapiens, sinoatrial node pacemaker cells express the canonical pacemaker-associated channel genes HCN1, HCN4, and CACNA1D, and the transcription factor TBX3.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:1ee9aa735bef921e8c37
claim_id: claim:1ee9aa735bef921e8c37
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, atrioventricular bundle cells are defined by enrichment of GJA5, CRNDE, and CNTN5.
span_literal:
AV bundle cells formed a distinct cluster defined by an enrichment of GJA5 (which encodes the gap junction protein Cx40), CRNDE and CNTN5


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:3b311ccade465b48538a
claim_id: claim:3b311ccade465b48538a
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, glial cells are defined by expression of PLP1, NRXN1, and NRXN3.
span_literal:
Based on recent studies of the heart and the gut that defined cells expressing PLP1 , NRXN1 and NRXN3 as glial cells


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:8ca58972aeeeebe97e70
claim_id: claim:8ca58972aeeeebe97e70
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
FB4 was named as FB4_activated on the basis of increased expression of TGFβ-responsive FB activation signature genes ( POSTN , TNC , COL1A1 , COL1A2 , COL3A1 and FN1 ), which includes genes encoding ECM proteins, compared with other FBs

summary:
In Homo sapiens, activated fibroblast 4 (FB4_activated) is marked by increased expression of POSTN, TNC, COL1A1, COL1A2, COL3A1, and FN1 compared with other fibroblasts.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:0ca3d2d3fb85121f5a43
claim_id: claim:0ca3d2d3fb85121f5a43
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
vCM3_stressed on the basis of expression of CM stress markers ( NPPB , LMCD1 , XIRP2 , ACTA1 and PFKP

summary:
In Homo sapiens, stressed ventricular cardiomyocyte 3 (vCM3_stressed) is marked by expression of the cardiomyocyte stress markers NPPB, LMCD1, XIRP2, ACTA1, and PFKP.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:f0f218e94fb3c90a5857
claim_id: claim:f0f218e94fb3c90a5857
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
other aCMs identified major markers for P cells such as genes encoding ion channel subunits ( CACNA1D and CACNA2D2 ) and TFs ( ISL1 , TBX3 and SHOX2

summary:
In Homo sapiens, pacemaker cells are marked by differential chromatin accessibility at CACNA1D, CACNA2D2, ISL1, TBX3, and SHOX2 compared with other atrial cardiomyocytes.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:923a05eb18e795c0eeec
claim_id: claim:923a05eb18e795c0eeec
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
both the SAN and AVN P cells showed downregulation of the sodium channel gene SCN5A and upregulation of the L-type calcium channel gene CACNA1D

summary:
In Homo sapiens, sinoatrial node and atrioventricular node pacemaker cells show downregulation of SCN5A and upregulation of CACNA1D compared with other cardiomyocytes.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:6a6efc227154b0c4ab5f
claim_id: claim:6a6efc227154b0c4ab5f
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
Two classical hyperpolarization-activated cyclic nucleotide-gated (HCN) pacemaker channel genes ( HCN1 and HCN4 ) were enriched in P cells from both nodes

summary:
In Homo sapiens, pacemaker cells from both the sinoatrial node and atrioventricular node are enriched for the hyperpolarization-activated cyclic nucleotide-gated channel genes HCN1 and HCN4.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:2fea666f7d8eebb4a5e6
claim_id: claim:2fea666f7d8eebb4a5e6
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, CACNA1G is highly expressed in sinoatrial node pacemaker cells only.
span_literal:
CACNA1G , which encodes the T-type calcium channel α-subunit (Ca V 3.1) and is crucial in pacemaking in rodents 6 , was highly expressed in SAN P cells


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:7a72d714e6d732a49296
claim_id: claim:7a72d714e6d732a49296
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
KCNJ5 , a G protein-coupled inwardly rectifying potassium (GIRK) channel subunit was upregulated in both P cell types

summary:
In Homo sapiens, KCNJ5 is upregulated in both sinoatrial node and atrioventricular node pacemaker cells.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:e99c98c4955299b1d7ba
claim_id: claim:e99c98c4955299b1d7ba
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal: KCNN2 was highly expressed in both P cell types, whereas KCNK13 was specific to AVN P cells
summary:
In Homo sapiens, KCNN2 is highly expressed in both pacemaker cell types, whereas KCNK13 is specific to atrioventricular node pacemaker cells.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:6a450775bf4e0fac440f
claim_id: claim:6a450775bf4e0fac440f
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal: ANO6 , which encodes a calcium-activated chloride channel, was upregulated in SAN and AVN P cells
summary:
In Homo sapiens, ANO6 is upregulated in sinoatrial node pacemaker cells, atrioventricular node pacemaker cells, and atrioventricular bundle cells.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:942982ed897fb6db58ac
claim_id: claim:942982ed897fb6db58ac
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, ANO6 is upregulated in atrioventricular bundle cells.
span_literal:
ANO6 , which encodes a calcium-activated chloride channel, was upregulated in SAN and AVN P cells and in AV bundle cells


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:f1e4f9c7ffadf960be85
claim_id: claim:f1e4f9c7ffadf960be85
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal: bundle cells were marked by the expression of the high-conductance gap junction subunit Cx40
summary:
In Homo sapiens, atrioventricular bundle cells are marked by expression of the high-conductance gap junction subunit connexin 40 (GJA5).


