# claims

claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:210991a96616a5172fbd
claim_id: claim:210991a96616a5172fbd
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
This is followed by a rostro-caudal patterning event, stemming in differentiation of the late rostral epiblast into rostral presumptive neuroectoderm (HESX1, SHISA2 and CYP26A1) eventually leading to the formation of Forebrain / Midbrain neurectoderm (PAX6,OTX2 and DLK1).

summary:
In Homo sapiens, rostral presumptive neuroectoderm cells express HESX1, SHISA2, and CYP26A1, and forebrain/midbrain neurectoderm cells express PAX6, OTX2, and DLK1.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:30ce78eecb8b2e6cab37
claim_id: claim:30ce78eecb8b2e6cab37
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
summary: In Homo sapiens, caudal presumptive neurectoderm cells express HOXA1, CRABP2, and FST.
span_literal:
Similarly, late caudal epiblasts differentiate into caudal presumptive neurectoderm (HOXA1,CRABP2 and FST) eventually propagating towards hindbrain neurectoderm (SOX1,HOXA2 and CRABP2).


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:839a4aa17ea2e4ee5848
claim_id: claim:839a4aa17ea2e4ee5848
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
PAX6 marks the dorsal territory in regions A and B, while NKX2-1 marks the ventral territory in regions D and E.

summary:
In Homo sapiens, PAX6 marks the dorsal telencephalic territory and NKX2-1 marks the ventral telencephalic territory.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:916c14fc0fad0406b9da
claim_id: claim:916c14fc0fad0406b9da
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
We found the telencephalic marker FOXG1 to be enriched in the vTel cultures while the diencephalic marker FOXD1 was upregulated in the vDienc cultures, confirming the regional patterning of the cultures

summary:
In Homo sapiens, FOXG1 is a telencephalic marker enriched in ventral telencephalic cells, while FOXD1 is a diencephalic marker upregulated in ventral diencephalic cells.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:5ff6596bf1069aedc68c
claim_id: claim:5ff6596bf1069aedc68c
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
We identified HESX1, SHISA2, FEZF1, LHX5 and CYP26A1 as pre-neuralising factors specifically expressed in the rostral cells.

summary:
In Homo sapiens, HESX1, SHISA2, FEZF1, LHX5, and CYP26A1 are pre-neuralising factors specifically expressed in rostral cells.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:fff1b8d8ee534c4409fc
claim_id: claim:fff1b8d8ee534c4409fc
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
summary: In Homo sapiens, pre-neuralised caudal cells express high levels of CRABP2.
span_literal:
pre-neuralised caudal cells express high levels of CRABP2; a transport protein which facilitates RA transfer and binding to its nuclear receptor complex


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:7c2684840337861e930f
claim_id: claim:7c2684840337861e930f
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal: including the co-expression of FGF8, 17, and 19 in the midbrain and MHB clusters
summary:
In Homo sapiens, midbrain and midbrain-hindbrain boundary clusters co-express FGF8, FGF17, and FGF19.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:ef28e9f8640d1d2cd67d
claim_id: claim:ef28e9f8640d1d2cd67d
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal: localized expression patterns of WNT5A, BMP1, SHH, SLIT1/2/3, and PDGFC in the floor plate clusters
summary:
In Homo sapiens, floor plate cells show localized expression of WNT5A, BMP1, SHH, SLIT1, SLIT2, SLIT3, and PDGFC.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:c62992c6cab3b8903c83
claim_id: claim:c62992c6cab3b8903c83
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal: we observed distinct expression of WNT7A, WNT7B, RSPO1, RSPO2, and RSPO3 in the Forebrain cluster
summary:
In Homo sapiens, the forebrain cluster shows distinct expression of WNT7A, WNT7B, RSPO1, RSPO2, and RSPO3.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:a1b0d730d6bb73b87f38
claim_id: claim:a1b0d730d6bb73b87f38
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
Temporal mapping of gene expression patterns in the C-region of the R/C MiSTR (i.e. the region harbouring the presumptive MHB) confirmed PAX2 as the earliest marker of the presumptive MHB at d5, followed by expression of PAX5, PAX8, EN1 and FGF8 at day 5-9 and subsequently by WNT1, FGF17, EN1 and EN2 marking the mature MHB structure at day 14

summary:
In Homo sapiens, PAX2 is the earliest marker of the presumptive midbrain-hindbrain boundary, followed by PAX5, PAX8, EN1, and FGF8, and subsequently WNT1, FGF17, EN1, and EN2 marking the mature midbrain-hindbrain boundary.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:c4a076fb48e5714f8b4f
claim_id: claim:c4a076fb48e5714f8b4f
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
The early OTX2+ population showed a trajectory towards the rostral MHB and subsequently towards midbrain and thalamic neurons. The early GBX2+ population showed a trajectory towards the caudal MHB and subsequently towards hindbrain neurons

summary:
In Homo sapiens, the early OTX2-positive population gives rise to rostral midbrain-hindbrain boundary cells, while the early GBX2-positive population gives rise to caudal midbrain-hindbrain boundary cells.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:d24e8df8ba8cae849706
claim_id: claim:d24e8df8ba8cae849706
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
The early OTX2+ population showed a trajectory towards the rostral MHB and subsequently towards midbrain and thalamic neurons. The early GBX2+ population showed a trajectory towards the caudal MHB and subsequently towards hindbrain neurons

summary:
In Homo sapiens, the early GBX2-positive population gives rise to caudal midbrain-hindbrain boundary cells.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:18f20e3099edfdbdb93a
claim_id: claim:18f20e3099edfdbdb93a
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal: OTX2 was the top transcription factor regulon identified in the rMHB cluster
summary:
In Homo sapiens, OTX2 is the top transcription factor regulon identified in the rostral midbrain-hindbrain boundary cluster.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:d42d3eee73a5c9e6c231
claim_id: claim:d42d3eee73a5c9e6c231
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal: we identified MSX1 and MSX2 as key transcription factors in the cMHB population
summary:
In Homo sapiens, MSX1 and MSX2 are key transcription factors in the caudal midbrain-hindbrain boundary population.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:643ab21ee709d1893d72
claim_id: claim:643ab21ee709d1893d72
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
emergence of segregated rostral MHB (OTX2+/WNT1+) and caudal MHB (GBX2+/FGF8+/FGF17+) populations at day 9, with EN1 and PAX8 being expressed on both sides of the boundary

summary:
In Homo sapiens, the rostral midbrain-hindbrain boundary is marked by OTX2 and WNT1, while the caudal midbrain-hindbrain boundary is marked by GBX2, FGF8, and FGF17, with EN1 and PAX8 expressed on both sides.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:bf1d4d0da88a3c347230
claim_id: claim:bf1d4d0da88a3c347230
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
emergence of segregated rostral MHB (OTX2+/WNT1+) and caudal MHB (GBX2+/FGF8+/FGF17+) populations at day 9, with EN1 and PAX8 being expressed on both sides of the boundary

summary:
In Homo sapiens, the caudal midbrain-hindbrain boundary is marked by GBX2, FGF8, and FGF17, with EN1 and PAX8 expressed on both sides of the boundary.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:ca6f1fab1f371d15415f
claim_id: claim:ca6f1fab1f371d15415f
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
Cell clusters were annotated using the expression of marker proteins: CD19 and CD20 for B cells, CD16 and CD56 for NK cells, CD14 and CD11c for CD14+ monocytes, CD3 and CD4 for CD4+ T cells, CD3 and CD8a for CD8+ T cells, and CD45RA and CD45RO for naïve and memory T cells, respectively

summary:
In Homo sapiens peripheral blood mononuclear cells, B cells are marked by CD19 and CD20 protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:4d126fee2c562788ec22
claim_id: claim:4d126fee2c562788ec22
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
Cell clusters were annotated using the expression of marker proteins: CD19 and CD20 for B cells, CD16 and CD56 for NK cells, CD14 and CD11c for CD14+ monocytes, CD3 and CD4 for CD4+ T cells, CD3 and CD8a for CD8+ T cells, and CD45RA and CD45RO for naïve and memory T cells, respectively

summary:
In Homo sapiens peripheral blood mononuclear cells, natural killer cells are marked by CD16 and CD56 protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:d3d0c32f62186ea89ae8
claim_id: claim:d3d0c32f62186ea89ae8
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
Cell clusters were annotated using the expression of marker proteins: CD19 and CD20 for B cells, CD16 and CD56 for NK cells, CD14 and CD11c for CD14+ monocytes, CD3 and CD4 for CD4+ T cells, CD3 and CD8a for CD8+ T cells, and CD45RA and CD45RO for naïve and memory T cells, respectively

summary:
In Homo sapiens peripheral blood mononuclear cells, CD14-positive monocytes are marked by CD14 and CD11c protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:25a348088dc0600af0a5
claim_id: claim:25a348088dc0600af0a5
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
summary:
In Homo sapiens peripheral blood mononuclear cells, CD4-positive T cells are marked by CD3 and CD4 protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:3a40806bce41404c3782
claim_id: claim:3a40806bce41404c3782
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
summary:
In Homo sapiens peripheral blood mononuclear cells, CD8-positive T cells are marked by CD3 and CD8a protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:809baab465ccb9bbb0be
claim_id: claim:809baab465ccb9bbb0be
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
summary:
In Homo sapiens peripheral blood mononuclear cells, naive T cells are marked by CD45RA protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:0c33ac0e66d1b14f6f77
claim_id: claim:0c33ac0e66d1b14f6f77
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
summary:
In Homo sapiens peripheral blood mononuclear cells, memory T cells are marked by CD45RO protein expression.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:0d02bdaebed91e6b8be1
claim_id: claim:0d02bdaebed91e6b8be1
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
Cluster 3 cells (Fig. 2D, 2E) expressed chemokine receptor CCR6 (indicating tissue-specific homing properties) and C-type lectin receptor CD161 (KLRB1) and CD127 (IL7R) on their surface constituted ~9.9% of CD4+ T cells

summary:
In Homo sapiens, CD4-positive T cell cluster 3 (memory cells including T helper 17 cells) expresses CCR6, KLRB1 (CD161), and IL7R (CD127).


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:929d72e96bcbdd6e1bdf
claim_id: claim:929d72e96bcbdd6e1bdf
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal: Cluster 5 cells expressed marker genes of MAIT cells (RORC, KLRB1, and CCR6 (33))
summary:
In Homo sapiens, mucosal-associated invariant T cells express the marker genes RORC, KLRB1, and CCR6.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:e31741f7addbf1882b45
claim_id: claim:e31741f7addbf1882b45
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
clusters 2, 3, and 6 cells were mostly from the baseline condition and enriched for KLF2, which encodes a transcription factor important for NK cell survival

summary:
In Homo sapiens, resting natural killer cells are enriched for KLF2, a transcription factor important for natural killer cell survival.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:706bdce9a1788c3a7616
claim_id: claim:706bdce9a1788c3a7616
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
Cluster 0 cells expressed genes associated with age-associated B cells (ABC) (38–40) and DN2 cells (41) (e.g., TLR7, PRDM1, TGAX/CD11c and TBX21/T-bet).

summary:
In Homo sapiens, activated B cell cluster 0 expressed genes associated with age-associated B cells and double negative 2 cells, including TLR7, PRDM1, ITGAX/CD11c, and TBX21/T-bet.


claim_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54:claim:8feceb860167cff57dcd
claim_id: claim:8feceb860167cff57dcd
paper_key: biorxiv:9f9eded3-6d6e-1014-996d-af8f6f192d54
span_literal:
Cluster 3 cells expressed additional markers associated with DN2 cells, such as FCRL5 and TRAF5, but lacked the expression of TLR7, ITGAX, and TBX21.

summary:
In Homo sapiens, activated B cell cluster 3 expressed FCRL5 and TRAF5 (markers of double negative 2 cells) but lacked expression of TLR7, ITGAX, and TBX21.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:2eed10a1a0ca5253309c
claim_id: claim:2eed10a1a0ca5253309c
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
Both clusters contained cells expressing lytic and latent KSHV genes (Figures 3, S5) and both clusters express endothelial markers PECAM1(CD31), PDPN, LYVE-1, and CD36 (Figure S6).

summary:
In Homo sapiens Kaposi sarcoma, both KSHV-infected cell clusters express the endothelial cell markers PECAM1, PDPN, LYVE1, and CD36.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:770475d9e66aeb0af8a1
claim_id: claim:770475d9e66aeb0af8a1
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
In the CD34-cluster, housekeeping genes were suppressed while cellular proliferation factors were enriched including EP300 and CREBBP, along with factors like DTX1, DTX4, HEY1, and CTNNB1 that regulate the NOTCH and WNT signaling pathways (Figure 4).

summary:
In Homo sapiens Kaposi sarcoma, the CD34-negative lymphatic endothelial cell cluster is enriched in EP300, CREBBP, DTX1, DTX4, HEY1, and CTNNB1.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:3f0ded2bc02f3c67e20d
claim_id: claim:3f0ded2bc02f3c67e20d
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
The CD34+ cluster of KSHV expressing cells exhibited high expression of GAPDH and ACTB as well as CD90, PROX1, CD36, PDPN, LYVE1, and the viral gene K5 (Figure S5-S8).

summary:
In Homo sapiens Kaposi sarcoma, the CD34-positive KSHV-infected vascular endothelial cell cluster exhibits high expression of GAPDH, ACTB, CD90, PROX1, CD36, PDPN, and LYVE1.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:3d9ea916397f858b9ee6
claim_id: claim:3d9ea916397f858b9ee6
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
CD34+ vascular endothelial cells can be distinguished from CD34+ telocytes by the expression of CD31+, PDPN+, and LYVE+, and the absence of PDGFRA (19).

summary:
In Homo sapiens, CD34-positive vascular endothelial cells can be distinguished from CD34-positive telocytes by expression of CD31, PDPN, and LYVE1, and the absence of PDGFRA.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:9554676cb76d79da5d58
claim_id: claim:9554676cb76d79da5d58
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
In addition to viral genes, several cellular genes were commonly expressed in the KSHV-positive cells including prospero homeobox protein 1 (PROX1), mannose receptor C-type 1 (MRC1; CD206), fms-related tyrosine kinase 4 (FLT4), and Kir2.1 inward-rectifier potassium channel (KCNJ2) (Table S1).

summary:
In Homo sapiens Kaposi sarcoma, KSHV-positive cells commonly express prospero homeobox protein 1 (PROX1), mannose receptor C-type 1 (MRC1), fms-related tyrosine kinase 4 (FLT4), and Kir2.1 inward-rectifier potassium channel (KCNJ2).


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:0b1172860be024fe0a6b
claim_id: claim:0b1172860be024fe0a6b
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
Differential expression analysis revealed 1,022 significantly enriched genes in KSHV+ cells in Cluster 15 cells including several voltage gated ion channel (VGSC) genes with SCN9A as a top biomarker candidate along with KSHV genes LANA and Kaposin (Figure 5, Table S1).

summary:
In Homo sapiens Kaposi sarcoma, KSHV-positive cells show SCN9A as a top cellular biomarker candidate.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:23b88724b05d1cfb54fe
claim_id: claim:23b88724b05d1cfb54fe
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
The KSHV genes LANA and K12 were the top viral biomarkers and the voltage-gated sodium channel SCN9A (Nav1.7) emerged as the top, non KSHV biomarker.

summary:
In Homo sapiens Kaposi sarcoma, the voltage-gated sodium channel SCN9A emerged as the top non-KSHV biomarker of KSHV-positive cells.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:c2b4cdaa79edb5edd399
claim_id: claim:c2b4cdaa79edb5edd399
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
However the KSHV+ clusters diverged dramatically into CD34-lymphatic endothelial cells (black cluster) and CD34+ vascular endothelial cells (red cluster).

summary:
In Homo sapiens Kaposi sarcoma, KSHV-positive clusters diverge into CD34-negative lymphatic endothelial cells and CD34-positive vascular endothelial cells.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:3c01cfb9523c8e0779f9
claim_id: claim:3c01cfb9523c8e0779f9
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
The CD34+ cluster was enriched in CD90 and S100A6 and genes related to angiogenesis and production of extracellular vesicles.

summary:
In Homo sapiens Kaposi sarcoma, the CD34-positive vascular endothelial cell cluster is enriched in CD90 and S100A6.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:3ae88be96cc228cd9ce2
claim_id: claim:3ae88be96cc228cd9ce2
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
summary: In Homo sapiens Kaposi sarcoma tumors, macrophages express IL10 and IL1B.
span_literal:
In samples in which KSHV+ cells were rare, macrophages expressing IL10 and IL1B, and CD8+ T lymphocytes were significantly more abundant than in samples in which KSHV+ cells were prevalent (Figure 6B).


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:3a431db00b9b35760e89
claim_id: claim:3a431db00b9b35760e89
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
Of the transcripts associated with the inflammatory subtype, we detected cell migration-inducing and hyaluronan-binding protein (KIAA1199; CEMIP) expression in all KS tumor samples, in both CD34+ and CD34-clusters.

summary:
In Homo sapiens Kaposi sarcoma, cell migration-inducing and hyaluronan-binding protein (CEMIP) is expressed in both CD34-positive and CD34-negative KSHV-infected cell clusters.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:a92d644316e1554138b2
claim_id: claim:a92d644316e1554138b2
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal: LY6H was enriched in CD34+ clusters.
summary:
In Homo sapiens Kaposi sarcoma, LY6H is enriched in CD34-positive KSHV-infected vascular endothelial cells.


claim_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f:claim:82a4555bcbf7d737c662
claim_id: claim:82a4555bcbf7d737c662
paper_key: biorxiv:a0900ed8-7609-1014-846c-dd411913591f
span_literal:
Additionally, the proliferative subtype transcript annexin A8-like 1 (ANXA8L1) was detected in non-infected epithelial cells and keratinocytes in all of our samples.

summary:
In Homo sapiens Kaposi sarcoma, annexin A8-like 1 (ANXA8L1) is expressed in non-infected epithelial cells and keratinocytes.


claim_key: biorxiv:a350e679-6eb1-1014-96d5-c0b9bbcd470a:claim:25f7a8a15aeffe61fcc9
claim_id: claim:25f7a8a15aeffe61fcc9
paper_key: biorxiv:a350e679-6eb1-1014-96d5-c0b9bbcd470a
span_literal: MUC2 and SPINK4
summary:
In Homo sapiens pancreatic cancer, MUC2 and SPINK4 are positive markers of resistance to gemcitabine plus nab-paclitaxel (AG) in pancreatic ductal adenocarcinoma.


claim_key: biorxiv:a3afea1b-6cbb-1014-91c3-a771a94d8f08:claim:ba307e119814ef4ca620
claim_id: claim:ba307e119814ef4ca620
paper_key: biorxiv:a3afea1b-6cbb-1014-91c3-a771a94d8f08
span_literal:
Alveolar type 2 cells within single cell suspensions of enzymatically digested cryobanked distal lung tissue retained expression of the pan-epithelial marker CD326 and the AT2 cell surface antigen recognized by monoclonal antibody HTII-280, allowing antibody-mediated enrichment and downstream analysis.

summary:
In Homo sapiens, alveolar type 2 cells express the pan-epithelial marker CD326 (EPCAM) and the alveolar type 2 cell surface antigen recognized by monoclonal antibody HTII-280.


claim_key: biorxiv:a3afea1b-6cbb-1014-91c3-a771a94d8f08:claim:c5185c90996542650f95
claim_id: claim:c5185c90996542650f95
paper_key: biorxiv:a3afea1b-6cbb-1014-91c3-a771a94d8f08
summary: In Homo sapiens, epithelial cells are positively selected by the pan-epithelial cell marker CD326.
span_literal:
Further FACS depletion of cells staining for either CD45, CD235a and CD31, elimination of dead cells staining for DAPI, and positive selection for the pan-epithelial cell marker CD326, led to highly enriched epithelial cell fraction.


claim_key: biorxiv:a3afea1b-6cbb-1014-91c3-a771a94d8f08:claim:efbf00b6eac0fe272b11
claim_id: claim:efbf00b6eac0fe272b11
paper_key: biorxiv:a3afea1b-6cbb-1014-91c3-a771a94d8f08
span_literal:
Epithelial cells were further subdivided based upon their staining with the AT2-specific monoclonal antibody, HTII-280[41].

summary:
In Homo sapiens, alveolar type 2 cells are identified by the alveolar type 2-specific monoclonal antibody HTII-280.


claim_key: biorxiv:a4dfbfd9-7f07-1014-9596-9cebe6ee6cbb:claim:adbd3425ef64c40652f9
claim_id: claim:adbd3425ef64c40652f9
paper_key: biorxiv:a4dfbfd9-7f07-1014-9596-9cebe6ee6cbb
span_literal:
LDHB and SELL were highly expressed in CD4 naïve T cells, whereas CD4 EM cells were characterized by high expression levels of HLA-DRA and GZMK.

summary:
In Homo sapiens, CD4 naïve T cells are marked by high expression of LDHB and SELL, whereas CD4 effector memory T cells are characterized by high expression of HLA-DRA and GZMK.


claim_key: biorxiv:a4dfbfd9-7f07-1014-9596-9cebe6ee6cbb:claim:b225706bf5c22ab3f262
claim_id: claim:b225706bf5c22ab3f262
paper_key: biorxiv:a4dfbfd9-7f07-1014-9596-9cebe6ee6cbb
span_literal:
LDHB and SELL were highly expressed in CD4 naïve T cells, whereas CD4 EM cells were characterized by high expression levels of HLA-DRA and GZMK.

summary:
In Homo sapiens, CD4 effector memory T cells are characterized by high expression of HLA-DRA and GZMK, in contrast to CD4 naïve T cells.


claim_key: biorxiv:a4dfbfd9-7f07-1014-9596-9cebe6ee6cbb:claim:df6135984df448fd0f5a
claim_id: claim:df6135984df448fd0f5a
paper_key: biorxiv:a4dfbfd9-7f07-1014-9596-9cebe6ee6cbb
summary: In Homo sapiens, T helper 2 cells were identified based on the expression of STAT6 and GATA3.
span_literal:
Among the activated CD4+ T cells, Th2 cells were identified based on the expression of STAT6 and GATA3 and Th17 cells were annotated based on the expression levels of RORA and STAT3.


claim_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56:claim:a8736f3eda1db8503f49
claim_id: claim:a8736f3eda1db8503f49
paper_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56
span_literal:
downregulation of the endothelial tip cell marker gene ESM1 and upregulation of the endothelial-to-mesenchymal transition (EndMT) marker genes S100A4 and COL3A1 provide further evidence for the impact of EndMT on CCM pathogenesis

summary:
In Homo sapiens blood vessel organoids, ESM1 is a positive marker of endothelial tip cells, while S100A4 and COL3A1 are positive markers of endothelial-to-mesenchymal transition.


claim_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56:claim:a096f55ca5dfb0c443aa
claim_id: claim:a096f55ca5dfb0c443aa
paper_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56
span_literal:
downregulation of the endothelial tip cell marker gene ESM1 and upregulation of the endothelial-to-mesenchymal transition (EndMT) marker genes S100A4 and COL3A1 provide further evidence for the impact of EndMT on CCM pathogenesis

summary:
In Homo sapiens blood vessel organoids, S100A4 and COL3A1 are positive markers of endothelial-to-mesenchymal transition cells.


claim_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56:claim:e19343cef6e2ae1c3c6e
claim_id: claim:e19343cef6e2ae1c3c6e
paper_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56
span_literal:
One of the consistently upregulated genes in EC cluster 9 was KLF2, highlighting the pivotal role of MEKK3-KLF2/4 signaling in CCM disease

summary:
In Homo sapiens blood vessel organoids, KLF2 is consistently upregulated in endothelial cell cluster 9 across all three CCM knockout genotypes.


claim_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56:claim:2171e15b03db659b0aba
claim_id: claim:2171e15b03db659b0aba
paper_key: biorxiv:a54482c5-73e0-1014-b3b0-b8dec8f62e56
span_literal:
Among the most up- or downregulated genes in this fibroblast cell cluster (Fig. 6A and S3) were EBF1, COL3A1, and DLK1, which were similarly deregulated in all three KO genotypes

summary:
In Homo sapiens blood vessel organoids, EBF1, COL3A1, and DLK1 are among the most differentially expressed genes in the fibroblast cell cluster across all three CCM knockout genotypes.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:81d1413dfac9391adff0
claim_id: claim:81d1413dfac9391adff0
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
we used nephroblastoma overexpressed/cysteine-rich protein 61/connective tissue growth factor/nephroblastoma overexpressed gene-3 (NOV, also known as CCN3) as a marker for the DZ, and sulfotransferase 2A1 (SULT2A1) as a marker for the FZ

summary:
In Homo sapiens, NOV (also known as CCN3) is used as a positive marker for the definitive zone of the adrenal cortex, and SULT2A1 is used as a positive marker for the fetal zone of the adrenal cortex.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:fb496ba25e3fe3f8bf74
claim_id: claim:fb496ba25e3fe3f8bf74
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
we used nephroblastoma overexpressed/cysteine-rich protein 61/connective tissue growth factor/nephroblastoma overexpressed gene-3 (NOV, also known as CCN3) as a marker for the DZ, and sulfotransferase 2A1 (SULT2A1) as a marker for the FZ

summary:
In Homo sapiens, SULT2A1 (sulfotransferase 2A1) is used as a positive marker for the fetal zone of the adrenal cortex.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:70d0e1e1b8e6ba0395f9
claim_id: claim:70d0e1e1b8e6ba0395f9
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
In our scRNA-seq dataset, HOPX was consistently one of the most differentially-expressed markers of the DZ compared to the FZ in all ages studied

summary:
In Homo sapiens, HOPX is a positive marker of the definitive zone compared to the fetal zone in the developing adrenal cortex.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:0f7475327929637f1ae2
claim_id: claim:0f7475327929637f1ae2
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
Across all stages, cells of the FZ region showed high expression of genes encoding the key enzymes needed for DHEA synthesis (STAR, CYP11A1, CYP17A1, POR, CYB5A) as well as of SULT2A1 (encoding sulfotransferase 2A1), which is required for sulfation of DHEA to DHEA-S and protects the developing fetus from androgen exposure

summary:
In Homo sapiens, fetal zone cells of the adrenal cortex show high expression of STAR, CYP11A1, CYP17A1, POR, CYB5A, and SULT2A1.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:49f0f2269e53d4923a7f
claim_id: claim:49f0f2269e53d4923a7f
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
As expected, HSD3B2 expression was low in the FZ during development, resulting in the likely shuttling of steroid precursors (e.g. pregnenolone) into the androgen pathway.

summary:
In Homo sapiens, HSD3B2 expression is low in fetal zone cells of the adrenal cortex during development.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:068c8241b07f66ed6b58
claim_id: claim:068c8241b07f66ed6b58
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
The high expression of STAR and CYP11A1 in the FZ cluster was mirrored by high expression of the ACTH receptor and its accessory protein (MRAP) suggesting not only that the FZ has the capacity to be highly biosynthetically active but also that FZ DHEA synthesis may be ACTH-dependent.

summary:
In Homo sapiens, fetal zone cells of the adrenal cortex show high expression of STAR, CYP11A1, MC2R (the adrenocorticotropic hormone receptor), and MRAP (melanocortin 2 receptor accessory protein).


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:b9f0e1b7e25850fc98ef
claim_id: claim:b9f0e1b7e25850fc98ef
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
However, by 19wpc, HOPX expression was relatively reduced (Fig.4b, Fig. 5f) and localized within a zona glomerulosa-like cluster that also expressed HSD3B2, CYP11B2, and the orphan nuclear receptors NR4A1 (NURR77)/NR4A2 (NUR1)

summary:
In Homo sapiens, the zona glomerulosa-like cluster of the adrenal cortex at 19 weeks post conception expresses HOPX, HSD3B2, CYP11B2, NR4A1, and NR4A2.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:a714b177d21f0b5e5b09
claim_id: claim:a714b177d21f0b5e5b09
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
HOPX is emerging as a key embryonic and adult stem cell marker involved in stem cell maintenance/quiescence

summary:
In Homo sapiens, HOPX is a positive marker of stem cells involved in stem cell maintenance and quiescence.


claim_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474:claim:c2d127a5d0ac22e06133
claim_id: claim:c2d127a5d0ac22e06133
paper_key: biorxiv:a63583e3-6c7b-1014-a201-b82bec671474
span_literal:
Of note, an emergent population of NOV positive/HOPX negative cells was identified by scRNA seq at 19wpc, which was located just central to the peripheral HOPX positive cells on dual-labeled IHC

summary:
In Homo sapiens, an emergent population of NOV-positive and HOPX-negative cells was identified in the adrenal cortex at 19 weeks post conception, located central to the peripheral HOPX-positive definitive zone cells.


claim_key: biorxiv:a6f25093-6d09-1014-a4b3-a2ea051baaac:claim:19983442fe71864ece46
claim_id: claim:19983442fe71864ece46
paper_key: biorxiv:a6f25093-6d09-1014-a4b3-a2ea051baaac
span_literal:
This analysis revealed six genes— UNC5B, TLR3, PCDH19, PROCR, SLITRK6, and SEMA6B —that were consistently enriched in the high-shift subgroup across all three patient datasets

summary:
In Homo sapiens, UNC5B, TLR3, PCDH19, PROCR, SLITRK6, and SEMA6B are surface markers enriched in pre-treatment high phenotypic shift cells compared to low phenotypic shift cells in hormone receptor positive metastatic breast cancer patients treated with palbociclib.


claim_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd:claim:56ad2b3e0e2582584429
claim_id: claim:56ad2b3e0e2582584429
paper_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd
span_literal: T cells expressed CD3D, CD8A, and CD4 genes.
summary:
In Homo sapiens nasopharyngeal carcinoma single-cell RNA sequencing data, T cells expressed CD3D, CD8A, and CD4 genes.


claim_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd:claim:0fc7c717e6f8b0d3275e
claim_id: claim:0fc7c717e6f8b0d3275e
paper_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd
span_literal: Myeloid cells expressed C1QB, LYZ, and AIF1 genes.
summary:
In Homo sapiens nasopharyngeal carcinoma single-cell RNA sequencing data, myeloid cells expressed C1QB, LYZ, and AIF1 genes.


claim_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd:claim:2f694ccdd3358622b190
claim_id: claim:2f694ccdd3358622b190
paper_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd
span_literal: B cells expressed MS4A1 and CD79A genes.
summary:
In Homo sapiens nasopharyngeal carcinoma single-cell RNA sequencing data, B cells expressed MS4A1 and CD79A genes.


claim_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd:claim:ae1ea7cc53b88b0d803f
claim_id: claim:ae1ea7cc53b88b0d803f
paper_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd
span_literal: Epithelial cells specifically expressed KRT5 and EPCAM genes.
summary:
In Homo sapiens nasopharyngeal carcinoma single-cell RNA sequencing data, epithelial cells specifically expressed KRT5 and EPCAM genes.


claim_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd:claim:1678d6042c2c2ce620f6
claim_id: claim:1678d6042c2c2ce620f6
paper_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd
span_literal: Fibroblasts expressed DCN and COL1A1 genes.
summary:
In Homo sapiens nasopharyngeal carcinoma single-cell RNA sequencing data, fibroblasts expressed DCN and COL1A1 genes.


claim_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd:claim:6758f95102cdc0c28f8f
claim_id: claim:6758f95102cdc0c28f8f
paper_key: biorxiv:a6ffed23-717d-1014-ae02-d2e67f78dddd
span_literal: Mast cells expressed CPA3, TPSAB1, and MS4A2 as marker genes.
summary:
In Homo sapiens nasopharyngeal carcinoma single-cell RNA sequencing data, mast cells expressed CPA3, TPSAB1, and MS4A2 as marker genes.


claim_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d:claim:b48d8a44f7fb4149a950
claim_id: claim:b48d8a44f7fb4149a950
paper_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d
span_literal:
These included RPE65 for RPE cells, FBLN1 for fibroblasts, TYR for melanocytes, FLT1 for vascular endothelial cells, F13A1 for macrophages, CD247 for T cells, SCN7A for Schwann cells, ACTA2 for pericytes and smooth muscle cells, and BANK1 for B cells (Figure 1D).

summary:
In Homo sapiens retinal pigment epithelium and choroid, RPE65 is a marker gene for retinal pigment epithelium cells.


claim_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d:claim:b6df5b952e26f8090b86
claim_id: claim:b6df5b952e26f8090b86
paper_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d
summary:
In Homo sapiens retinal pigment epithelium and choroid, FLT1 is a marker gene for vascular endothelial cells.


claim_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d:claim:a3f25a9d8fc568df6c6c
claim_id: claim:a3f25a9d8fc568df6c6c
paper_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d
summary:
In Homo sapiens retinal pigment epithelium and choroid, ACTA2 is a marker gene for pericytes and smooth muscle cells.