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:d707d35968f8cafca821
claim_id: claim:d707d35968f8cafca821
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, KCND2 is specifically expressed in atrioventricular bundle cells.
span_literal:
KCND2 , a gene associated with nocturnal atrial fibrillation 20 and Brugada syndrome, was also specifically expressed in AV bundle cells


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:8724064c43eacd63f4a4
claim_id: claim:8724064c43eacd63f4a4
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
the GIRK channel subunit KCNJ3 and two classically neuron-associated calcium channel subunits ( CACNA1E and CACNA1B ) were more highly expressed in Purkinje cells than in vCMs

summary:
In Homo sapiens, KCNJ3, CACNA1E, and CACNA1B are more highly expressed in Purkinje cells than in ventricular cardiomyocytes.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:553584826b7e9f4b8c01
claim_id: claim:553584826b7e9f4b8c01
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
AV bundle and Purkinje cells were enriched for GJA5 expression, whereas P cells expressed the ultra-low conductance gap junction subunit GJC1 (which encodes Cx45)

summary:
In Homo sapiens, atrioventricular bundle cells and Purkinje cells are enriched for GJA5 expression, whereas pacemaker cells express the ultra-low conductance gap junction subunit GJC1.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:0fcbb559184b69998c2f
claim_id: claim:0fcbb559184b69998c2f
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
The glutamate transporter SLC1A3 and synthetic enzyme GLS , as well as synaptic vesicle genes such as SNAP25 and STX7 , were expressed in both SAN and AVN P cells

summary:
In Homo sapiens, the glutamate transporter SLC1A3, the synthetic enzyme GLS, and the synaptic vesicle genes SNAP25 and STX7 are expressed in both sinoatrial node and atrioventricular node pacemaker cells.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:43322bc567343ce345dd
claim_id: claim:43322bc567343ce345dd
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, NC2_glial_NGF+ cells express genes involved in the glutamate–glutamine cycle.
span_literal:
NC2_glial_NGF + cells expressed genes involved in the glutamate–glutamine cycle, the means by which astroglia replenish glutamine pools for neighbouring glutamatergic neurons


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:ff64efb93abee0c8013f
claim_id: claim:ff64efb93abee0c8013f
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, NC2_glial_NGF+ cells express SLC1A2, GLUL, and SLC38A9.
span_literal:
the glutamate reuptake transporter EAAT2 (encoded by SLC1A2 ), glutamine synthetase (encoded by GLUL ), which remakes glutamine from glutamate, and the glutamine transporter (encoded by SLC38A9 ), which releases extracellular glutamine


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:684387e69890c7936f26
claim_id: claim:684387e69890c7936f26
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, pacemaker cells express the glutamine transporter SLC38A1 and the glutaminase GLS.
span_literal:
P cells expressed glutamine transporter (encoded by SLC38A1 ) and glutaminase (encoded by GLS ), which converts glutamine to the active neurotransmitter glutamate


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:fc1c2d02e4a577f9ff49
claim_id: claim:fc1c2d02e4a577f9ff49
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
summary: In Homo sapiens, the NC2_glial_NGF+ glial cell population expresses the neurexins NRXN1 and NRXN3.
span_literal:
This glial population expresses neurexins ( NRXN1 and NRXN3 ), which form trans-synaptic complexes with cell adhesion molecules


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:4b226aefe9d290c2ec3b
claim_id: claim:4b226aefe9d290c2ec3b
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
The neuropeptide somatostatin (encoded by SST ), previously identified as a marker of RAGP neuronal populations in pig 33 , was highly correlated with the pan-neuronal cytoskeletal score

summary:
In Homo sapiens, right atrial ganglionated plexus neuronal cells show SST expression highly correlated with the pan-neuronal cytoskeletal score.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:09aed5b98bc5fa699f02
claim_id: claim:09aed5b98bc5fa699f02
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
SLC18A3 , SLC5A7 , CHAT and ACHE , the catecholamine synthetic enzymes TH and DDC and the sympathetic co-transmitter neuropeptide Y (encoded by NPY

summary:
In Homo sapiens, right atrial ganglionated plexus neurons express the cholinergic markers SLC18A3, SLC5A7, CHAT, and ACHE, the catecholamine synthetic enzymes TH and DDC, and the sympathetic co-transmitter neuropeptide Y (NPY).


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:78be253b323ce7487ec5
claim_id: claim:78be253b323ce7487ec5
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal: NGF was more highly expressed in NC2_glial_NGF + cells than in CMs and other neural cells
summary:
In Homo sapiens, NC2_glial_NGF+ cells express NGF more highly than cardiomyocytes and other neural cells.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:9dac2f6bffdac633a365
claim_id: claim:9dac2f6bffdac633a365
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
vCM3 was renamed as vCM3_stressed based on the specific expression of NPPB , which encodes B-type natriuretic peptide (BNP), which is a diagnostic marker for HF and a valuable prognostic predictor for the entire spectrum of disease severity and expressed in stressed CMs

summary:
In Homo sapiens, stressed ventricular cardiomyocyte 3 (vCM3_stressed) is marked by specific expression of NPPB, which encodes B-type natriuretic peptide.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:94f0ea0ebc2901003c46
claim_id: claim:94f0ea0ebc2901003c46
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
compared with other vCMs, vCM3_stressed cells expressed higher levels of genes encoding receptors for IL-6, TNFSF12 and IL-1 ( IL6R , TNFRSF12A , and IL1R1 and IL1RAP , respectively)

summary:
In Homo sapiens, stressed ventricular cardiomyocyte 3 (vCM3_stressed) expresses higher levels of IL6R, TNFRSF12A, IL1R1, and IL1RAP compared with other ventricular cardiomyocytes.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:15e79830c5674b95f78e
claim_id: claim:15e79830c5674b95f78e
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
Within the group of receptors were the classical acetylcholine muscarinic (M 2 ) (encoded by CHRM2 ) and catecholamine β (encoded by ADRB1 ) receptors, which are responsible for mediating the major heart-rate-modulating effects of the autonomic nervous system (ANS)

summary:
In Homo sapiens, cardiac conduction system cells express the muscarinic acetylcholine receptor M2 (CHRM2) and the beta-adrenergic receptor (ADRB1).