claim_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d:claim:7f304210b709946baf4a
claim_id: claim:7f304210b709946baf4a
paper_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d
span_literal:
Comparing these two clusters revealed 18 differentially expressed genes (Data S3), including higher expression of SULF1 and WFDC1 in macular RPE and KCNIP4 and VEPH1 in peripheral RPE as previously reported.23

summary:
In Homo sapiens, macular retinal pigment epithelium shows higher expression of SULF1 and WFDC1 compared to peripheral retinal pigment epithelium.


claim_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d:claim:d75f3787e39f78b3d162
claim_id: claim:d75f3787e39f78b3d162
paper_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d
span_literal:
Comparing these two clusters revealed 18 differentially expressed genes (Data S3), including higher expression of SULF1 and WFDC1 in macular RPE and KCNIP4 and VEPH1 in peripheral RPE as previously reported.23

summary:
In Homo sapiens, peripheral retinal pigment epithelium shows higher expression of KCNIP4 and VEPH1 compared to macular retinal pigment epithelium.


claim_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d:claim:bcf8cd1e4bc373e9853e
claim_id: claim:bcf8cd1e4bc373e9853e
paper_key: biorxiv:a83150af-6e3c-1014-8107-a71f7784ca4d
summary: In Homo sapiens, retinal pigment epithelium cells show specific expression of SLC16A8 and TSPAN10.
span_literal:
scRNA-seq demonstrated RPE-specific expression of SLC16A8 and TSPAN10 and glia-specific expression of APOE, in line with prior reports.46,47


claim_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a:claim:3214e53f3fce846c4d40
claim_id: claim:3214e53f3fce846c4d40
paper_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a
span_literal:
Notably, analysis of NKX6-2 in our cohort revealed significant enrichment in Gastric IPMN compared to Intestinal and Pancreaticobiliary subtypes as well as in LGD compared to HGD

summary:
In Homo sapiens, NKX6-2 is enriched in gastric intraductal papillary mucinous neoplasm cells compared to intestinal and pancreaticobiliary subtypes.


claim_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a:claim:b617b5a695767f64dcb2
claim_id: claim:b617b5a695767f64dcb2
paper_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a
span_literal: This work also identified HOXB3 and ZNF117 as markers for LGD.
summary:
In Homo sapiens, HOXB3 and ZNF117 were identified as markers for low-grade dysplasia intraductal papillary mucinous neoplasm cells.


claim_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a:claim:2ca57741a58998663583
claim_id: claim:2ca57741a58998663583
paper_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a
span_literal:
Separating samples based on dysplasia, the authors identified gastric isthmus-pit (GIP) phenotype with high NKX6-2 in LGD IPMN with associated plasma cell infiltrates, while elevated CLDN4 and CEACAM6 in HGD IPMN and invasive carcinoma.

summary:
In Homo sapiens, NKX6-2 is highly expressed in low-grade dysplasia intraductal papillary mucinous neoplasm cells with a gastric isthmus-pit phenotype.


claim_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a:claim:878f50ba9589a38e15c7
claim_id: claim:878f50ba9589a38e15c7
paper_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a
span_literal:
Separating samples based on dysplasia, the authors identified gastric isthmus-pit (GIP) phenotype with high NKX6-2 in LGD IPMN with associated plasma cell infiltrates, while elevated CLDN4 and CEACAM6 in HGD IPMN and invasive carcinoma.

summary:
In Homo sapiens, CLDN4 and CEACAM6 are elevated in high-grade dysplasia intraductal papillary mucinous neoplasm cells and invasive carcinoma.


claim_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a:claim:3cd8f0e9ddfe387c8394
claim_id: claim:3cd8f0e9ddfe387c8394
paper_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a
span_literal:
Loss of NKX6-2 was also associated with increased epithelial-mesenchymal transition (EMT) markers consistent with cell state changes toward invasive cancer.

summary:
In Homo sapiens, loss of NKX6-2 is associated with epithelial-mesenchymal transition in intraductal papillary mucinous neoplasm cells progressing toward invasive cancer.


claim_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a:claim:84c9ab130df3eedcdcec
claim_id: claim:84c9ab130df3eedcdcec
paper_key: biorxiv:a9567cc0-6e50-1014-9a45-a24404db0d1a
span_literal:
Notable features include a striking absence of CD8+ cytotoxic lymphocytes (CTLs) and early infiltration of Foxp3+ T-regulatory (T-reg) cells, macrophages, and myeloid-derived suppressor cells (MDSCs) which are considered tumor-promoting immune cells.

summary:
In Homo sapiens, Foxp3 is a positive marker of T-regulatory cells in the pancreatic intraepithelial neoplasia microenvironment.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:8018f62dff1d87fc4fab
claim_id: claim:8018f62dff1d87fc4fab
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
Moreover, binomial differential expression was performed to detect differentially expressed markers for each cluster. The metastasis associated lung adenocarcinoma transcript-1 (MALAT1) was detected to be a marker for cluster 4.

summary:
In Homo sapiens, metastasis associated lung adenocarcinoma transcript 1 (MALAT1) was detected as a positive marker for circulating tumor cell cluster 4 in breast cancer.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:01c5787cf37cafe5719e
claim_id: claim:01c5787cf37cafe5719e
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
Based on the binomial differential expression, cells in cluster 3 express significantly less DGKD and PTCRA but significantly more KRT18 (Figure 4d-4f).

summary:
In Homo sapiens, circulating tumor cell cluster 3 expresses significantly less diacylglycerol kinase delta (DGKD) and pre T cell antigen receptor alpha (PTCRA) but significantly more keratin 18 (KRT18).


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:320a1cff5c8c7b3affad
claim_id: claim:320a1cff5c8c7b3affad
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
The generated RPART decision tree (Figure 3b) included four decision nodes: MALAT1, SYNE2, SLC25A39 and CFLAR.

summary:
In Homo sapiens, the RPART decision tree for predicting circulating tumor cell cluster 1 versus cluster 4 identity included MALAT1, SYNE2, SLC25A39, and CFLAR as decision nodes.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:2f686c7276f07e3fedaf
claim_id: claim:2f686c7276f07e3fedaf
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
The network of the down-regulated genes in cluster 2 (Figure 7b) highlighted thymidylate synthetase (TYMS) as a hub gene in addition to a set of highly connected genes involved in DNA synthesis and replication.

summary:
In Homo sapiens, thymidylate synthetase (TYMS) was highlighted as a hub gene among down-regulated genes in myxoid liposarcoma cell cluster 2.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:425700d0814ba6dffee3
claim_id: claim:425700d0814ba6dffee3
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal: TYMS is up-regulated in cluster 3 (fig 7c).
summary:
In Homo sapiens, thymidylate synthetase (TYMS) is up-regulated in myxoid liposarcoma cell cluster 3.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:48c23c1a6a200bb21b85
claim_id: claim:48c23c1a6a200bb21b85
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
The generated RPART decision tree (fig 7d) included two decision nodes: Aurora Kinase A (AURKA) and Cell Division Cycle 27 (CDC27).

summary:
In Homo sapiens, the RPART decision tree for predicting myxoid liposarcoma cell cluster 2 versus cluster 3 identity included Aurora Kinase A (AURKA) and Cell Division Cycle 27 (CDC27) as decision nodes.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:b5cfd1399578cd80f7c3
claim_id: claim:b5cfd1399578cd80f7c3
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
The networking analysis outcome (Supplementary Table. S1) nominated a panel of 18 hub genes, including PLK1, CDC20, KIF2C, BUB1, AURKB, and PTTG1 as potential biomarkers for cluster 2 cells.

summary:
In Homo sapiens, PLK1, CDC20, KIF2C, BUB1, AURKB, and PTTG1 were nominated as potential biomarkers for myxoid liposarcoma cell cluster 2.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:5fe7dd9b708a8d3edc9a
claim_id: claim:5fe7dd9b708a8d3edc9a
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
The networking analysis suggested five genes; PF4, PPBP, ITGA2B, FERMT3 and SELP as central hub nodes (Figure 3a).

summary:
In Homo sapiens, PF4, PPBP, ITGA2B, FERMT3, and SELP were identified as central hub nodes among up-regulated differentially expressed genes in circulating tumor cell cluster 4.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:51b7cf559d677ae1edc8
claim_id: claim:51b7cf559d677ae1edc8
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
However, four genes (CTNNB1, ILK, TGFB1 and ZEB2) have been classified as significantly up-regulated in cluster 4, these genes exhibit similar expression patterns to the genes in the second GF-subset.

summary:
In Homo sapiens, CTNNB1, ILK, TGFB1, and ZEB2 have been classified as significantly up-regulated in circulating tumor cell cluster 4.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:deb56a68f5ec421f1ca8
claim_id: claim:deb56a68f5ec421f1ca8
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
Seven EMT genes (AKT1, EGFR, EPAS1, ERBB2, HIF1A, SMAD3, and MET) were relatively up-regulated in cluster 3 comparing to cluster 4.

summary:
In Homo sapiens, seven epithelial-mesenchymal transition genes (AKT1, EGFR, EPAS1, ERBB2, HIF1A, SMAD3, and MET) were relatively up-regulated in circulating tumor cell cluster 3 compared to circulating tumor cell cluster 4.


claim_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0:claim:9eb5cb0e929e7515f3ff
claim_id: claim:9eb5cb0e929e7515f3ff
paper_key: biorxiv:a96dba70-6cf7-1014-a294-bf2ca6d364a0
span_literal:
Five genes (RPS27A, TUBA1B, RPL4, RPL34 and RPS12) have been classified as significantly up-regulated in cluster 3 whereas 748 genes were significantly up-regulated in the cluster 4 (Supplementary Data S2).

summary:
In Homo sapiens, RPS27A, TUBA1B, RPL4, RPL34, and RPS12 have been classified as significantly up-regulated in circulating tumor cell cluster 3 compared to circulating tumor cell cluster 4.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:183037c43e1443ce4fac
claim_id: claim:183037c43e1443ce4fac
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal:
activated NK cells identified by the expression of KIR2DL4, GPR183, GRP171, CD69, and IFNG, resting NK cells marked by GZMK, TTC38, CD160, and PLEKNF1

summary:
In Homo sapiens, activated natural killer cells are identified by the expression of KIR2DL4, GPR183, GPR171, CD69, and IFNG, while resting natural killer cells are marked by GZMK, TTC38, CD160, and PLEKF1.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:ffef5b0d79102f3a15c4
claim_id: claim:ffef5b0d79102f3a15c4
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal:
KIR2DL4+ GPR171+ activated NK cells were lessened in proportion with the progression of the disease from normal colon to colon cancer and liver metastasis cancer, whereas GZMK+ resting NK cells increased

summary:
In Homo sapiens, KIR2DL4 and GPR171 are positive markers of activated natural killer cells, while GZMK is a positive marker of resting natural killer cells in colon cancer liver metastasis.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:558bba5c661eba8c08a5
claim_id: claim:558bba5c661eba8c08a5
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal:
KIR2DL4+ GPR171+ activated NK cells were lessened in proportion with the progression of the disease from normal colon to colon cancer and liver metastasis cancer, whereas GZMK+ resting NK cells increased

summary:
In Homo sapiens, GZMK is a positive marker of resting natural killer cells in colon cancer liver metastasis.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:1640de66d4b45bb394ed
claim_id: claim:1640de66d4b45bb394ed
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal:
Marker genes of activated NK cells (KIR2DL4 and GPR171) exhibited a gradient descent expression pattern, whereas the expression of resting NK cell marker genes (GZMK) exhibited a gradient rise pattern

summary:
In Homo sapiens, KIR2DL4 and GPR171 are marker genes of activated natural killer cells, while GZMK is a marker gene of resting natural killer cells.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:5ce15693f192bf6d8164
claim_id: claim:5ce15693f192bf6d8164
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal:
we identified the tendency of NK cells to differentiate to an resting state with decreasing expression of activated marker KIR2DL4 as well as typical functional NK cell markers: NKG2D(Yu et al., 2023) and NKG2A which are only triggered by cell-to-cell interactions as validated by FACS

summary:
In Homo sapiens, tumor-educated natural killer cells shift to a resting state with decreased expression of activated marker KIR2DL4 and functional markers NKG2D and NKG2A.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:8c6da9ee06942c65f400
claim_id: claim:8c6da9ee06942c65f400
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal:
We discovered that GZMK+ resting NK cells increased significantly in tumor tissues and were enriched in the tumor regions of both diseases.

summary:
In Homo sapiens, GZMK-positive resting natural killer cells are enriched in tumor regions of colon cancer and liver metastasis.


claim_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a:claim:747748c07f5ef4399884
claim_id: claim:747748c07f5ef4399884
paper_key: biorxiv:a9b298c9-7797-1014-9b95-8bbbe23c746a
span_literal: KIR2DL4+ activated NK cells exhibited the opposite position and relevance.
summary:
In Homo sapiens, KIR2DL4-positive activated natural killer cells are enriched in non-tumor regions and associated with better prognosis.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:4f8c431507e9c2e998bf
claim_id: claim:4f8c431507e9c2e998bf
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
scATAC-seq analysis of 50:50 mixtures identified two distinct populations of cells, which demonstrated high accessibility of open chromatin regions linked either to monocyte-specific genes (i.e. CD14, CSF1R, TREML4), or to T cell-specific genes (i.e. CD3E, CD4, CD8A; Supplementary Fig. 2a and Methods).

summary:
In Homo sapiens, monocytes are marked by high chromatin accessibility at CD14, CSF1R, and TREML4, while T cells are marked by high chromatin accessibility at CD3E, CD4, and CD8A.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:b71ada950849dcb9f9b4
claim_id: claim:b71ada950849dcb9f9b4
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
Clusters 2-4 demonstrated accessibility at cis- elements neighboring key myeloid progenitor genes, including KIT, GATA1, TAL1, and SPI1, while Clusters 14-16 demonstrated accessibility at cis-elements neighboring B cell genes, including CD19, EBF1, and LYN

summary:
In Homo sapiens, myeloid progenitor cells show chromatin accessibility at KIT, GATA1, TAL1, and SPI1.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:d6f61bbfdd5ad65b9099
claim_id: claim:d6f61bbfdd5ad65b9099
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
the CD34 gene score identified hematopoietic progenitors, the CD14 gene score identified monocyte and myeloid dendritic cells (mDCs), and the CD20 gene score identified B cells

summary:
In Homo sapiens, hematopoietic progenitor cells are identified by CD34 gene activity score, monocytes and myeloid dendritic cells are identified by CD14 gene activity score, and B cells are identified by CD20 gene activity score.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:176d06f6e80b87f55565
claim_id: claim:176d06f6e80b87f55565
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
genome-wide accessibility at binding sites for GATA2, a lineage-determining factor for megakaryocyte, erythrocyte, and basophil lineages25, was increased in megakaryocyte-erythroid progenitors (MEPs), in basophils, and in common myeloid progenitors (CMPs), as expected

summary:
In Homo sapiens, megakaryocyte-erythroid progenitors show increased genome-wide accessibility at GATA2 binding sites.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:5850f948ab982de589b6
claim_id: claim:5850f948ab982de589b6
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
genome-wide accessibility at binding sites for GATA2, a lineage-determining factor for megakaryocyte, erythrocyte, and basophil lineages25, was increased in megakaryocyte-erythroid progenitors (MEPs), in basophils, and in common myeloid progenitors (CMPs), as expected

summary:
In Homo sapiens, common myeloid progenitors show increased genome-wide accessibility at GATA2 binding sites.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:eb69b8e0bbe7529613b0
claim_id: claim:eb69b8e0bbe7529613b0
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
the accessibility of binding sites for EBF1, the lineage-determining factor for B cells26, was increased in naïve, memory, and plasma B cells, as well as in early B cell progenitors

summary:
In Homo sapiens, naïve B cells, memory B cells, plasma B cells, and early B cell progenitors show increased accessibility at EBF1 binding sites.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:5803770cfe996a431aa1
claim_id: claim:5803770cfe996a431aa1
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
mDCs and B cells shared activity at sites containing BCL11A, SPI1, and IRF factor motifs, but demonstrated unique activity at sites containing motifs for CEBP factors and EBF1, respectively

summary:
In Homo sapiens, myeloid dendritic cells show unique activity at CEBP factor motif sites, while B cells show unique activity at EBF1 motif sites; both share activity at BCL11A, SPI1, and IRF motif sites.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:9e6b43aa315963b59867
claim_id: claim:9e6b43aa315963b59867
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
mDCs and B cells shared activity at sites containing BCL11A, SPI1, and IRF factor motifs, but demonstrated unique activity at sites containing motifs for CEBP factors and EBF1, respectively

summary:
In Homo sapiens, B cells show unique activity at EBF1 motif sites and share activity at BCL11A, SPI1, and IRF motif sites with myeloid dendritic cells.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:905007c122898ee422b8
claim_id: claim:905007c122898ee422b8
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
TBX21- and EOMES-bound sites were active in both NK and T cell populations; however, only T cells showed accessibility at sites containing motifs for the T cell lineage-determining factor TCF7

summary:
In Homo sapiens, natural killer cells and T cells show activity at TBX21- and EOMES-bound sites, but only T cells show accessibility at TCF7 motif sites.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:6e6322e2cefe5998608b
claim_id: claim:6e6322e2cefe5998608b
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
TBX21- and EOMES-bound sites were active in both NK and T cell populations; however, only T cells showed accessibility at sites containing motifs for the T cell lineage-determining factor TCF7

summary:
In Homo sapiens, T cells show activity at TBX21- and EOMES-bound sites and accessibility at TCF7 motif sites, distinguishing them from natural killer cells.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:6913278e135fe2182baa
claim_id: claim:6913278e135fe2182baa
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
cis-elements that were accessible early in the trajectory included enhancers for EBF1, RUNX1, IL7R, RAG2, and MEF2C, factors that are critical for B cell lineage specification and diversity

summary:
In Homo sapiens, early B cell progenitors show accessible enhancers for EBF1, RUNX1, IL7R, RAG2, and MEF2C, which are critical for B cell lineage specification.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:1f3edb751008e301b761
claim_id: claim:1f3edb751008e301b761
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
~3,500 cis-elements that were accessible late in the trajectory included elements proximal to PRDM1, a critical transcription factor for plasma cell fate, and the plasma cell-specific marker SDC1 (CD138).

summary:
In Homo sapiens, plasma B cells show accessible cis-elements proximal to PRDM1 and the plasma cell-specific marker SDC1 (CD138).