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:0e7a7d70ec1c984772b5
claim_id: claim:0e7a7d70ec1c984772b5
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
P cells, including angiotensin II (encoded by AGTR1 ), calcitonin gene-related peptide (encoded by CALCRL ), glucagon-like peptide 1 (encoded b y GLP1R ), parathyroid hormone (encoded by PTH1R ) and vasoactive intestinal peptide (encoded by VIPR2

summary:
In Homo sapiens, pacemaker cells express receptors for neurohumoral ligands including AGTR1, CALCRL, GLP1R, PTH1R, and VIPR2.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:74844b478f2675f62acb
claim_id: claim:74844b478f2675f62acb
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal: CCS cells ( ADGRL3 , ADGRG6 and CELSR1
summary:
In Homo sapiens, cardiac conduction system cells highly express the adhesion G-protein-coupled receptors ADGRL3, ADGRG6, and CELSR1.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:93240c8af5fbda3f86c2
claim_id: claim:93240c8af5fbda3f86c2
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
our results indicated that FOXP2, a TF associated with language centre development in the brain, is a key TF targeting major P cell ion channel genes such as HCN1 and CACNA1D , as well as TBX3

summary:
In Homo sapiens, pacemaker cells express FOXP2, a key transcription factor targeting major pacemaker cell ion channel genes HCN1 and CACNA1D, as well as TBX3.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:6f29e0d2f9bef556d60b
claim_id: claim:6f29e0d2f9bef556d60b
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal: PRDM6
summary:
In Homo sapiens, pacemaker cells express PRDM6, which regulates multiple genes encoding ion channels and G-protein-coupled receptors.


claim_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93:claim:b0317edd129f90b98306
claim_id: claim:b0317edd129f90b98306
paper_key: hca:0462_10.1038_s41586-023-06311-1_b735ac2f93
span_literal:
CREB5 , which encodes cAMP-responsive element-binding protein 5 and is associated with atrial fibrillation 27 , was also one of the TFs highly expressed in P cells compared with other aCMs

summary:
In Homo sapiens, CREB5 is highly expressed in pacemaker cells compared with other atrial cardiomyocytes.


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:b6e034dafd7ef0a8ec7b
claim_id: claim:b6e034dafd7ef0a8ec7b
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal: KRT1 mapped into the suprabasal epithelial region, and KRT15 into the basal epithelial layer.
summary:
In Homo sapiens oral mucosa, KRT1 is a marker of the suprabasal epithelial region, and KRT15 is a marker of the basal epithelial layer.


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:53a73c0a465b67ea2844
claim_id: claim:53a73c0a465b67ea2844
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
summary: In Homo sapiens oral mucosa, KRT13 and KRT4 are markers restricted to the sulcular epithelium.
span_literal:
They also show distinct keratin signatures with KRT13 and KRT4 being restricted to the sulcular epithelium and KRT18 specific to the junctional epithelium


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:1357de4aeacb8af7c213
claim_id: claim:1357de4aeacb8af7c213
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
summary: In Homo sapiens oral mucosa, SOX9 shows restricted expression in the junctional epithelium.
span_literal:
Interestingly, SOX9 shows a restricted expression to the junctional epithelium, and it is known to be expressed in stem cells/progenitors in several tissues such as gut and skin


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:7793fac437b5b178f4f9
claim_id: claim:7793fac437b5b178f4f9
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
We also analysed the basal proliferative epithelial progenitor layer, which shows high expression of KRT8, IGFBP2, FOXP2, and NEFM (neurofilament medium chain)

summary:
In Homo sapiens oral mucosa, the basal proliferative epithelial progenitor layer shows high expression of KRT8, IGFBP2, FOXP2, and NEFM (neurofilament medium chain).


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:74f58ce1350ede9102fe
claim_id: claim:74f58ce1350ede9102fe
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
we identified a rare disease-associated epithelial proliferative population characterised by TOP2A and CENPF expression.

summary:
In Homo sapiens oral mucosa, a rare disease-associated epithelial proliferative population is characterised by TOP2A and CENPF expression.


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:7595f48136f47ba571fd
claim_id: claim:7595f48136f47ba571fd
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
Fibroblast 2 ( GREM1 + , SFRP1 + ) showed an increased spatial enrichment in the subepithelial region compared to the other subtypes, and a substantial enrichment in the sulcular stroma, suggestive of a role in epithelial maintenance.

summary:
In Homo sapiens oral mucosa, fibroblast 2 is marked by GREM1 and SFRP1 expression and is enriched in the subepithelial region.


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:a140bbe600a491151cea
claim_id: claim:a140bbe600a491151cea
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
These fibroblasts were mainly located in regions that co-localised with other immune cell types, and are characterised by expression of RAC2, LCP1, and TNFRS11B , a negative regulator of bone resorption and key regulator of osteoclast activity as previously described

summary:
In Homo sapiens oral mucosa, fibroblast 5 is characterised by expression of RAC2, LCP1, and TNFRSF11B.


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:0c09d63f8179f803e4c1
claim_id: claim:0c09d63f8179f803e4c1
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
This immune-effector profile is also shown by a higher expression of chemokines such as CXCL8 and CXCL10, and ALOX5AP, which encodes arachidonate 5-lipoxygenase-activating protein.

summary:
In Homo sapiens oral mucosa, fibroblast 5 shows higher expression of CXCL8, CXCL10, and ALOX5AP (arachidonate 5-lipoxygenase-activating protein).


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:916ccd95e08a5711d1cb
claim_id: claim:916ccd95e08a5711d1cb
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
We used RAC2 and LCP1 to label this population, and CD14 and CD79A for macrophages and B cells, respectively.

summary:
In Homo sapiens oral mucosa, RAC2 and LCP1 label fibroblast 5, CD14 labels macrophages, and CD79A labels B cells.


claim_key: hca:0463_10.7554_elife.81525_0f73520e7f:claim:f59900cea58e36a78dff
claim_id: claim:f59900cea58e36a78dff
paper_key: hca:0463_10.7554_elife.81525_0f73520e7f
span_literal:
From these, CDKN2B, IL1A, IL1B, and VAMP8 specifically localised in the junctional epithelium region

summary:
In Homo sapiens oral mucosa, periodontitis risk genes CDKN2B, IL1A, IL1B, and VAMP8 specifically localise in the junctional epithelium region.


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:0adea2a29fd07c6c6a7c
claim_id: claim:0adea2a29fd07c6c6a7c
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
span_literal:
Some cells in this cluster expressed CD1C, XCR1 , CLEC9A and CD141 ( THBD ) ( Fig. 3C ) indicating that it included cDC1 and cDC2 cells ( Fig. S13E-F ).

summary:
In Homo sapiens kidney, conventional dendritic cell type 1 expresses XCR1, CLEC9A, and THBD (CD141), while conventional dendritic cell type 2 expresses CD1C.


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:87208723682704f7aa53
claim_id: claim:87208723682704f7aa53
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
span_literal:
MNPa and MNPb ( Fig. S13I ), including anti-microbial genes such as S100A8 and S100A9 , IL1B and lysozyme ( LYZ

summary:
In Homo sapiens kidney, mononuclear phagocyte a expresses anti-microbial genes S100A8, S100A9, IL1B, and LYZ.


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:97cd634e68b22d18301b
claim_id: claim:97cd634e68b22d18301b
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
span_literal:
MNPb ( Fig. S13I ), including anti-microbial genes such as S100A8 and S100A9 , IL1B and lysozyme ( LYZ

summary:
In Homo sapiens kidney, mononuclear phagocyte b expresses anti-microbial genes S100A8, S100A9, IL1B, and LYZ.


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:53b34e2ce5639c9f0c9e
claim_id: claim:53b34e2ce5639c9f0c9e
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
summary: In Homo sapiens kidney, mononuclear phagocyte d expresses MRC1, C1QC, CD163, and MAF.
span_literal:
MNPd was the only mature kidney MNP cluster with similarity to fetal kidney Mphage1 ( S16C ), and both clusters expressed MRC1 , C1QC, CD163 , and MAF ( Figs. 3C , S16D ).


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:b1b997e8cda07b69744b
claim_id: claim:b1b997e8cda07b69744b
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
summary: In Homo sapiens kidney, pelvic epithelium is marked by KRT17 and expresses CXCL8 and LCN2.
span_literal:
We validated this, demonstrating that CK17 ( KRT17 )+ cells (a marker of PE) in human kidney pelvis express CXCL8 and LCN2 ( Fig. 4B , S19A) .


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:47f2f2587676ecbaf3f3
claim_id: claim:47f2f2587676ecbaf3f3
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
span_literal:
In mature kidneys, we observed higher expression of the flagellin receptor TLR5 , and its down-stream signalling molecule MyD88 , in the PE compared with the proximal nephron epithelium ( Fig. S10D ).

summary:
In Homo sapiens mature kidney, pelvic epithelium shows higher expression of TLR5 and MYD88 compared with proximal nephron epithelium.


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:434c31bf8ad541bdf96b
claim_id: claim:434c31bf8ad541bdf96b
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
span_literal:
CX3CL1 was expressed in CNT and PE, and its receptor CX3CR1 on monocyte-derived macrophages (MNPa-b) and DCs.

summary:
In Homo sapiens kidney, connecting tubule and pelvic epithelium express CX3CL1, while monocyte-derived macrophages (mononuclear phagocyte a and mononuclear phagocyte b) and dendritic cells express CX3CR1.


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:16ddf9bcd9c654e9715c
claim_id: claim:16ddf9bcd9c654e9715c
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
summary: In Homo sapiens kidney, mononuclear phagocyte d shows little expression of CX3CR1.
span_literal:
Notably, MNPd showed little expression of CX3CR1 , and in human kidney sections there were few CD206/163 positive cells in the medulla and pelvis compared to the cortex ( Fig. S18D ).


claim_key: hca:0464_10.1126_science.aat5031_cfde7f776b:claim:596614f851b2489189dc
claim_id: claim:596614f851b2489189dc
paper_key: hca:0464_10.1126_science.aat5031_cfde7f776b
summary: In Homo sapiens kidney, mononuclear phagocyte d differentially expresses RUNX1.
span_literal:
Of note, RUNX1 , a TF used to fate-map yolk sac-derived cells ( 20 ), was differentially expressed in MNPd ( Fig. S13H ), raising the possibility that they may populate the kidney pre-natally.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:f057e77248020b707fb0
claim_id: claim:f057e77248020b707fb0
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
S2 cells (marked by F3 , NPY , and FOXL1 ) expressed markers akin to a peri-cryptal telocyte population

summary:
In Homo sapiens, stromal 2 fibroblasts are marked by F3, NPY, and FOXL1, expressing markers akin to a peri-cryptal telocyte population.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:c605ba03a735871278a2
claim_id: claim:c605ba03a735871278a2
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, BEST4/OTOP2 cells express CA7, CA4, BEST4, and OTOP2.
span_literal:
One cluster expressed enterocyte ( CA7, CA4 ) genes along with a distinct transcriptional signature including BEST4 and OTOP2 which was in keeping with recently described BEST4/OTOP2 cells


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:c683e7d0c7e407b7625c
claim_id: claim:c683e7d0c7e407b7625c
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, epithelial cells are marked by EPCAM and FABP1.
span_literal:
Compartments included differential expression of epithelial ( EPCAM, FABP1), fibroblast ( THY1, COL1A2, VIM) , myofibroblast ( VIM, FOXF1, TAGLN ), endothelium ( PECAM1, CDH5, CLDN5 ), pericyte ( KCNJ8, ABCC9, TGS5 ), neural/glial ( PHOX2B, HAND2, TUBB2B) , immune ( PTPRC ) and muscle ( MYH11, ACTG2 ) genes