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:07d30a6f13937d1f459d
claim_id: claim:07d30a6f13937d1f459d
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
9 T cell clusters (high accessibility of CD3E, CD8A, and CD4 enhancers), 2 natural killer (NK) cell clusters (high accessibility of KLRC1 and NCR1 enhancers), B cells and plasma cells (high accessibility of CD19 and SDC1 enhancers, respectively), myeloid cells that comprised mDCs and tissue macrophages (high accessibility of CD86, CSF1R, and FLT3 enhancers), stromal endothelial cells and fibroblasts (high accessibility of CD31 and COL1A2 enhancers, respectively), and 4 tumor cell clusters (high accessibility of KRT14 enhancers

summary:
In Homo sapiens, T cells in the tumor microenvironment show high accessibility of CD3E, CD8A, and CD4 enhancers.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:c7fb37042c5c6e24387f
claim_id: claim:c7fb37042c5c6e24387f
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
span_literal:
9 T cell clusters (high accessibility of CD3E, CD8A, and CD4 enhancers), 2 natural killer (NK) cell clusters (high accessibility of KLRC1 and NCR1 enhancers), B cells and plasma cells (high accessibility of CD19 and SDC1 enhancers, respectively), myeloid cells that comprised mDCs and tissue macrophages (high accessibility of CD86, CSF1R, and FLT3 enhancers), stromal endothelial cells and fibroblasts (high accessibility of CD31 and COL1A2 enhancers, respectively), and 4 tumor cell clusters (high accessibility of KRT14 enhancers

summary:
In Homo sapiens, natural killer cells in the tumor microenvironment show high accessibility of KLRC1 and NCR1 enhancers.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:01b07fe1052539c71111
claim_id: claim:01b07fe1052539c71111
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary:
In Homo sapiens, plasma cells in the tumor microenvironment show high accessibility of SDC1 enhancers.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:78f3d0413274d8102bcf
claim_id: claim:78f3d0413274d8102bcf
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary:
In Homo sapiens, myeloid cells comprising myeloid dendritic cells and tissue macrophages in the tumor microenvironment show high accessibility of CD86, CSF1R, and FLT3 enhancers.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:4e5197c07b69aec89613
claim_id: claim:4e5197c07b69aec89613
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary:
In Homo sapiens, endothelial cells in the tumor microenvironment show high accessibility of CD31 enhancers.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:75870388530de0a4fed2
claim_id: claim:75870388530de0a4fed2
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary:
In Homo sapiens, fibroblasts in the tumor microenvironment show high accessibility of COL1A2 enhancers.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:80495c141a7951eda56c
claim_id: claim:80495c141a7951eda56c
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary: In Homo sapiens, naïve CD8+ T cells show high accessibility of CCR7 and TCF7 enhancers.
span_literal:
CD8+ T cell states included naïve T cells (high accessibility of CCR7 and TCF7 enhancers), effector T cells (high accessibility of EOMES and IFNG enhancers), memory T cells (high accessibility of EOMES enhancers, but low accessibility of effector gene enhancers), and exhausted T cells (TEx; high accessibility of cis-elements proximal to inhibitory receptor genes PDCD1, CTLA4, and HAVCR2, and to T cell dysfunction genes CD101 and CD3849


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:91eea8a50c46edc6eb34
claim_id: claim:91eea8a50c46edc6eb34
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary:
In Homo sapiens, exhausted CD8+ T cells show high accessibility of cis-elements proximal to PDCD1, CTLA4, HAVCR2, CD101, and CD38.


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:7992ed5b16b41ba7ec91
claim_id: claim:7992ed5b16b41ba7ec91
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary: In Homo sapiens, regulatory T cells show high accessibility of FOXP3 and CTLA4 enhancers.
span_literal:
Tregs (high accessibility of FOXP3 and CTLA4 enhancers), T helper 1 (Th1) cells (high accessibility of IFNG and TBX21 enhancers), T helper 17 (Th17) cells (high accessibility of IL17A and CTSH enhancers), and T follicular helper (Tfh) cells (high accessibility of CXCR5, IL21, and BTLA enhancers


claim_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a:claim:989890f824f85cebfedc
claim_id: claim:989890f824f85cebfedc
paper_key: biorxiv:ab05f819-6c04-1014-81aa-9646e853264a
summary:
In Homo sapiens, T follicular helper cells show high accessibility of CXCR5, IL21, and BTLA enhancers.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:6aa13b94f66ccde5d648
claim_id: claim:6aa13b94f66ccde5d648
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
Marker genes include ANGPTL7 and COMP in the basal outer root sheath, VEGFA and CA9 in the companion layer, GAL and CRCT1 in Henle’s layer, TGFA in Huxley’s layer, KRT73 in the cuticle, LEF1 and KRT83 in the cortex, keratin-associated proteins (KRTAPs) together with SCYGR8 in the medulla, and TOP2A in the matrix cells.

summary:
In Homo sapiens skin, ANGPTL7 and COMP are markers of basal outer root sheath cells of the hair follicle.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:ea47d08399f33389b430
claim_id: claim:ea47d08399f33389b430
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
Dermal papilla cells expressed specific markers including IGFBP3, DKK2, RSPO4, and EDN3 (Fig. 4c and d).

summary:
In Homo sapiens skin, dermal papilla cells express specific markers including IGFBP3, DKK2, RSPO4, and EDN3.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:bcea91a72c097b90f858
claim_id: claim:bcea91a72c097b90f858
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
In this regressing follicle, we observed expression of SULT1E1, THBS1, PAPLN, and CLU, reflecting the dynamic transcriptional landscape associated with hair-cycle progression (Fig. 4f).

summary:
In Homo sapiens skin, catagen hair follicle cells express SULT1E1, THBS1, PAPLN, and CLU, reflecting hair-cycle progression.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:20c89be996ca3ba9fcc1
claim_id: claim:20c89be996ca3ba9fcc1
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
summary: In Homo sapiens skin, a Merkel cell cluster is characterized by strong expression of CCER2.
span_literal:
This cluster is characterized by strong expression of CCER2 (Fig. 6b), a gene that is poorly characterized overall46 and, to our knowledge, has not been reported in skin.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:ea6369069c5905066add
claim_id: claim:ea6369069c5905066add
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
summary: In Homo sapiens skin, KRT20 is a well-established marker for Merkel cells.
span_literal:
In addition, the cluster shows co-expression of KRT20 (Fig. 6b), a well-established marker for Merkel cells47,48.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:04714b8e989c7e2b21e8
claim_id: claim:04714b8e989c7e2b21e8
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
Moreover, sebaceous progenitor cells and the junctional zone display strong enrichment for PTN and C1QTNF12 (Fig. 5h), both of which are spatially validated in Visium HD sections, highlighting their role as early lineage markers (Fig. 5i) and showing how high-resolution spatial transcriptomics enables precise mapping of cell states45.

summary:
In Homo sapiens skin, sebaceous progenitor cells display strong enrichment for PTN and C1QTNF12, highlighting their role as early lineage markers.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:1474793854d1253f0213
claim_id: claim:1474793854d1253f0213
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
Among the 177 samples, a single sample (GSM505054057) unexpectedly harbors two distinct cancer-associated fibroblast (CAF) clusters (RGS5⁺, MCAM⁺, NOTCH3+, CHI3L1⁺, TMEM158⁺)71,72 that together represent ∼0.8 % of the cells (∼1473 cells) (Supplementary Fig. 16).

summary:
In Homo sapiens skin, cancer-associated fibroblast clusters are positive for RGS5, MCAM, NOTCH3, CHI3L1, and TMEM158.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:1a55d048832dba16b1b4
claim_id: claim:1a55d048832dba16b1b4
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
summary: In Homo sapiens skin, a rare Merkel cell population is positive for KRT20 and CCER2.
span_literal:
In the HSCA core we uncovered a rare KRT20⁺/CCER2⁺ Merkel-cell population that had not been reported in any individual dataset or in previous studies.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:2eac09dcf54b7ea48f98
claim_id: claim:2eac09dcf54b7ea48f98
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
Within the hair shaft, KRT83⁺ cortex cells preferentially engaged in neuregulin (NRG) signaling, while adjacent LEF1+ cortex cells relied on canonical WNT cues, indicating a functional split between cortical subpopulations (Fig. 4g).

summary:
In Homo sapiens skin, KRT83-positive cortex cells and LEF1-positive cortex cells represent functionally distinct cortical subpopulations of the hair shaft.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:5da9008cb84587cfff1e
claim_id: claim:5da9008cb84587cfff1e
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
Within the hair shaft, KRT83⁺ cortex cells preferentially engaged in neuregulin (NRG) signaling, while adjacent LEF1+ cortex cells relied on canonical WNT cues, indicating a functional split between cortical subpopulations (Fig. 4g).

summary:
In Homo sapiens skin, LEF1-positive cortex cells represent a functionally distinct cortical subpopulation of the hair shaft.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:7b8e84a5bffe325ce179
claim_id: claim:7b8e84a5bffe325ce179
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
span_literal:
upper, middle, and lower sub-regions, each suggesting a distinct transcriptional signature (e.g., GAL

summary:
In Homo sapiens skin, the upper Henle's layer sub-region is enriched for GAL, the middle Henle's layer sub-region for CRCT1, and the lower Henle's layer sub-region for RHCGG.


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:c51b8129f422e8377218
claim_id: claim:c51b8129f422e8377218
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
summary: In Homo sapiens skin, the middle Henle's layer sub-region is enriched for CRCT1.
span_literal:
middle, and lower sub-regions, each suggesting a distinct transcriptional signature (e.g., GAL enriched in the upper zone, CRCT1


claim_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33:claim:074ee3218aa825b83c18
claim_id: claim:074ee3218aa825b83c18
paper_key: biorxiv:ab2a1489-7001-1014-b2bf-f5e47d205c33
summary: In Homo sapiens skin, the lower Henle's layer sub-region shows elevated RHCGG expression.
span_literal:
lower sub-regions, each suggesting a distinct transcriptional signature (e.g., GAL enriched in the upper zone, CRCT1 in the middle zone, and elevated RHCGG


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:21e98da31b94cb87c551
claim_id: claim:21e98da31b94cb87c551
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
summary: In Homo sapiens, oligodendrocyte progenitor cells are marked by CSPG4, PCDH15, PDGFRA, and PTPRZ1.
span_literal:
cells expressing markers for OPCs (CSPG4, PCDH15, PDGFRa, PTPRZ1) or MOL (ANLN, CNP, MBP, PLP1) clustered well in both the human and mouse integrated datasets


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:0752b537e7354ecfe437
claim_id: claim:0752b537e7354ecfe437
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
cells expressing myelin marker transcripts (ANLN, CNP, GSN, MBP, PLLP, PLP1) distributed similar across human and mouse MOL

summary:
In Homo sapiens, mature oligodendrocytes express the myelin marker transcripts ANLN, CNP, GSN, MBP, PLLP, and PLP1.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:c8f12e92d0d47b2db760
claim_id: claim:c8f12e92d0d47b2db760
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
multiple myelin-related transcripts displayed exclusive or predominant expression in MOL of only one of the species, as exemplified by PMP2, PADI2, CA2, TSPAN2 and GJC3

summary:
In Homo sapiens, mature oligodendrocytes display exclusive or predominant expression of PMP2 and PADI2 compared to mouse mature oligodendrocytes. In Homo sapiens, mature oligodendrocytes display negative or very low expression of TSPAN2 and GJC3 compared to mouse mature oligodendrocytes.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:0f635df619d43c5a1d39
claim_id: claim:0f635df619d43c5a1d39
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
PMP2/Pmp2 mRNA is expressed in human but not mouse MOL and PMP2 protein was identified in human but not mouse myelin.

summary:
In Homo sapiens, mature oligodendrocytes express PMP2 mRNA, and PMP2 protein is identified in human central nervous system myelin.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:c1a7d4701548a2235fe9
claim_id: claim:c1a7d4701548a2235fe9
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
TSPAN2/Tspan2 and GJC3/Gjc3 transcripts are expressed in mouse but not human MOL and their protein products TSPAN2 and GJC3 are identified in mouse but not human myelin.

summary:
In Homo sapiens, mature oligodendrocytes do not express TSPAN2 or GJC3 transcripts, and their protein products are not identified in human myelin.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:12bea4e4c4e60dd176d2
claim_id: claim:12bea4e4c4e60dd176d2
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
the subpopulations were defined by varying degrees of expression of other transcripts, including the myelin-related CD9 and OPALIN (cluster 0), APOD, KLK6 and S100B (cluster 1), APOE and CST3 (cluster 2), CA2 and PTGS (cluster 3), and SIRT2 and NFASC (cluster 4)

summary:
In Homo sapiens, mature oligodendrocyte subpopulation cluster 0 is defined by expression of CD9 and OPALIN.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:e019fa230af9dbcdb485
claim_id: claim:e019fa230af9dbcdb485
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
the subpopulations were defined by varying degrees of expression of other transcripts, including the myelin-related CD9 and OPALIN (cluster 0), APOD, KLK6 and S100B (cluster 1), APOE and CST3 (cluster 2), CA2 and PTGS (cluster 3), and SIRT2 and NFASC (cluster 4)

summary:
In Homo sapiens, mature oligodendrocyte subpopulation cluster 1 is defined by expression of APOD, KLK6, and S100B.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:946f8ee3cedb0ae92960
claim_id: claim:946f8ee3cedb0ae92960
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
the subpopulations were defined by varying degrees of expression of other transcripts, including the myelin-related CD9 and OPALIN (cluster 0), APOD, KLK6 and S100B (cluster 1), APOE and CST3 (cluster 2), CA2 and PTGS (cluster 3), and SIRT2 and NFASC (cluster 4)

summary:
In Homo sapiens, mature oligodendrocyte subpopulation cluster 2 is defined by expression of APOE and CST3.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:8f6ffbc9a6b2574a855d
claim_id: claim:8f6ffbc9a6b2574a855d
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
summary:
In Homo sapiens, mature oligodendrocyte subpopulation cluster 3 is defined by expression of CA2 and PTGS.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:f4ff92bdd9399681f1e4
claim_id: claim:f4ff92bdd9399681f1e4
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
summary:
In Homo sapiens, mature oligodendrocyte subpopulation cluster 4 is defined by expression of SIRT2 and NFASC.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:5aaeee386bba137086de
claim_id: claim:5aaeee386bba137086de
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
All cells in all clusters also express high levels of known myelin-related marker transcripts (CNP, PLP1, MBP, MAG, CLDN11).