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:262495f960c9ad769086
claim_id: claim:262495f960c9ad769086
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
Progenitor and differentiated intestinal smooth muscle cells (iSMCs) were respectively marked by genes such as PLPP2 and ACTA2

summary:
In Homo sapiens, progenitor intestinal smooth muscle cells are marked by PLPP2 and differentiated intestinal smooth muscle cells are marked by ACTA2.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:f29b47d5c1fbca5916c4
claim_id: claim:f29b47d5c1fbca5916c4
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
we identified a unique colonic rather than SI-specific glial population serving as the sole GFRA3 source during development

summary:
In Homo sapiens, a colonic lymphoid-associated glial population is the sole source of GFRA3 during intestinal development.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:1f7b16d8d5a294b2fc21
claim_id: claim:1f7b16d8d5a294b2fc21
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
monocytes were identified by high expression of CD14 in comparison to macrophages as well as FCN1 a key gene expressed in colonic monocytes in colorectal cancer ( Zhang et al., 2020 ) alongside transcription of Myeloid Inhibitory C-type Lectin like receptor (MICL encoded by CLEC12A ) reported in this cell type

summary:
In Homo sapiens, monocytes are identified by high expression of CD14, FCN1, and CLEC12A compared to macrophages.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:58a90afa638ba5196658
claim_id: claim:58a90afa638ba5196658
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
Two clusters represented DCs, by expression of the pan-marker ETV6 ( Robbins et al., 2008 ) were divided into conventional DC ( FLT3 ) and plasmocytic DCs ( PTCRA, LILRA4 )

summary:
In Homo sapiens, dendritic cells express the pan-marker ETV6, with conventional dendritic cells marked by FLT3 and plasmacytoid dendritic cells marked by PTCRA and LILRA4.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:b21646092cab3afdf516
claim_id: claim:b21646092cab3afdf516
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
B cells were seen with expression of genes including CD19 , and clustered into cells which had more mature B cells markers ( CD19hi, CD79A, IGHD ) and a cluster with a more naive appearance; relatively lower expression of CD19, expressing light chain IGLL1 , and other genes reported in naive B cells such as VPREB3

summary:
In Homo sapiens, mature B cells are marked by high CD19, CD79A, and IGHD, while pre-B cells express lower CD19, IGLL1, and VPREB3.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:262b13f1a2ba5204674c
claim_id: claim:262b13f1a2ba5204674c
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, type 3 innate lymphoid cells are marked by KIT, KLRB1, RORC, and ID2.
span_literal:
The final cluster expressed KIT highlighting it as a ILC cell which together with KLRB1 , RORC and ID2 demonstrated this to be of the ILC-3 subtype


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:35b2019cd8abb7685e63
claim_id: claim:35b2019cd8abb7685e63
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, lymphatic endothelial cells are marked by PROX1, PDPN, and LYVE1.
span_literal:
one further group of cells was distinct from the vascular ECs and had specific expression of genes such as PROX1, PDPN and very high expression of LYVE1 which are known to be markers of lymphatic ECs


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:65d1bbd1bb8c03c49e6f
claim_id: claim:65d1bbd1bb8c03c49e6f
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
span_literal:
PHOX2B which is seen in enteric nervous system (ENS) progenitors and was thus termed “glial progenitors

summary:
In Homo sapiens, glial progenitors express PHOX2B, a gene seen in enteric nervous system progenitors.


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:6efc4754e75b67ec6f05
claim_id: claim:6efc4754e75b67ec6f05
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, intra-ganglionic glial cells are marked by ENTPD2.
span_literal:
ENTPD2 expression has previously been reported in intra-ganglionic glia and so cells expressing this were annotated as such


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:20a4d7c16055e35c1aec
claim_id: claim:20a4d7c16055e35c1aec
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, interneurons are identified by expression of TAC1 and PENK.
span_literal:
interneurons were identified by expression of tachkinin ( TAC1 ) and enkephalin ( PENK ), inhibitory motor neuron by expression of nitric oxide ( NOS1 ) and VIP and excitory motor neurons by expression of CASZ1


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:d753d3d399742a9fb30c
claim_id: claim:d753d3d399742a9fb30c
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, interstitial cells of Cajal are marked by KIT, ANO1, and SPON2.
span_literal:
a second cluster expressing KIT alongside ANO1 and SPON2 – resembling the Interstitial cells of Cajal


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:02d2acc0ada62d4b5678
claim_id: claim:02d2acc0ada62d4b5678
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, enteroendocrine D-cells are marked by SST.
span_literal:
Somatostatin ( SST, D-cells), serotonin (TPH1, Enterochromaffin cells), cholecystokinin ( CCK , I cells), Peptide YY/ glucagon ( PYY , GCG L-Cells), Neurotensin ( NTS , N cells) and co-expression of Motilin and Ghrelin was seen in the same cluster and annotated as A-Cell/M-Cells


claim_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941:claim:7245c5e0a02e393ccd52
claim_id: claim:7245c5e0a02e393ccd52
paper_key: hca:0465_10.1016_j.cell.2020.12.016_af8ed7d941
summary: In Homo sapiens, Paneth cells express DEFA5 and DEFA6 and are specific to the small intestine.
span_literal:
The final cluster was small intestinal specific and expressed defensins ( DEFA5, DEFA6 ) in keeping with Paneth cells


claim_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad:claim:840d0f3b02845b984820
claim_id: claim:840d0f3b02845b984820
paper_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad
span_literal:
the expression of EC hallmark gene eNOS was significantly decreased by H + T, evident not only by the reduced average mRNA level in single ECs, but also by the lowered percentage of ECs that express eNOS, following a time-dependent manner.

summary:
In Homo sapiens, endothelial nitric oxide synthase (eNOS) is a hallmark gene of endothelial cells, and its expression is decreased in dysfunctional endothelial cells.


claim_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad:claim:2f3cc6adfb146500a3b6
claim_id: claim:2f3cc6adfb146500a3b6
paper_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad
span_literal:
pro-inflammatory and pro-fibrotic genes (e.g., ICAM1, FN1 , and SERPINE1 ) were increased in mRNA levels in single ECs and in percentage of ECs with positive expression across time

summary:
In Homo sapiens, intercellular adhesion molecule 1 (ICAM1), fibronectin 1 (FN1), and SERPINE1 are pro-inflammatory and pro-fibrotic marker genes that are increased in dysfunctional endothelial cells.


claim_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad:claim:b1f9103f2d4aa4042c50
claim_id: claim:b1f9103f2d4aa4042c50
paper_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad
span_literal:
the mesenchymal marker smooth muscle cell actin (α-SMA, encoded by ACTA2 ) was induced in a much slower pattern, i.e., from 0.2% of control ECs to 1.4% of cells after 7 days of H + T treatment

summary:
In Homo sapiens, alpha-smooth muscle actin (ACTA2) is a mesenchymal marker gene induced in endothelial cells undergoing endothelial-mesenchymal transition.


claim_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad:claim:fa8bad1312da775b5559
claim_id: claim:fa8bad1312da775b5559
paper_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad
span_literal:
we performed shared nearest neighbor (SNN) clustering and visually selected clusters showing high expression levels of CDH5 , which encodes VE-cad

summary:
In Homo sapiens, CDH5, which encodes VE-cadherin, is used to identify endothelial cells from single-cell RNA sequencing data.


claim_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad:claim:b652c5a3897408a3bfc9
claim_id: claim:b652c5a3897408a3bfc9
paper_key: hca:0466_10.1038_s41467-020-18957-w_ce0dae83ad
span_literal: eNOS, encoded by NOS3 , and many EC function markers decreased
summary:
In Homo sapiens, endothelial nitric oxide synthase, encoded by NOS3, is an endothelial cell function marker that decreased in dysfunctional endothelial cells.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:528f91c8597dc37eedf6
claim_id: claim:528f91c8597dc37eedf6
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function.

summary:
In Homo sapiens, the colonic crypt niche mesenchymal cell (S2) expresses SOX6, F3 (CD142), and WNT genes.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:cfcf56cae7d2e8226668
claim_id: claim:cfcf56cae7d2e8226668
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases.

summary:
In Homo sapiens, the activated mesenchymal population (S4) expresses tumor necrosis factor superfamily member 14 (TNFSF14), interleukin-33, and lysyl oxidases.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:6b6f00300beb193d7ca6
claim_id: claim:6b6f00300beb193d7ca6
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
Violin plots for pan-fibroblast marker genes vimentin ( VIM ) and collagen types 1 and 3 ( COL1A2 , COL3A1 ) across clusters.

summary:
In Homo sapiens, pan-fibroblast marker genes include vimentin (VIM), collagen type I alpha 2 chain (COL1A2), and collagen type III alpha 1 chain (COL3A1).


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:686f993eae96b61b47df
claim_id: claim:686f993eae96b61b47df
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
summary: In Homo sapiens, myofibroblasts are marked by high expression of MYH11 and ACTG2.
span_literal:
We designated one cluster myofibroblasts (MFs) based on high expression of contractile genes (e.g., MYH11 and ACTG2 ), while the remaining clusters designated stromal 1–4 (hereafter S1–S4) expressed fibroblast-associated but not contractile genes and showed dissimilar transcriptional profiles and ontology enrichment


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:79ac5ecac35e17c9ea3a
claim_id: claim:79ac5ecac35e17c9ea3a
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
summary: In Homo sapiens, endothelial cells show marked expression of PECAM1.
span_literal:
Two clusters of endothelial cells showed marked expression of PECAM1 , glial cells showed S100B expression, pericytes expressed RGS5 , and plasma cells were identified by SDC1 expression.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:14da244f9bf952f89805
claim_id: claim:14da244f9bf952f89805
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal: Examples of preferentially induced genes included APOE , CCL8 , FABP5 , ADAMDEC1
summary:
In Homo sapiens, the stromal 1 subset (S1) preferentially expresses APOE, CCL8, FABP5, and ADAMDEC1.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:4afdab9df58b86bdcab8
claim_id: claim:4afdab9df58b86bdcab8
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
S2, marked by expression of the transcription factor SOX6 ( Figure 1 Dii), consisted of two similar sub-clusters designated 2a and 2b ( Figure 1 B).

summary:
In Homo sapiens, the stromal 2 subset (S2) is marked by expression of the transcription factor SOX6.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:8dcf77c0dd3b75312da1
claim_id: claim:8dcf77c0dd3b75312da1
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
S2 had high expression of transforming growth factor β (TGF-β) superfamily ligands ( BMP2 and BMP5 ), non-canonical Wnt ligands ( WNT5A and WNT5B ), and the secreted Wnt antagonist FRZB

summary:
In Homo sapiens, the stromal 2 subset (S2) has high expression of BMP2, BMP5, WNT5A, WNT5B, and FRZB.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:909912b1076634d27525
claim_id: claim:909912b1076634d27525
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
summary: In Homo sapiens, the stromal 2 subset (S2) expresses high levels of periostin (POSTN).
span_literal:
S2 also expressed high levels of periostin ( POSTN ) ( Figure 1 D, ii), which is essential for tissue repair but can also promote tumorigenesis


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:0649b4f94a9498dc564d
claim_id: claim:0649b4f94a9498dc564d
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
We detected S1 markers ( ADAMDEC1 , DCN , SLIT2 , CXCL12 ) in mesenchymal cells distributed throughout the lamina propria, while S2 markers ( F3 [ CD142 ], WNT5A , WNT5B , BMP2 , BMP5 , FRZB , POSTN , HSD17B2 ) were restricted to a smaller sub-population in close proximity to the epithelial monolayer.

summary:
In Homo sapiens, the stromal 1 subset (S1) is marked by ADAMDEC1, DCN, SLIT2, and CXCL12, while the stromal 2 subset (S2) is marked by F3 (CD142), WNT5A, WNT5B, BMP2, BMP5, FRZB, POSTN, and HSD17B2.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:c1adb9e34b458c47425e
claim_id: claim:c1adb9e34b458c47425e
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
We detected S1 markers ( ADAMDEC1 , DCN , SLIT2 , CXCL12 ) in mesenchymal cells distributed throughout the lamina propria, while S2 markers ( F3 [ CD142 ], WNT5A , WNT5B , BMP2 , BMP5 , FRZB , POSTN , HSD17B2 ) were restricted to a smaller sub-population in close proximity to the epithelial monolayer.