summary:
In Homo sapiens, all mature oligodendrocyte subpopulations express high levels of the myelin-related marker transcripts CNP, PLP1, MBP, MAG, and CLDN11.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:e7ca0b4c0a2a9e50e25c
claim_id: claim:e7ca0b4c0a2a9e50e25c
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
Marker genes used for annotating the oligodendrocyte lineage were CSPG4, PCDH15, PDGFRa, PTPRZ1 and VCAN for OPCs, BCAS1, ENPP6 and GPR17 for NFO, and CA2, CLDN11, CNP, CMTM5, MAG, MBP, MOBP, PLP1 and SIRT2 for MOL.

summary:
In Homo sapiens, oligodendrocyte progenitor cells are annotated by marker genes CSPG4, PCDH15, PDGFRA, PTPRZ1, and VCAN.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:f4f68f82d4dd25c28b99
claim_id: claim:f4f68f82d4dd25c28b99
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
Marker genes used for annotating the oligodendrocyte lineage were CSPG4, PCDH15, PDGFRa, PTPRZ1 and VCAN for OPCs, BCAS1, ENPP6 and GPR17 for NFO, and CA2, CLDN11, CNP, CMTM5, MAG, MBP, MOBP, PLP1 and SIRT2 for MOL.

summary:
In Homo sapiens, newly formed oligodendrocytes are annotated by marker genes BCAS1, ENPP6, and GPR17.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:d48621f14a92e963530c
claim_id: claim:d48621f14a92e963530c
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
Marker genes used for annotating the oligodendrocyte lineage were CSPG4, PCDH15, PDGFRa, PTPRZ1 and VCAN for OPCs, BCAS1, ENPP6 and GPR17 for NFO, and CA2, CLDN11, CNP, CMTM5, MAG, MBP, MOBP, PLP1 and SIRT2 for MOL.

summary:
In Homo sapiens, mature oligodendrocytes are annotated by marker genes CA2, CLDN11, CNP, CMTM5, MAG, MBP, MOBP, PLP1, and SIRT2.


claim_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57:claim:2d59dcf58313f18e7931
claim_id: claim:2d59dcf58313f18e7931
paper_key: biorxiv:acd52af7-6c95-1014-8d0b-873ff14c4a57
span_literal:
the higher abundance of PADI2 in human compared to mouse myelin goes along with a higher abundance of PADI2/Padi2 mRNA in human compared to mouse MOL.

summary:
In Homo sapiens, mature oligodendrocytes express higher levels of PADI2 mRNA compared to mouse mature oligodendrocytes.


claim_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22:claim:362eb728a3d78d063104
claim_id: claim:362eb728a3d78d063104
paper_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22
span_literal:
One of the 105 highly variable genes is SLC11A1, which encodes a member of the solute carrier family 11, a family of proton-coupled divalent metal ion transporters (Fig. 4c).

summary:
In Homo sapiens, SLC11A1, encoding solute carrier family 11 member A1, is identified as a highly variable gene specific to classical monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22:claim:a26db4b310aac7750631
claim_id: claim:a26db4b310aac7750631
paper_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22
span_literal:
Another gene in this list of 105 highly variable genes is TREM1, which encodes triggering receptor expressed on myeloid cells 1 and is an ancestral predictor for malaria susceptibility (Fig. 4d).

summary:
In Homo sapiens, TREM1, encoding triggering receptor expressed on myeloid cells 1, is identified as a highly variable gene specific to classical monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22:claim:6c9dc29218673a409e82
claim_id: claim:6c9dc29218673a409e82
paper_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22
span_literal:
Another gene ILB1 is on their list of ancestral malaria predictor genes as well as on our list of 105 highly variable genes linked to cell type.

summary:
In Homo sapiens, ILB1 is identified as a highly variable gene linked to cell type, localized to classical monocytes in peripheral blood mononuclear cells.


claim_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22:claim:84fbaa33b1649be5d359
claim_id: claim:84fbaa33b1649be5d359
paper_key: biorxiv:ad26cde3-7040-1014-a3a5-9f8011665a22
span_literal:
We additionally found one gene, RNF17, which showed distinct specificity by sex:age:ancestry (Fig. 4e, f).

summary:
In Homo sapiens, RNF17 shows distinct specificity by sex, age, and ancestry in peripheral blood mononuclear cells.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:41d43d3f7d95ca8db228
claim_id: claim:41d43d3f7d95ca8db228
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
In particular, genes associated with tissue trafficking (CXCR4, CCL5, KLF2, ITGA4, ITGB1, CD69) and cytotoxicity (GZMK, KLRG1, GZMA) were upregulated in MS/CIS

summary:
In Homo sapiens, CD8+ T cells from multiple sclerosis/clinically isolated syndrome patients show upregulated expression of CXCR4, CCL5, KLF2, ITGA4, ITGB1, CD69, GZMK, KLRG1, and GZMA compared to healthy control/other neuroinflammatory disorder participants.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:c154527624e7f5e2105c
claim_id: claim:c154527624e7f5e2105c
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
In contrast, genes associated with naïve status (CCR7, SELL, LEF1) and TCR signaling (CD8B, CD3D, CD3E, LCK, ZAP70, LAT) were downregulated relative to HC/OND participants.

summary:
In Homo sapiens, CD8+ T cells from multiple sclerosis/clinically isolated syndrome patients show downregulated expression of CCR7, SELL, LEF1, CD8B, CD3D, CD3E, LCK, ZAP70, and LAT compared to healthy control/other neuroinflammatory disorder participants.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:a25a9d47a7d29919e854
claim_id: claim:a25a9d47a7d29919e854
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
A similar profile was observed amongst CD4+ T cells from blood and CSF of MS/CIS patients, including increased expression of genes related to tissue migration (ITGB1, CD69, ITGA4, CXCR3, CXCR4) and cytokine secretion (IL32, GZMK) and reduced naïve status (CCR7, LEF1, SELL, TCF7) and TCR signaling (LCK)

summary:
In Homo sapiens, CD4+ T cells from multiple sclerosis/clinically isolated syndrome patients show increased expression of ITGB1, CD69, ITGA4, CXCR3, CXCR4, IL32, and GZMK and reduced expression of CCR7, LEF1, SELL, TCF7, and LCK compared to healthy control/other neuroinflammatory disorder participants.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:60632af51f237504ea87
claim_id: claim:60632af51f237504ea87
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
In particular, genes associated with cytotoxic CD8+ T cell function (CD8A, CD8B, NKG7, KLRD1, GZMA, GZMH, GZMM, GZMK, EOMES) and chemotaxis (CCL5, CCL4) were significantly increased in highly expanded T cells, whereas genes associated with naïve status were significantly reduced (IL7R, LTB, LDHB).

summary:
In Homo sapiens, highly expanded cerebrospinal fluid T cells show significantly increased expression of CD8A, CD8B, NKG7, KLRD1, GZMA, GZMH, GZMM, GZMK, EOMES, CCL5, and CCL4, and significantly reduced expression of IL7R, LTB, and LDHB compared to unexpanded T cells.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:f79cc8aa3aaf94d1519a
claim_id: claim:f79cc8aa3aaf94d1519a
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
Targeted gene expression analysis revealed increased expression of genes associated with effector/memory differentiation (EOMES, KLRG1, CCL5, CD27), tissue homing (CXCR3, CCR5), resident memory status (CD69, IGTAE), as well as inhibitory genes associated with chronic antigen exposure (HOPX, TIGIT, DUSP2, PDCD1, LAG3) in highly CSF-expanded CD8+ and CD4+ T cells

summary:
In Homo sapiens, highly cerebrospinal fluid-expanded CD8+ T cells show increased expression of EOMES, KLRG1, CCL5, CD27, CXCR3, CCR5, CD69, ITGAE, HOPX, TIGIT, DUSP2, PDCD1, and LAG3.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:7bbc6d17aba3e323334b
claim_id: claim:7bbc6d17aba3e323334b
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
Targeted gene expression analysis revealed increased expression of genes associated with effector/memory differentiation (EOMES, KLRG1, CCL5, CD27), tissue homing (CXCR3, CCR5), resident memory status (CD69, IGTAE), as well as inhibitory genes associated with chronic antigen exposure (HOPX, TIGIT, DUSP2, PDCD1, LAG3) in highly CSF-expanded CD8+ and CD4+ T cells

summary:
In Homo sapiens, highly cerebrospinal fluid-expanded CD4+ T cells show increased expression of EOMES, KLRG1, CCL5, CD27, CXCR3, CCR5, CD69, ITGAE, HOPX, TIGIT, DUSP2, PDCD1, and LAG3.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:1aa0f14952ee808460b0
claim_id: claim:1aa0f14952ee808460b0
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
In contrast, CSF-unexpanded T cells expressed higher levels of genes associated with naive/non-activation (SELL, CCR7, IL7R, TCF7, LEF1) as well as the integrin gene ITGB1.

summary:
In Homo sapiens, cerebrospinal fluid-unexpanded T cells express higher levels of SELL, CCR7, IL7R, TCF7, LEF1, and ITGB1 compared to highly expanded T cells.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:7c01003efff221a7602d
claim_id: claim:7c01003efff221a7602d
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
The overwhelming majority of the enriched and expanded clonotypes were found in cluster 1, which was defined by a significantly increased expression with a number of genes associated with cytotoxic effector CD8+ T cells, including CD8A, CD8B, PLEK, DUSP2, EOMES, GZMK, GZMA, GZMH, PRF1, NKG7, CCL5, and CCL4

summary:
In Homo sapiens, cerebrospinal fluid T cell cluster 1 enriched in expanded clonotypes is defined by significantly increased expression of CD8A, CD8B, PLEK, DUSP2, EOMES, GZMK, GZMA, GZMH, PRF1, NKG7, CCL5, and CCL4, consistent with cytotoxic effector CD8+ T cells.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:6d4e9aa2d3c2a78f9a12
claim_id: claim:6d4e9aa2d3c2a78f9a12
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
span_literal:
CD8+ T cells (Fig. 1E, Table S3) in the CSF displayed significantly increased expression of various genes relative to the peripheral blood, including genes associated with migration and trafficking (CXCR3, CXCR4, CCL4, ITGB1, ITGA4), signaling and activation (CD2, FYN, DUSP2), and cytotoxicity (GZMK, GZMA).

summary:
In Homo sapiens, cerebrospinal fluid CD8+ T cells display significantly increased expression of CXCR3, CXCR4, CCL4, ITGB1, ITGA4, CD2, FYN, DUSP2, GZMK, and GZMA relative to peripheral blood CD8+ T cells.


claim_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada:claim:252a7e3f134b58f37a08
claim_id: claim:252a7e3f134b58f37a08
paper_key: biorxiv:ae5f009e-6d7a-1014-8ed6-cd1c0d2e0ada
summary: In Homo sapiens, platelet cells are marked by high expression of PPBP and PF4.
span_literal:
Clusters of cells with a high expression of platelet markers, PPBP and PF4, or hemoglobin subunits (HBB, HBA1, HBA2) were omitted.


claim_key: biorxiv:ae94037e-6d11-1014-8c86-e625ada7cdce:claim:fc3ebab98c52a12419a3
claim_id: claim:fc3ebab98c52a12419a3
paper_key: biorxiv:ae94037e-6d11-1014-8c86-e625ada7cdce
span_literal:
All neuronal subsets expressed both NRXN2 and PIRT, although NRXN2 levels were lower overall (Fig. 2a).

summary:
In Homo sapiens dorsal root ganglia, all sensory neuron subsets express both NRXN2 and PIRT, confirming these genes as markers of sensory neurons.


claim_key: biorxiv:ae94037e-6d11-1014-8c86-e625ada7cdce:claim:3ef55785360c23729cec
claim_id: claim:3ef55785360c23729cec
paper_key: biorxiv:ae94037e-6d11-1014-8c86-e625ada7cdce
span_literal:
Immunostaining of DRG sections from human donors further confirmed protein expression of NRXN2 and PIRT across DRG neurons of different soma diameters (Fig. 2b).

summary:
In Homo sapiens, immunostaining of dorsal root ganglia sections confirmed protein expression of NRXN2 and PIRT across dorsal root ganglia neurons of different soma diameters.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:cbee53b82636b824f9a7
claim_id: claim:cbee53b82636b824f9a7
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
We then proceed to characterize the fibroblast cells expressing MOXD1 by co-staining the sections with PDGFRa (marker of fibroblasts) and alpha smooth muscle actin (α-SMA, a marker of myofibroblasts, which also marks pericytes and smooth muscle cells).

summary:
In Homo sapiens, platelet-derived growth factor receptor alpha is a marker of fibroblasts, and alpha smooth muscle actin is a marker of myofibroblasts, pericytes, and smooth muscle cells.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:1ee89f5e4c6c47e7680a
claim_id: claim:1ee89f5e4c6c47e7680a
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
We then proceed to characterize the fibroblast cells expressing MOXD1 by co-staining the sections with PDGFRa (marker of fibroblasts) and alpha smooth muscle actin (α-SMA, a marker of myofibroblasts, which also marks pericytes and smooth muscle cells).

summary:
In Homo sapiens, alpha smooth muscle actin is a marker of myofibroblasts, which also marks pericytes and smooth muscle cells.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:98feba6a4a07cbb2fa39
claim_id: claim:98feba6a4a07cbb2fa39
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
A closer inspection of this region showed high expression of the myofibroblast associated genes POSTN, ASPN, ACTA2 and TAGLN (Figure 8G) (11, 30).

summary:
In Homo sapiens, myofibroblasts show high expression of the myofibroblast-associated genes POSTN, ASPN, ACTA2, and TAGLN.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:126ca6f75ffea45d016b
claim_id: claim:126ca6f75ffea45d016b
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
Our results corfirmed that cells expressing myofibroblasts markers like POSTN and ASPN also expressed LTBP2, LTBP1, BGN, DPT and the highest levels of COL3A1 and COL8A1.

summary:
In Homo sapiens, myofibroblasts express markers POSTN, ASPN, LTBP2, LTBP1, BGN, DPT, COL3A1, and COL8A1.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:6b7a143f1852d1517a9d
claim_id: claim:6b7a143f1852d1517a9d
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
Cells in Cluster-4 expressed profibrotic and myofibroblast markers like TNC, collagens, SPARC, POSTN, FN1 and TPM2 in higher levels than cells in Cluster-3.

summary:
In Homo sapiens, myofibroblasts express profibrotic markers TNC, SPARC, POSTN, FN1, and TPM2 at high levels.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:cead9017dfdbb63d09c9
claim_id: claim:cead9017dfdbb63d09c9
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
Furthermore, we find that MOXD1 is also expressed at early stages of IPF suggesting that it can be used as an early biomarker of fibroblast pulmonary fibrosis.

summary:
In Homo sapiens, monooxygenase DBH like 1 (MOXD1) is expressed at early stages of idiopathic pulmonary fibrosis and can be used as an early biomarker of fibroblast pulmonary fibrosis.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:54a35280b4932b4383a3
claim_id: claim:54a35280b4932b4383a3
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
More importantly, we discover a point of transition between these two states, which is characterized by a significant decrease in ribosomal protein genes and a significant increase in copper-binding proteins.

summary:
In Homo sapiens, transitional fibroblasts are characterized by a significant decrease in ribosomal protein genes and a significant increase in copper-binding proteins.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:9c6b7c60093bca6e45a4
claim_id: claim:9c6b7c60093bca6e45a4
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
We examine the second most upregulated copper-binding protein, MOXD1, and find it to be fibroblast- and IPF-specific.

summary:
In Homo sapiens, monooxygenase DBH like 1 (MOXD1) is a fibroblast-specific and idiopathic pulmonary fibrosis-specific copper-binding protein.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:d25d7f09e7d724620d03
claim_id: claim:d25d7f09e7d724620d03
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
TIMP1, COL1A1, CTHRC1, TUBA1B, SH3BGRL3 and S100A16 were the top six differentially expressed genes between Cluster-3 and Cluster-4 (upregulated in Cluster-4).

summary:
In Homo sapiens, TIMP1, COL1A1, CTHRC1, TUBA1B, SH3BGRL3, and S100A16 are upregulated in Cluster-4 myofibroblast-like fibroblasts compared to Cluster-3 profibrotic fibroblasts.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:ac54f5b4085aa245b668
claim_id: claim:ac54f5b4085aa245b668
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
Briefly, fibroblasts in Cluster-1 had higher expression in 263 genes (FDR<0.05) with the highest being: ICAM1, CXCL1, CXCL2, CXCL3, CXCL8, CCL2, IL6, PTX3, IER3, GADD45B, THBS1, SOD2 and NFKBIA which are associated with immune response and regulation of inflammation (Figure 3 and Table S4).

summary:
In Homo sapiens, Cluster-1 fibroblasts (normal state) have higher expression of ICAM1, CXCL1, CXCL2, CXCL3, CXCL8, CCL2, IL6, PTX3, IER3, GADD45B, THBS1, SOD2, and NFKBIA, which are associated with immune response and regulation of inflammation.


claim_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe:claim:c98b75806f6d8976693b
claim_id: claim:c98b75806f6d8976693b
paper_key: biorxiv:b01f00d1-6e6e-1014-8e4a-e846f4b1debe
span_literal:
Among the 118 genes that were significantly upregulated in Cluster-2, CXCL14, SFRP2 and SFRP4 had higher expression levels in IPF samples.

summary:
In Homo sapiens, Cluster-2 fibroblasts show significant upregulation of CXCL14, SFRP2, and SFRP4, with higher expression levels in idiopathic pulmonary fibrosis samples.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:a0ece4a9b37bd00d67b9
claim_id: claim:a0ece4a9b37bd00d67b9
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Upregulation of LY6S indicates CD4+ and CD8+ T cell activation by IFN alpha and IL-1 (T4-a, T4-c, T8-a and T8-c).

summary:
In Homo sapiens, upregulation of LY6S indicates activation of CD4+ T cells by interferon alpha and interleukin-1.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:69ebaf6b50008c1215bd
claim_id: claim:69ebaf6b50008c1215bd
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Upregulation of LY6S indicates CD4+ and CD8+ T cell activation by IFN alpha and IL-1 (T4-a, T4-c, T8-a and T8-c).

summary:
In Homo sapiens, upregulation of LY6S indicates activation of CD8+ T cells by interferon alpha and interleukin-1.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:5e748f65140046782855
claim_id: claim:5e748f65140046782855
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
summary: In Homo sapiens, GBP2 is a marker of effector memory CD4+ T cells.
span_literal:
Upregulation of the effector memory T cell marker GBP2 indicates that T4-a and T4-c likely become effector memory CD4+ T cells.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:500282cbe6bc315f8860
claim_id: claim:500282cbe6bc315f8860
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
summary: In Homo sapiens, upregulation of granzyme B (GZMB) indicates cytotoxic CD8+ T cells.
span_literal:
Upregulation of the principal cytotoxic granzyme GZMB indicates that T8-c are likely cytotoxic CD8+ T cells.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:b923755f896b2f6aa22a
claim_id: claim:b923755f896b2f6aa22a
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
summary: In Homo sapiens, MRC1 (CD206) and CD209 are markers of M2 macrophages.
span_literal:
The Mac-c and Mac-e polarisations present with upregulated M2 macrophage marker (MRC1 (CD206) or CD209) expression, implicating them as M2 macrophages.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:94aee0499014eff996b1
claim_id: claim:94aee0499014eff996b1
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
summary: In Homo sapiens, upregulated expression of CXCL9 and CXCL10 is indicative of M1 macrophages.
span_literal:
Conversely, Mac-a presents with upregulated expression of pro-inflammatory CXCL9 and CXCL10 cytokines, indicative of M1 macrophages.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:681b050c8f71dc8846ee
claim_id: claim:681b050c8f71dc8846ee
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
IL-1 and GM-CSF- induced Mono-c and Mono-e polarisations upregulate M1 macrophage differentiation marker VCAN, suggesting monocyte to M1 macrophage differentiation.

summary:
In Homo sapiens, VCAN is an M1 macrophage differentiation marker upregulated in monocytes undergoing differentiation to M1 macrophages.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:1dcb73019bfbcd0c774a
claim_id: claim:1dcb73019bfbcd0c774a
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Both IL-1-induced Mono-c and IL-1 beta-induced Mac-c polarisations have upregulated monocyte/macrophage migration (JAML) and differentiation (MAFB) marker expression.

summary:
In Homo sapiens, JAML is a migration marker and MAFB is a differentiation marker of monocyte/macrophage polarisation states.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:288644c61d8c75cff787
claim_id: claim:288644c61d8c75cff787
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
All TNF- alpha and GM-CSF-stimulated myeloid cells upregulate the anti-apoptotic BCL2A1 gene, indicating a BCL2A1-mediated pro-survival mechanism.

summary:
In Homo sapiens, myeloid cells stimulated by tumor necrosis factor alpha and granulocyte-macrophage colony-stimulating factor upregulate the anti-apoptotic gene BCL2A1.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:1acf64c274b9a5db43c8
claim_id: claim:1acf64c274b9a5db43c8
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
TNF-alpha induces the expression of IL1RN (IL-1RA) and the pattern recognition receptors CLEC6A and CLEC4E in monocytes, macrophages and cDC2s, possibly suppressing IL-1 responses and priming myeloid cells for innate immune recognition and activation.

summary:
In Homo sapiens, tumor necrosis factor alpha induces expression of IL1RN, CLEC6A, and CLEC4E in monocytes, macrophages, and conventional dendritic cell type 2.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:28b17e821f3637bbff40
claim_id: claim:28b17e821f3637bbff40
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
TNF-alpha induces the expression of IL1RN (IL-1RA) and the pattern recognition receptors CLEC6A and CLEC4E in monocytes, macrophages and cDC2s, possibly suppressing IL-1 responses and priming myeloid cells for innate immune recognition and activation.

summary:
In Homo sapiens, tumor necrosis factor alpha induces expression of IL1RN, CLEC6A, and CLEC4E in macrophages.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:83c6f094246171d35154
claim_id: claim:83c6f094246171d35154
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
TNF-alpha induces the expression of IL1RN (IL-1RA) and the pattern recognition receptors CLEC6A and CLEC4E in monocytes, macrophages and cDC2s, possibly suppressing IL-1 responses and priming myeloid cells for innate immune recognition and activation.

summary:
In Homo sapiens, tumor necrosis factor alpha induces expression of IL1RN, CLEC6A, and CLEC4E in conventional dendritic cell type 2.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:e39a293fec3e1ebbb2c1
claim_id: claim:e39a293fec3e1ebbb2c1
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
IFN alpha and IL-1 beta upregulate cytotoxic granzyme GZMB expression in NK-a and NK-c cells, and the cytotoxicity regulator KLRB1 may govern the NK-c cytotoxic state.

summary:
In Homo sapiens, interferon alpha and interleukin-1 beta upregulate GZMB expression in natural killer cells, and KLRB1 may govern the cytotoxic state of natural killer cells.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:177e3055fd1db6f0661a
claim_id: claim:177e3055fd1db6f0661a
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
All immune cells express the TNF-alpha (TNFRSF1A and TNFRSF1B) and IFN alpha (IFNAR1 and IFNAR2) receptors and are enriched for these pathways, indicating they are primed to respond to secreted TNF-alpha and IFN alpha in the TME (Figure 6B-D).

summary:
In Homo sapiens, monocytes/macrophages, CD8+ T cells, and neutrophils in the medulloblastoma tumor microenvironment express TNFRSF1A, TNFRSF1B, IFNAR1, and IFNAR2.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:193e6139f4692492ea35
claim_id: claim:193e6139f4692492ea35
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Monocytes/macrophages and neutrophils express the CCL3 and CCL5 receptor CCR1, while CD8+ T cells express the CXCL10 receptor CXCR3 and the CCL4 and CCL5 receptor CCR5.

summary:
In Homo sapiens, monocytes/macrophages and neutrophils express CCR1, while CD8+ T cells express CXCR3 and CCR5 in the medulloblastoma tumor microenvironment.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:369967e483a38b21e539
claim_id: claim:369967e483a38b21e539
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Additionally, monocytes/macrophages and neutrophils express the main GM-CSF receptor CSF2RA and are enriched in the IL-3, IL-5 and GM-CSF signalling pathway, indicating potential to respond to secreted GM-CSF.

summary:
In Homo sapiens, monocytes/macrophages and neutrophils express the granulocyte-macrophage colony-stimulating factor receptor CSF2RA in the medulloblastoma tumor microenvironment.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:145fd59447bb52c5cdd4
claim_id: claim:145fd59447bb52c5cdd4
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Additionally, monocytes/macrophages and neutrophils express the main GM-CSF receptor CSF2RA and are enriched in the IL-3, IL-5 and GM-CSF signalling pathway, indicating potential to respond to secreted GM-CSF.

summary:
In Homo sapiens, neutrophils express the granulocyte-macrophage colony-stimulating factor receptor CSF2RA in the medulloblastoma tumor microenvironment.


claim_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092:claim:0fbb378a4e9b3cdbe8c6
claim_id: claim:0fbb378a4e9b3cdbe8c6
paper_key: biorxiv:b3e65ef0-6e38-1014-8f8f-a6ec49a73092
span_literal:
Finally, neutrophils express the IL-1 (IL1R2 and IL1RAP) and IL-6 (IL6R and IL6ST) receptors and are the only cell type enriched for these pathways, indicating a possible neutrophil specific response to ZIKV-induced medulloblastoma-secreted interleukins.

summary:
In Homo sapiens, neutrophils express the interleukin-1 receptors IL1R2 and IL1RAP and the interleukin-6 receptors IL6R and IL6ST in the medulloblastoma tumor microenvironment.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:a5e6e39247c75f3830b2
claim_id: claim:a5e6e39247c75f3830b2
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
C1Q A/B/C genes were exclusively expressed in microglia, while C3 was highly expressed in microglia and astrocytes.

summary:
In Homo sapiens, C1QA, C1QB, and C1QC genes were exclusively expressed in microglia, while C3 was highly expressed in microglia and astrocytes.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:ab6a166d4c03bd7e45a5
claim_id: claim:ab6a166d4c03bd7e45a5
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Complement receptor encoding genes (C3AR1, C5AR2, ITGAM, ITGAX, ITGB2, VSIG4) were predominantly expressed in microglia, while neurons expressed a set of brain-specific putative receptors (NPTX 1/2, NPTXR, NRP1).

summary:
In Homo sapiens, complement receptor encoding genes C3AR1, C5AR2, ITGAM, ITGAX, ITGB2, and VSIG4 were predominantly expressed in microglia.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:09e23f259965797b0fea
claim_id: claim:09e23f259965797b0fea
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Endothelial cells abundantly expressed key regulators (CD46, CD55, CD59, CFH), while neurons and OPCs expressed a set of putative regulators (CSMD 1/2/3, and SUSD4).

summary:
In Homo sapiens, endothelial cells abundantly expressed key complement regulators CD46, CD55, CD59, and CFH.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:3e773e596ef6f938902d
claim_id: claim:3e773e596ef6f938902d
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Endothelial cells abundantly expressed key regulators (CD46, CD55, CD59, CFH), while neurons and OPCs expressed a set of putative regulators (CSMD 1/2/3, and SUSD4).

summary:
In Homo sapiens, oligodendrocyte precursor cells expressed putative complement regulators CSMD1, CSMD2, CSMD3, and SUSD4.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:74ccccbbf1efc1afbcb0
claim_id: claim:74ccccbbf1efc1afbcb0
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal: In CP, exclusive expression of C1QA, C1QB, and C1QC in microglia was observed.
summary:
In Homo sapiens hippocampus, exclusive expression of C1QA, C1QB, and C1QC in microglia was observed in the classical pathway.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:152056065978e8962398
claim_id: claim:152056065978e8962398
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal: In LP, MASP1 was predominantly expressed in astrocytes, OPC and ependymal cells.
summary:
In Homo sapiens hippocampus, MASP1 was predominantly expressed in astrocytes, oligodendrocyte precursor cells, and ependymal cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:1402e87ef01b447ff233
claim_id: claim:1402e87ef01b447ff233
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
In AP, expression of CFB was dominant in endothelial cells and C3 was expressed predominantly in microglia.

summary:
In Homo sapiens hippocampus, CFB expression was dominant in endothelial cells and C3 was expressed predominantly in microglia.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:4a682aabc5f9bcaf87aa
claim_id: claim:4a682aabc5f9bcaf87aa
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
In CP, microglia exhibited highly expressed C1QA, C1QB, and C1QC, absent in other cell types; endothelial cells showed notable expression of C1S and C1R, while inhibitory neurons demonstrated high expression of C2.

summary:
In Homo sapiens hippocampus, microglia exhibited highly expressed C1QA, C1QB, and C1QC; endothelial cells showed notable expression of C1S and C1R; inhibitory neurons demonstrated high expression of C2.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:e248ec0b78d11a67a588
claim_id: claim:e248ec0b78d11a67a588
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal: In TP endothelial cells expressed C7, while ependymal cells abundantly expressed C5 and C6.
summary:
In Homo sapiens hippocampus, endothelial cells expressed C7, while ependymal cells abundantly expressed C5 and C6.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:33fc61c0074472741bd8
claim_id: claim:33fc61c0074472741bd8
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
genes encoding the components of C1q, C1QA, C1QB, and C1QC, were uniquely expressed in microglia (Fig. 1A,E).

summary:
In Homo sapiens hippocampus, genes encoding the components of C1q, C1QA, C1QB, and C1QC, were uniquely expressed in microglia.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:27beb6d262ef79bf8f44
claim_id: claim:27beb6d262ef79bf8f44
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Endothelial cells were the main expressors of C1R and C1S, encoding the serine proteases C1r and C1s that bind C1q to form the C1 complex.

summary:
In Homo sapiens hippocampus, endothelial cells were the main expressors of C1R and C1S, encoding the serine proteases C1r and C1s.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:5611a21111935e4c83b4
claim_id: claim:5611a21111935e4c83b4
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary: In Homo sapiens hippocampus, C2 was predominantly expressed by neurons and microglia.
span_literal:
C2, encoding C2, the protease component of the CP C3 convertase (C4b2a), was predominantly expressed by neurons and microglia.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:40445a4e0bc1fb9872ff
claim_id: claim:40445a4e0bc1fb9872ff
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
the genes encoding the C4A and C4B isotypes, C4A and C4B demonstrated different expression patterns, the former primarily expressed by astrocytes and the latter by ependymal cells.

summary:
In Homo sapiens hippocampus, C4A was primarily expressed by astrocytes and C4B was primarily expressed by ependymal cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:d8279c296dbe1cb47c0c
claim_id: claim:d8279c296dbe1cb47c0c
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
MASP1 was expressed primarily by astrocytes with low expression in a small proportion of ependymal cells and OPCs while MASP2 expression was not detected (Fig. 1B,F).

summary:
In Homo sapiens hippocampus, MASP1 was expressed primarily by astrocytes with low expression in ependymal cells and oligodendrocyte precursor cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:3c4cf64684bb0b65ddf9
claim_id: claim:3c4cf64684bb0b65ddf9
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
C3 (encoding C3, the core component of the complement system), was predominantly expressed in microglia (43.7% expressing C3 gene) with low expression in astrocytes (3.9% expression) (Fig. 1C,G).

summary:
In Homo sapiens hippocampus, C3 was predominantly expressed in microglia with low expression in astrocytes.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:7a783b23d70b06389c89
claim_id: claim:7a783b23d70b06389c89
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
CFB (encoding the AP serine protease factor B) was predominantly expressed in microglia while CFD (encoding factor D) was primarily expressed in endothelial cells (Fig. 1C,G).

summary:
In Homo sapiens hippocampus, CFB was predominantly expressed in microglia while CFD was primarily expressed in endothelial cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:423cb903e171f97c3606
claim_id: claim:423cb903e171f97c3606
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
C5 was the most widely expressed, detected consistently in all cell types, with astrocytes and ependymal cells the highest expressors followed by OPCs and oligodendrocytes (Fig. 1D,H).

summary:
In Homo sapiens hippocampus, C5 was the most widely expressed terminal pathway gene, with astrocytes and ependymal cells the highest expressors.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:a05598682655738d9e85
claim_id: claim:a05598682655738d9e85
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Expression of C6 was highest in ependymal cells while C7 expression was highest in endothelial cells.

summary:
In Homo sapiens hippocampus, expression of C6 was highest in ependymal cells while C7 expression was highest in endothelial cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:f1c37d752ab0a5fe3bfb
claim_id: claim:f1c37d752ab0a5fe3bfb
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Genes encoding the integrin receptors for C3 fragments CR3 and CR4 (ITGAM, ITGAX and ITGB2) were abundantly and exclusively (apart from low expression in T cells) expressed by microglia (Fig. 2A,B).

summary:
In Homo sapiens hippocampus, genes encoding the integrin receptors for C3 fragments CR3 and CR4 (ITGAM, ITGAX, and ITGB2) were abundantly and exclusively expressed by microglia.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:416105efea2001b36bf8
claim_id: claim:416105efea2001b36bf8
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
The VSIG4 gene, encoding the C3 fragment receptor CRIg (Complement Receptor of the Immunoglobulin Superfamily) was strongly and exclusively expressed in microglia (Fig. 2A,B).