summary:
In Homo sapiens, the stromal 2 subset (S2) is marked by F3 (CD142), WNT5A, WNT5B, BMP2, BMP5, FRZB, POSTN, and HSD17B2.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:efaff0894ed63cf3ad67
claim_id: claim:efaff0894ed63cf3ad67
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
Identification of SOX6 − ZEB2 + /ZEB1 − ZEB2 + S1 and SOX6 + ZEB2 − /ZEB1 + ZEB2 − S2 subsets in healthy human colon.

summary:
In Homo sapiens, the stromal 1 subset (S1) is SOX6-negative and ZEB2-positive, while the stromal 2 subset (S2) is SOX6-positive and ZEB2-negative in healthy colon.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:9d32a4d5be6d65cc75f3
claim_id: claim:9d32a4d5be6d65cc75f3
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
Identification of SOX6 − ZEB2 + /ZEB1 − ZEB2 + S1 and SOX6 + ZEB2 − /ZEB1 + ZEB2 − S2 subsets in healthy human colon.

summary:
In Homo sapiens, the stromal 2 subset (S2) is SOX6-positive, ZEB1-positive, and ZEB2-negative in healthy colon.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:4505f74805ed5c6800d2
claim_id: claim:4505f74805ed5c6800d2
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
Highly ranked S4 markers included fibroblastic reticular cell (FRC)-associated genes, lymphocyte trafficking cytokines ( CCL19 and CCL21 ), T cell co-stimulatory TNF-superfamily ligand ( TNFSF14/LIGHT) , the major histocompatibility complex (MHC) class II invariant chain ( CD74 ), the molecular chaperone clusterin ( CLU ), CD24, and interleukin-33 (IL-33)

summary:
In Homo sapiens, the stromal 4 subset (S4) is marked by CCL19, CCL21, TNFSF14 (LIGHT), CD74, CLU, CD24, and interleukin-33 (IL33).


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:b48d1e224a36740de62b
claim_id: claim:b48d1e224a36740de62b
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
We identified a colonic crypt niche mesenchymal S2 population, which expressed F3/CD142 and the transcription factor SOX6 located in direct proximity to epithelial cells

summary:
In Homo sapiens, the colonic crypt niche mesenchymal stromal 2 subset (S2) expresses F3 (CD142) and the transcription factor SOX6.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:13b8157cbf0c8f884ae5
claim_id: claim:13b8157cbf0c8f884ae5
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
Histogram comparisons of CCL19 and TNFSF14 (LIGHT) levels in healthy versus inflamed colonic mesenchyme marks the emergence of S4.

summary:
In Homo sapiens, CCL19 and TNFSF14 (LIGHT) mark the emergence of the stromal 4 subset (S4) in inflamed colonic mesenchyme.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:a99bfca7f67882e98a92
claim_id: claim:a99bfca7f67882e98a92
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
We observed several disease-associated changes in the UC stroma, exemplified by reduced S2 markers F3/CD142 and POSTN, increased BCL6 and PTGS2/COX-2 expression levels in S3, and markedly expanded S4.

summary:
In Homo sapiens, the stromal 2 subset (S2) is marked by F3 (CD142) and POSTN, while the stromal 3 subset (S3) shows increased BCL6 and PTGS2 (COX-2) expression in ulcerative colitis.


claim_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11:claim:748605f8967137bc222d
claim_id: claim:748605f8967137bc222d
paper_key: hca:0467_10.1016_j.cell.2018.08.067_51639edc11
span_literal:
We observed several disease-associated changes in the UC stroma, exemplified by reduced S2 markers F3/CD142 and POSTN, increased BCL6 and PTGS2/COX-2 expression levels in S3, and markedly expanded S4.

summary:
In Homo sapiens, the stromal 3 subset (S3) shows increased BCL6 and PTGS2 (COX-2) expression in ulcerative colitis.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:a5ffd6f596ed8006a09c
claim_id: claim:a5ffd6f596ed8006a09c
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
summary: In Homo sapiens, fibroblast state F2 (myofibroblast) is marked by ACTA2 and TAGLN expression.
span_literal:
Unbiased clustering, harmony integration to correct for batch effects, and subsequent DGE identified 13 distinct fibroblast cell states ([Fig. 2A](512579v1_fig2.tif)) marked by classical fibroblast markers (F1, ground state), ACTA2/TAGLN (F2, myofibroblasts), CCL2/THBS1 (F3), APOE/AGT (F4), DLK1/GPX3 (F5), PTGDS/GPC3 (F6), APOD/IGFBP5 (F7), GDF15/ATF5 (F8), FAP/POSTN (F9), ISG15/MX1 (F10), PLA2G2A (F11), PCOLCE2/MFAP5 (F12), and PRG4/CXCL14 (F13)


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:e64b9e5fd95a9ab39a23
claim_id: claim:e64b9e5fd95a9ab39a23
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
summary:
In Homo sapiens, fibroblast state F9 is marked by FAP (fibroblast activator protein) and POSTN (periostin) expression.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:724517770eeed1b97bc3
claim_id: claim:724517770eeed1b97bc3
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
Differential expression analysis from the cell surface protein data identified additional markers for the F2 (F11R) and F9 (THY1, CD276, LAMP1, CD63) states

summary:
In Homo sapiens, fibroblast state F2 (myofibroblast) is marked by F11R cell surface protein expression, while fibroblast state F9 is marked by THY1, CD276, LAMP1, and CD63 cell surface protein expression.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:f3813fc85a9e2ca59f52
claim_id: claim:f3813fc85a9e2ca59f52
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
Differential expression analysis from the cell surface protein data identified additional markers for the F2 (F11R) and F9 (THY1, CD276, LAMP1, CD63) states

summary:
In Homo sapiens, fibroblast state F9 (fibroblast activator protein/periostin fibroblast) is marked by THY1, CD276, LAMP1, and CD63 cell surface protein expression.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:3a23e98dd0b8b117a67a
claim_id: claim:3a23e98dd0b8b117a67a
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
Within the myeloid cell compartment, IL-1β expression was observed in CCR2+ monocytes, macrophages, and classic dendritic cells (DC2s)

summary:
In Homo sapiens, IL1B (interleukin 1 beta) is expressed in CCR2-positive monocytes within the myeloid cell compartment.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:76564efb9e203772a8f1
claim_id: claim:76564efb9e203772a8f1
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
Within the myeloid cell compartment, IL-1β expression was observed in CCR2+ monocytes, macrophages, and classic dendritic cells (DC2s)

summary:
In Homo sapiens, IL1B (interleukin 1 beta) is expressed in macrophages within the myeloid cell compartment.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:99c54dc5b540428a7023
claim_id: claim:99c54dc5b540428a7023
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
Within the myeloid cell compartment, IL-1β expression was observed in CCR2+ monocytes, macrophages, and classic dendritic cells (DC2s)

summary:
In Homo sapiens, IL1B (interleukin 1 beta) is expressed in classic dendritic cells (type 2 conventional dendritic cell).