summary:
In Homo sapiens hippocampus, the VSIG4 gene, encoding the C3 fragment receptor CRIg, was strongly and exclusively expressed in microglia.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:93fc5334b4a5977971e3
claim_id: claim:93fc5334b4a5977971e3
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Genes encoding the anaphylatoxin receptors (C3AR1, C5AR1, C5AR2) were all expressed predominantly on microglia, although for C5AR1 ependymal cells also showed strong expression.

summary:
In Homo sapiens hippocampus, genes encoding the anaphylatoxin receptors C3AR1, C5AR1, and C5AR2 were all expressed predominantly on microglia, although C5AR1 was also strongly expressed in ependymal cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:9ada29554a59adf6d65d
claim_id: claim:9ada29554a59adf6d65d
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
The genes encoding the neuropilins and neuronal pentraxins (NRP1, NRP2, NPTX1, NPTX2, NPTXR), putative complement receptors primarily expressed in brain, were widely expressed in brain cells, most abundantly in excitatory neurons (Fig.2A,B).

summary:
In Homo sapiens hippocampus, the genes encoding the neuropilins and neuronal pentraxins (NRP1, NRP2, NPTX1, NPTX2, NPTXR) were most abundantly expressed in excitatory neurons.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:44722110361132d62439
claim_id: claim:44722110361132d62439
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Microglia exhibited high expression of genes encoding complement receptors C3AR1, C5AR1, ITGAM, ITGAX, ITGB2 and VSIG4; excitatory neurons showed expression of NPTX1, NPTX2, NPTXR, and C1QBP; endothelial cells displayed notable expression of CALR and NRP1.

summary:
In Homo sapiens hippocampus, microglia exhibited high expression of complement receptor genes C3AR1, C5AR1, ITGAM, ITGAX, ITGB2, and VSIG4.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:883353ff71683df5573f
claim_id: claim:883353ff71683df5573f
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Microglia exhibited high expression of genes encoding complement receptors C3AR1, C5AR1, ITGAM, ITGAX, ITGB2 and VSIG4; excitatory neurons showed expression of NPTX1, NPTX2, NPTXR, and C1QBP; endothelial cells displayed notable expression of CALR and NRP1.

summary:
In Homo sapiens hippocampus, excitatory neurons showed expression of NPTX1, NPTX2, NPTXR, and C1QBP.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:732c4fec91966f519d72
claim_id: claim:732c4fec91966f519d72
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal: Oligodendrocytes expressed the highest levels of CR1, while ependymal cells expressed C5AR1.
summary:
In Homo sapiens hippocampus, oligodendrocytes expressed the highest levels of CR1, while ependymal cells expressed C5AR1.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:eaa740ffd42b9c4e1554
claim_id: claim:eaa740ffd42b9c4e1554
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Genes encoding the “classical” complement regulators (CD46, CD55, CD59, CFH, SERPING1) were most highly expressed in endothelial cells, but also in many other cell types at lower levels (Fig. 2C,D).

summary:
In Homo sapiens hippocampus, genes encoding the classical complement regulators CD46, CD55, CD59, CFH, and SERPING1 were most highly expressed in endothelial cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:04caf785657e216ad30d
claim_id: claim:04caf785657e216ad30d
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
CLU, encoding the terminal pathway regulator clusterin, was broadly expressed in all cell types, highest in astrocytes and ependymal cells, CFI was significantly expressed only in endothelial cells, while genes encoding other “classical” regulators, VTN, CFP, CFH1 – CFH5, were minimally expressed in brain cells (Fig. 2C,D).

summary:
In Homo sapiens hippocampus, CLU, encoding the terminal pathway regulator clusterin, was highest in astrocytes and ependymal cells, and CFI was significantly expressed only in endothelial cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:ada02b030d76a8c9f32f
claim_id: claim:ada02b030d76a8c9f32f
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Of the putative regulators, genes encoding the CUB and Sushi Multiple Domain (CSMD; CSMD1 – CSMD3) and Sushi Domain Containing 4 (SUSD4; SUSD4) proteins were expressed by all cell types, most abundantly by OPCs and neurons, while SRPX2 was expressed in a small subset of astrocytes and endothelial cells (Fig. 2C,D).

summary:
In Homo sapiens hippocampus, CSMD1, CSMD2, CSMD3, and SUSD4 were most abundantly expressed by oligodendrocyte precursor cells and neurons, while SRPX2 was expressed in a small subset of astrocytes and endothelial cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:555ffb8f5f00849c7fc0
claim_id: claim:555ffb8f5f00849c7fc0
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Endothelial cells showed high expression of CD46, CD55, CD59, CFH, CFI, SERPING1 and SRPX2, while astrocytes exhibited notable expression of CLU and SRPX2.

summary:
In Homo sapiens hippocampus, endothelial cells showed high expression of CD46, CD55, CD59, CFH, CFI, SERPING1, and SRPX2.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:4b2025dfc580d21dfcd7
claim_id: claim:4b2025dfc580d21dfcd7
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal: Excitatory neurons predominantly expressed CFP, CSMD1, CSMD2, CSMD3 and SUSD4.
summary:
In Homo sapiens hippocampus, excitatory neurons predominantly expressed CFP, CSMD1, CSMD2, CSMD3, and SUSD4.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:72f3d573ff457d2d384f
claim_id: claim:72f3d573ff457d2d384f
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal: The CSMD1-3 genes were also highly expressed by OPC.
summary:
In Homo sapiens hippocampus, the CSMD1, CSMD2, and CSMD3 genes were also highly expressed by oligodendrocyte precursor cells.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:76d6364e32620e611f65
claim_id: claim:76d6364e32620e611f65
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Cell types were additionally annotated based on the expression of known marker genes: RBFOX3, SLC17A7 (excitatory neurons); RBFOX3, GAD1, GAD2 (inhibitory neurons); GFAP, AQP4, SLC1A2 (astrocytes); CX3CR1, P2RY12, APBB1IP (microglia); MOG, MBP, MOBP, PLP1 (oligodendrocytes); PDGFRA, CSPG4, OLIG1 (OPCs); CLDN5, VWF, PECAM1, FLT1 (endothelial cells); CFAP54, FOXJ1, RSPH1 (ependymal cells); and TRBC2, CD3D, CD3E (T cells).

summary:
In Homo sapiens hippocampus, excitatory neurons were annotated based on expression of RBFOX3 and SLC17A7.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:2c9b26e6f30a81a51c37
claim_id: claim:2c9b26e6f30a81a51c37
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Cell types were additionally annotated based on the expression of known marker genes: RBFOX3, SLC17A7 (excitatory neurons); RBFOX3, GAD1, GAD2 (inhibitory neurons); GFAP, AQP4, SLC1A2 (astrocytes); CX3CR1, P2RY12, APBB1IP (microglia); MOG, MBP, MOBP, PLP1 (oligodendrocytes); PDGFRA, CSPG4, OLIG1 (OPCs); CLDN5, VWF, PECAM1, FLT1 (endothelial cells); CFAP54, FOXJ1, RSPH1 (ependymal cells); and TRBC2, CD3D, CD3E (T cells).

summary:
In Homo sapiens hippocampus, inhibitory neurons were annotated based on expression of RBFOX3, GAD1, and GAD2.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:193a431a40fcebb9b0a6
claim_id: claim:193a431a40fcebb9b0a6
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
span_literal:
Cell types were additionally annotated based on the expression of known marker genes: RBFOX3, SLC17A7 (excitatory neurons); RBFOX3, GAD1, GAD2 (inhibitory neurons); GFAP, AQP4, SLC1A2 (astrocytes); CX3CR1, P2RY12, APBB1IP (microglia); MOG, MBP, MOBP, PLP1 (oligodendrocytes); PDGFRA, CSPG4, OLIG1 (OPCs); CLDN5, VWF, PECAM1, FLT1 (endothelial cells); CFAP54, FOXJ1, RSPH1 (ependymal cells); and TRBC2, CD3D, CD3E (T cells).

summary:
In Homo sapiens hippocampus, astrocytes were annotated based on expression of GFAP, AQP4, and SLC1A2.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:1e1affad2767258e182e
claim_id: claim:1e1affad2767258e182e
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary:
In Homo sapiens hippocampus, microglia were annotated based on expression of CX3CR1, P2RY12, and APBB1IP.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:38e7f17e2341a0aa03f9
claim_id: claim:38e7f17e2341a0aa03f9
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary:
In Homo sapiens hippocampus, oligodendrocytes were annotated based on expression of MOG, MBP, MOBP, and PLP1.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:b633f075677561133a55
claim_id: claim:b633f075677561133a55
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary:
In Homo sapiens hippocampus, oligodendrocyte precursor cells were annotated based on expression of PDGFRA, CSPG4, and OLIG1.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:9b28c5eb4ccd56365b53
claim_id: claim:9b28c5eb4ccd56365b53
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary:
In Homo sapiens hippocampus, endothelial cells were annotated based on expression of CLDN5, VWF, PECAM1, and FLT1.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:d6759e92a0c4cd6d1831
claim_id: claim:d6759e92a0c4cd6d1831
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary:
In Homo sapiens hippocampus, ependymal cells were annotated based on expression of CFAP54, FOXJ1, and RSPH1.


claim_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6:claim:acc4091654e4d9f29120
claim_id: claim:acc4091654e4d9f29120
paper_key: biorxiv:b60c0833-6df2-1014-8865-f92ffff4fcc6
summary: In Homo sapiens hippocampus, excitatory neurons predominantly expressed NPTX1, NPTX2, and NPTXR.
span_literal:
Excitatory neurons predominantly expressed NPTX1, NPTX2, and NPTXR; the other complement receptor genes, ITGB2, ITGAX and VISG4, were highly expressed in microglia, demonstrating cell-type-specific gene expression patterns.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:56505cd5b0697a14c889
claim_id: claim:56505cd5b0697a14c889
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
α clusters showed features of stem/progenitor cells (s/p), including a high proliferation score, strong enrichment of proliferation and stem marker gene expression (TK1, EZH2, AURKA, HES4), long RNA velocity vectors showing a multidirectional pattern, and a prominent G2/M transcriptional profile.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, stem/progenitor cells are marked by positive expression of TK1, EZH2, AURKA, and HES4.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:43a19f2ca234d0441c4c
claim_id: claim:43a19f2ca234d0441c4c
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
β and δ clusters were the most adenocarcinoma-like, featuring a high AR signature score, low NE score, strong enrichment of ACPC marker gene expression (AR, KLK3), no enrichment of the G2/M state, a low proliferation score compared to the progenitor group, and a more uniform direction of RNA velocity vectors.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, adenocarcinoma-like cells are marked by positive expression of AR and KLK3.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:d27aa53c9470db0275ad
claim_id: claim:d27aa53c9470db0275ad
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
The γ subclusters showed the most neuroendocrine-like differentiation with a high NE score, a low AR signature score, strong enrichment of NE marker gene expression (CHGA, SCG2), no enrichment of the G2/M state, a low proliferation score, and a uniform direction of short RNA velocity vectors.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, neuroendocrine-like cells are marked by positive expression of CHGA and SCG2.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:152cc9143c02ad1a9cb6
claim_id: claim:152cc9143c02ad1a9cb6
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
Clusters-3 in both models were distinguished as the most neuroendocrine-like, exhibiting a relative absence of REST activity and high activity scores for TFs such as NRF1, HES4 and ONECUT2

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, neuroendocrine-like cells exhibit negative REST activity and positive NRF1, HES4, and ONECUT2 transcription factor activity.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:d90cb80bc5a89c90b3ff
claim_id: claim:d90cb80bc5a89c90b3ff
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
Inferred TF activities in subclusters 1.1 and 2.1, were consistent with a stem-like phenotype and included WNT pathway effectors such as TCF7 and TCF7L2, and retinoid X receptors

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, stem-like cells show positive transcription factor activity of TCF7 and TCF7L2.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:04d5046828adc94d3f63
claim_id: claim:04d5046828adc94d3f63
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
co-occurred with TFs determining luminal epithelial (FOXA1, AR, NR3C1) and neural (NR2F1, ASCL1) lineages

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, stem-like cells show co-occurring positive transcription factor activity of luminal epithelial factors FOXA1, AR, and NR3C1, and neural factors NR2F1 and ASCL1.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:2c3cafb28f5086692033
claim_id: claim:2c3cafb28f5086692033
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal: we identified MAP3K5/ASK1 as a top differentially expressed gene marking cluster III of PC35-2
summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, MAP3K5 (also known as ASK1) is a positive marker of cluster III cells.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:2da02d9a6dbc659961b4
claim_id: claim:2da02d9a6dbc659961b4
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
Subpopulations were identified by marker gene expression: AR to mark ACPC lineage; SCG2 to mark NEPC lineage; TK1, EZH2 and AURKA and EdU incorporation to mark stem-like/progenitors.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, AR marks adenocarcinoma prostate cancer cells, SCG2 marks neuroendocrine prostate cancer cells, and TK1, EZH2, and AURKA mark stem-like/progenitor cells.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:ef45a06fe9a59e2ca9de
claim_id: claim:ef45a06fe9a59e2ca9de
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
Subpopulations were identified by marker gene expression: AR to mark ACPC lineage; SCG2 to mark NEPC lineage; TK1, EZH2 and AURKA and EdU incorporation to mark stem-like/progenitors.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, SCG2 marks neuroendocrine prostate cancer cells.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:2016d6904719019e40c5
claim_id: claim:2016d6904719019e40c5
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
Subpopulations were identified by marker gene expression: AR to mark ACPC lineage; SCG2 to mark NEPC lineage; TK1, EZH2 and AURKA and EdU incorporation to mark stem-like/progenitors.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer organoids, TK1, EZH2, and AURKA mark stem-like/progenitor cells.


claim_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081:claim:3ee322ad25a654ceb1f4
claim_id: claim:3ee322ad25a654ceb1f4
paper_key: biorxiv:b629f2a0-6f39-1014-bcfe-d40330cad081
span_literal:
We found Aurora Kinase A, a regulator of mitotic progression, stem cell self-renewal, and asymmetric division (David M Glover, 1995; Eterno et al., 2016; Wang et al., 2019), to be expressed and restricted to the stem/progenitors.

summary:
In Homo sapiens metastatic castration-resistant prostate cancer, Aurora Kinase A (AURKA) is positively expressed and restricted to stem/progenitor cells.


claim_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4:claim:0628e2f98d521fd10681
claim_id: claim:0628e2f98d521fd10681
paper_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4
summary: In Homo sapiens prostate cancer tissue, panCK26, S6, and NaKATPase are markers of epithelial cells.
span_literal:
epithelial cell markers (panCK26, S6, NaKATPase), basal cell markers (p63, CK5), a cancer cell marker (AMACR), and T cell markers (CD3, CD4, CD8, FOXP3, CD68)


claim_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4:claim:4f217e8963c4cd89193b
claim_id: claim:4f217e8963c4cd89193b
paper_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4
span_literal:
epithelial cell markers (panCK26, S6, NaKATPase), basal cell markers (p63, CK5), a cancer cell marker (AMACR), and T cell markers (CD3, CD4, CD8, FOXP3, CD68)

summary:
In Homo sapiens prostate cancer tissue, AMACR (alpha-methylacyl-CoA racemase) is a marker of cancer cells.


claim_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4:claim:a5a8c2afedb80744cac1
claim_id: claim:a5a8c2afedb80744cac1
paper_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4
summary: In Homo sapiens prostate tissue, cancerous epithelial cells are negative for p63 and CK5.
span_literal:
CE cells were negative for both markers (p63⁻, CK5⁻) and N-CE cells positive for ≥ 1 marker (p63⁺ or CK5⁺).


claim_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4:claim:cc151a42febc323189be
claim_id: claim:cc151a42febc323189be
paper_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4
summary: In Homo sapiens prostate cancer tissue, T-helper cells are positive for CD3 and CD4.
span_literal:
T-helper cells (TH: CD3⁺CD4⁺), T-regulatory cells (Treg: CD3⁺CD4⁺FOXP3⁺), and macrophages (CD68⁺) were labeled.


claim_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4:claim:6f89bee2114ffb689fbf
claim_id: claim:6f89bee2114ffb689fbf
paper_key: biorxiv:b71d9b5e-6f1d-1014-9408-ec8c7da502b4
span_literal:
AMACR (alpha-methylacyl-CoA racemase), a key enzyme involved in fatty-acid metabolism, serves as a well-established diagnostic biomarker that is markedly overexpressed in prostate-cancer epithelium compared with benign glands [34].