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:50e35ec0e14256a58951
claim_id: claim:50e35ec0e14256a58951
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
We show that IL-1β is selectively expressed by CCR2+ monocytes and macrophages in the human heart consistent with our prior mouse studies

summary:
In Homo sapiens, IL1B (interleukin 1 beta) is selectively expressed by CCR2-positive monocytes in the human heart.


claim_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30:claim:0402a5570b3e13bbb7c1
claim_id: claim:0402a5570b3e13bbb7c1
paper_key: hca:0469_10.1101_2022.10.17.512579_e7abedbc30
span_literal:
We show that IL-1β is selectively expressed by CCR2+ monocytes and macrophages in the human heart consistent with our prior mouse studies

summary:
In Homo sapiens, IL1B (interleukin 1 beta) is selectively expressed by macrophages in the human heart.


claim_key: hca:0470_10.21203_rs.3.rs-2402606_v1_8de4ac8813:claim:2f30519a95bfb7c491c9
claim_id: claim:2f30519a95bfb7c491c9
paper_key: hca:0470_10.21203_rs.3.rs-2402606_v1_8de4ac8813
span_literal:
We identified a disease-associated fibroblast trajectory marked by cell surface expression of fibroblast activator protein (FAP), which diverged into distinct myofibroblasts and pro-fibrotic fibroblast populations, the latter resembling matrifibrocytes.

summary:
In Homo sapiens, disease-associated fibroblasts are marked by cell surface expression of fibroblast activator protein (FAP), diverging into myofibroblasts and pro-fibrotic fibroblasts.


claim_key: hca:0470_10.21203_rs.3.rs-2402606_v1_8de4ac8813:claim:9f162bc4cb707206abca
claim_id: claim:9f162bc4cb707206abca
paper_key: hca:0470_10.21203_rs.3.rs-2402606_v1_8de4ac8813
span_literal:
Pro-fibrotic fibroblasts were transcriptionally similar to cancer associated fibroblasts and expressed high levels of collagens and periostin (POSTN), thymocyte differentiation antigen 1 (THY-1), and endothelin receptor A (EDNRA) predicted to be driven by a RUNX1 gene regulatory network.

summary:
In Homo sapiens, pro-fibrotic fibroblasts express high levels of periostin (POSTN), thymocyte differentiation antigen 1 (THY-1), and endothelin receptor A (EDNRA), predicted to be driven by a RUNX1 gene regulatory network.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:914ced562b033022b684
claim_id: claim:914ced562b033022b684
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
We identified CD56 bright NK cells in the scRNA-seq data using the high expression of IL7RA ( IL7R ), CD62L ( SELL ), NKG2A ( KLRC1 ), and granzyme K ( GZMK )

summary:
In Homo sapiens, CD56 bright natural killer cells are identified by high expression of IL7R, SELL, KLRC1, and GZMK.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:d99ff723350137b00e9b
claim_id: claim:d99ff723350137b00e9b
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
summary: In Homo sapiens, CD56 bright natural killer cells highly express XCL1 and XCL2.
span_literal:
XCL1 and XCL2 from C chemokine family are also highly expressed in “CD56 bright NK” cluster consistent with previous data obtained using mass spectrometry


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:69b6479fcd19b567edb4
claim_id: claim:69b6479fcd19b567edb4
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
Functionally matured NK cells with high expression of CX3CR1 , HAVCR2 (TIM-3), and ZEB2 represents terminally differentiated status with the unique transcriptional profile.

summary:
In Homo sapiens, terminally differentiated natural killer cells are marked by high expression of CX3CR1, HAVCR2, and ZEB2.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:3fde895631a79ba5bf8e
claim_id: claim:3fde895631a79ba5bf8e
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
summary: In Homo sapiens, adaptive natural killer cells are marked by high expression of KLRC2 (NKG2C).
span_literal:
This cluster featured with high expression of KLRC2 (NKG2C), which has been used as a marker for the adaptive NK cells resulting from human cytomegalovirus (HCMV) infection


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:baf592a30eba81d85b40
claim_id: claim:baf592a30eba81d85b40
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
Previous work from Schlums et al. 42 has discovered that adaptive NK cells from HCMV + donors express less FcεRγ ( FCER1G ), SYK ( SYK ), EAT-2 ( SH2D1B ), and PLZF ( ZBTB16 ) compared to other NK subsets.

summary:
In Homo sapiens, adaptive natural killer cells express less FCER1G, SYK, SH2D1B, and ZBTB16 compared to other natural killer cell subsets.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:e519747ca14574739a6a
claim_id: claim:e519747ca14574739a6a
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal: The high expression of transcription factor ZEB2 indicated terminal maturity of this cluster
summary:
In Homo sapiens, terminal natural killer cells are marked by high expression of the transcription factor ZEB2.


claim_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944:claim:fd1c2a813f5eb08395fc
claim_id: claim:fd1c2a813f5eb08395fc
paper_key: hca:0471_10.1038_s41467-019-11947-7_0514f87944
span_literal:
To further support the identification of the terminally matured cluster, we demonstrate increased expression of CX3CR1 and HAVCR2 (TIM-3), both of which mark the mature NK population with full responsiveness

summary:
In Homo sapiens, terminally matured natural killer cells show increased expression of CX3CR1 and HAVCR2 (TIM-3).