summary:
In Homo sapiens, AMACR (alpha-methylacyl-CoA racemase) is a positive marker of prostate cancer epithelial cells compared with benign gland cells.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:3cd732b8f7a90787fea9
claim_id: claim:3cd732b8f7a90787fea9
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal: colonocyte-like (FABP1, CEACAM7, ANPEP, SI)
summary:
In Homo sapiens colorectal cancer, colonocyte-like cancer cells are marked by FABP1, CEACAM7, ANPEP, and SI.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:882bb923f2dc2b0330e3
claim_id: claim:882bb923f2dc2b0330e3
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal: Goblet-like (MUC2, FCGBP, ZG16, ATOH1)
summary:
In Homo sapiens colorectal cancer, goblet-like cancer cells are marked by MUC2, FCGBP, ZG16, and ATOH1.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:89f01e1b111e2a445974
claim_id: claim:89f01e1b111e2a445974
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal: TA-like (TOP2A, UBE2C, PCLAF, HELLS, TK1)
summary:
In Homo sapiens colorectal cancer, transit-amplifying-like cancer cells are marked by TOP2A, UBE2C, PCLAF, HELLS, and TK1.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:b22de86855922ff0caee
claim_id: claim:b22de86855922ff0caee
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal:
There are highly mitotic/proliferative clusters (LGR5, TOP2A, MKI67) of both COAD and READ that resemble highly aggressive and invasive cancer cells.

summary:
In Homo sapiens colorectal cancer, highly mitotic/proliferative cancer cells express LGR5, TOP2A, and MKI67.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:4eeaa971bb2774845d1c
claim_id: claim:4eeaa971bb2774845d1c
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal:
These include T cells - CD4 (CD4), CD8 (CD8A), and T regulatory cells (FOXP3) - as well as NK cells (NKG7, TYROBP).

summary:
In Homo sapiens, CD4 T cells are marked by CD4, CD8 T cells by CD8A, T regulatory cells by FOXP3, and natural killer cells by NKG7 and TYROBP.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:2bc66807cbe90c686c63
claim_id: claim:2bc66807cbe90c686c63
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
summary: In Homo sapiens, naïve B cells are marked by IGHD and TCL1A.
span_literal:
B cells are represented as naïve (IGHD, TCL1A), memory (CD27,CD44), and activated (CD69, CD83) subsets, while plasma cells (JCHAIN) express immunoglobulins such as IgA (IGHA1), IgG (IGHG1), and IgM (IGHM).


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:60b506615dcee2b9d0a5
claim_id: claim:60b506615dcee2b9d0a5
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
summary: In Homo sapiens, monocytes are marked by VCAN and CD14.
span_literal:
The myeloid lineage encompasses monocytes (VCAN, CD14), macrophages (C1QA, C1QB), mast cells (TPSB2, CPA3), and dendritic cells, including classical (CLEC9A, CD1C) and plasmacytoid subsets (IL3RA, GZMB), as well as eosinophils (CLC, CCR3) and neutrophils (CXCR2, FCGR3B).


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:c3a9fdb11d40cbf32d5c
claim_id: claim:c3a9fdb11d40cbf32d5c
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
summary: In Homo sapiens, gamma-delta T cells are marked by TRDV1 and TRGC1.
span_literal:
Specialized populations such as gamma-delta T cells (TRDV1, TRGC1) and innate lymphoid cells (ILCs; IL4I1, KIT) are also depicted, along with immune cell developmental stages, such as progenitors (CD24, AXL) and stem-like cells (LEF1), and cycling states (MKI67, CDK1).


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:6de8b1f90af611c2ca5e
claim_id: claim:6de8b1f90af611c2ca5e
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal:
TAN markers (OLR1, PLAU, VEGFA) were highly upregulated in TAN, whereas CXCR2, a marker of mature neutrophils, was highly expressed in blood neutrophils but downregulated in TAN (Figure 4F).

summary:
In Homo sapiens, tumor-associated neutrophils are marked by positive expression of OLR1, PLAU, and VEGFA, whereas CXCR2, a marker of mature neutrophils, is downregulated in tumor-associated neutrophils compared to blood neutrophils.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:adce88626770166f3ffe
claim_id: claim:adce88626770166f3ffe
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal:
From TAN1, neutrophils diverged into two trajectories: one leading to a putative pro-tumor TAN phenotype (TAN4) characterized by high IL1A expression, a key driver of emergency myelopoiesis that fuels inflammation and immunosuppression in the TME28, and another toward a phenotype defined by high expression of antigen-presentation-associated markers, such as HLA-DRA (TAN2/TAN3) (Figure 4J).

summary:
In Homo sapiens colorectal cancer, the putative pro-tumor tumor-associated neutrophil 4 phenotype is characterized by high IL1A expression, while tumor-associated neutrophil 2/tumor-associated neutrophil 3 are defined by high expression of the antigen-presentation-associated marker HLA-DRA.


claim_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e:claim:069035f34bb5d3be1331
claim_id: claim:069035f34bb5d3be1331
paper_key: biorxiv:b7d0eaf3-6f9e-1014-bc01-ef7867d59c7e
span_literal:
From TAN1, neutrophils diverged into two trajectories: one leading to a putative pro-tumor TAN phenotype (TAN4) characterized by high IL1A expression, a key driver of emergency myelopoiesis that fuels inflammation and immunosuppression in the TME28, and another toward a phenotype defined by high expression of antigen-presentation-associated markers, such as HLA-DRA (TAN2/TAN3) (Figure 4J).

summary:
In Homo sapiens colorectal cancer, tumor-associated neutrophil 2/tumor-associated neutrophil 3 are defined by high expression of the antigen-presentation-associated marker HLA-DRA.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:e31c88b5bcd3889bb7ed
claim_id: claim:e31c88b5bcd3889bb7ed
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
span_literal: CD86 for M1, CD206 for M2a and CD163 for M2c
summary:
In Homo sapiens, CD86 is a marker for M1 macrophages, CD206 (MRC1) is a marker for M2a macrophages, and CD163 is a marker for M2c macrophages.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:3408e6ebe1cf1b743a31
claim_id: claim:3408e6ebe1cf1b743a31
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
span_literal:
Among the proteins that were highly upregulated in the M1 macrophages compared to both M2a and M2c macrophages (Table S1) were CD86, which is used as a surface marker for the M1 state (FDR < 1.09×10−3 and Log2FC > 3.38), as well as a number of well-studied inflammatory proteins, such as GBP1, IDO1, ISG15, and MX154,55 (GBP1: FDR < 2.31×10−4 and Log2FC > 4.12; IDO1: FDR < 4.21×10−3 and Log2FC > 6.54; ISG15: FDR < 5.66×10−4 and Log2FC > 5.01; MX1: FDR < 7.18×10−4 and Log2FC > 5.70).

summary:
In Homo sapiens, CD86, GBP1, IDO1, ISG15, and MX1 are upregulated in M1 macrophages compared to both M2a and M2c macrophages.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:b830cab99c3bae796bc2
claim_id: claim:b830cab99c3bae796bc2
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
span_literal:
Analogously, IL-4 and IL-13 treated macrophages had highly upregulated levels of several surface proteins that were used in previous studies as markers for immunosuppressive M2a macrophages. These included CD209, CD206/MRC1 and CD163 (CD209: FDR < 5.74×10−5 and Log2FC > 5.39; MRC1: FDR < 1.27×10−3 and Log2FC > 1.90; CD163: FDR < 2.05×10−2 and Log2FC > 3.77)28,56,57.

summary:
In Homo sapiens, CD209, CD206/MRC1, and CD163 are upregulated surface protein markers for immunosuppressive M2a macrophages.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:07574b1141ae56014e9e
claim_id: claim:07574b1141ae56014e9e
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
summary: In Homo sapiens, CD209 and CD163 are significantly upregulated surface markers in M2c macrophages.
span_literal:
Similarly, M2c macrophages had a significantly upregulated expression of surface markers CD209 and CD163 (CD209: FDR < 4.93×10−4 and Log2FC > 3.36; CD163: FDR < 2.63×10−3 and Log2FC > 5.47).


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:07801adf5ccd087b830d
claim_id: claim:07801adf5ccd087b830d
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
summary: In Homo sapiens, macrophage cells express the myeloid markers AIF1, CD14, and LYZ.
span_literal:
Macrophage cells identified this way expressed myeloid markers AIF1, CD14 and LYZ (Figure S4C)16,17,111.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:8680eca9ef823ed7e946
claim_id: claim:8680eca9ef823ed7e946
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
span_literal:
cells characterized by high expression of tumor markers (EPCAM, KRT19 and MLANA, or AFP, GPC3 and VIL1

summary:
In Homo sapiens, tumor cells are characterized by high expression of EPCAM, KRT19, MLANA, AFP, GPC3, and VIL1.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:0257e4cf5d8bb73c2901
claim_id: claim:0257e4cf5d8bb73c2901
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
span_literal:
markers that relate to functionally well-characterized in vitro polarization states, such as CD206 after exposure to IL-4 and/or IL-13, or CD163 after exposure to both IL-4 and IL-10 stimuli are regularly used in immunohistochemistry (IHC) characterizations of clinical samples14,15.

summary:
In Homo sapiens, CD206 is a marker for macrophages polarized with interleukin-4 and/or interleukin-13, and CD163 is a marker for macrophages polarized with both interleukin-4 and interleukin-10.


claim_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a:claim:00060dcc6285e6849eb5
claim_id: claim:00060dcc6285e6849eb5
paper_key: biorxiv:b88cbe76-6c0b-1014-a018-e498be98267a
span_literal:
markers that relate to functionally well-characterized in vitro polarization states, such as CD206 after exposure to IL-4 and/or IL-13, or CD163 after exposure to both IL-4 and IL-10 stimuli are regularly used in immunohistochemistry (IHC) characterizations of clinical samples14,15.

summary:
In Homo sapiens, CD163 is a marker for macrophages polarized with both interleukin-4 and interleukin-10.


claim_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07:claim:bec1d4961130311a3110
claim_id: claim:bec1d4961130311a3110
paper_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07
span_literal: RBM47, ABR, and RNF144B were positively correlated with macrophages
summary:
In Homo sapiens, macrophages are positively correlated with expression of RBM47, ABR, and RNF144B in myocardial infarction.


claim_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07:claim:4d49fd032f20fccd8c70
claim_id: claim:4d49fd032f20fccd8c70
paper_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07
span_literal: FN1 and COL6A3 showed a strong positive correlation with T follicular helper (TFH) cells
summary:
In Homo sapiens, T follicular helper cells show a strong positive correlation with FN1 and COL6A3 expression in myocardial infarction.


claim_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07:claim:54796438c2f8254be750
claim_id: claim:54796438c2f8254be750
paper_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07
span_literal: POSTN and TBC1D8 exhibited a significant negative correlation with T cells
summary:
In Homo sapiens, T cells exhibit a significant negative correlation with POSTN and TBC1D8 expression in myocardial infarction.


claim_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07:claim:8aad9deff1adf3765f66
claim_id: claim:8aad9deff1adf3765f66
paper_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07
span_literal: COL1A1 and DPYSL3 showed positive correlations with B cells
summary:
In Homo sapiens, B cells show positive correlations with COL1A1 and DPYSL3 expression in myocardial infarction.


claim_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07:claim:0cbf94f85b429f3cdd53
claim_id: claim:0cbf94f85b429f3cdd53
paper_key: biorxiv:b9f9eea1-7c5b-1014-87f0-cbc500249f07
span_literal: SDC2, C5AR1, and GPC6 were positively correlated with dendritic cells
summary:
In Homo sapiens, dendritic cells are positively correlated with SDC2, C5AR1, and GPC6 expression in myocardial infarction.


claim_key: biorxiv:ba2fe3cc-7145-1014-8950-ece91a9c7114:claim:f709e9ed5593534b8b8d
claim_id: claim:f709e9ed5593534b8b8d
paper_key: biorxiv:ba2fe3cc-7145-1014-8950-ece91a9c7114
span_literal:
the subset of clusters with high gene activity for T-cell markers (CD4, CD8A, CD3E) and high fraction of cells previously annotated as T-cell was selected

summary:
In Homo sapiens, T cells are identified by high gene activity of the T-cell markers CD4, CD8A, and CD3E.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:44f3c1f7d59041288f2d
claim_id: claim:44f3c1f7d59041288f2d
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
In acinar cells (Figure 3, A-B), we observe significant down-regulation of key function genes including CELA2A and AMY2B, alongside up-regulation of stress-response genes such as RPL13 and RPS3A.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, acinar cells show significant down-regulation of CELA2A and AMY2B and up-regulation of RPL13 and RPS3A compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:77c39b43b7ead3b07f82
claim_id: claim:77c39b43b7ead3b07f82
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Beta cells (Figure 3, C-D) show alterations in endocrine function genes including down-regulation of CLPS and PRSS1, and up-regulation of CTRB2 and CELA3B, with corresponding pathway enrichment in pancreatic secretion, diabetes-related pathways, and various digestion and absorption pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, beta cells show down-regulation of CLPS and PRSS1 and up-regulation of CTRB2 and CELA3B compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:780220f5cfbf3ec1e4b8
claim_id: claim:780220f5cfbf3ec1e4b8
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Ductal cells (Figure 3, E-F) demonstrate significant changes in genes such as down-regulated CLPS and PNLIP, up-regulated HSPB1 and TMBIM1, with pathway enrichment strongly focused on pancreatic secretion, fat and protein digestion and absorption pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, ductal cells show down-regulation of CLPS and PNLIP and up-regulation of HSPB1 and TMBIM1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:d4b7cbcc1469b156c83d
claim_id: claim:d4b7cbcc1469b156c83d
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
immune cells show extensive transcriptional changes including up-regulation of MIF and PPDPF, and down-regulation of CLPS and PRSS1, with pathway enrichment in pancreatic secretion, digestive and metabolic pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma pancreatic tissue, immune cells show up-regulation of MIF and PPDPF and down-regulation of CLPS and PRSS1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:7b0cadfa55e18a72bcff
claim_id: claim:7b0cadfa55e18a72bcff
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
CD8 T cells (Figure 5, A-B) show activation of inflammatory genes including up-regulation of ZFP36, CMC1 and TSC22D3, together with down-regulation of MT-ND1.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, CD8 T cells show up-regulation of ZFP36, CMC1, and TSC22D3 and down-regulation of MT-ND1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:beee5daa76e5a1a410f0
claim_id: claim:beee5daa76e5a1a410f0
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
CD8 TEM cells (Figure 5, C-D) exhibit changes in up-regulated ZFP36 and down-regulated AKR1C3 expression, with pathway enrichment in malaria, leishmaniasis, and legionellosis pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, CD8 effector memory T cells show up-regulation of ZFP36 and down-regulation of AKR1C3 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:7ee3bf7367a82e0fbdb9
claim_id: claim:7ee3bf7367a82e0fbdb9
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
NK cells (Figure 5, E-F) demonstrate alterations in down-regulated RAB34, S100B and CX3CR1 genes, together with up-regulated BTG1 genes, with extensive enrichment in diverse pathways including phototransduction, pertussis, renin secretion, and various metabolic and immune signaling pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, natural killer cells show down-regulation of RAB34, S100B, and CX3CR1 and up-regulation of BTG1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:0ce0337b22e2073149cd
claim_id: claim:0ce0337b22e2073149cd
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
CD4 T cells (Figure 6, A-B) display up-regulation of RPL13A, NBEAL1 and down-regulation of RPS4Y1, accompanied by enrichment in IL-17 signaling pathway, Coronavirus disease-COVID-19, and Salmonella infection pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, CD4 T cells show up-regulation of RPL13A and NBEAL1 and down-regulation of RPS4Y1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:ce438c42919e589281a3
claim_id: claim:ce438c42919e589281a3
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
CD4 TCM cells (Figure 6, C-D) exhibit changes in up-regulated RPL13A, RPL36A and down-regulated RPS4Y1 expression, with pathway enrichment in prostate cancer, toxoplasmosis, and infectious disease-related pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, CD4 central memory T cells show up-regulation of RPL13A and RPL36A and down-regulation of RPS4Y1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:2260a78e9277f815f975
claim_id: claim:2260a78e9277f815f975
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
HSPCs (Figure 7, A-B) display up-regulation of RPL32 and RPS15, and down-regulation of SNCG, WFDC2 and BPIFB1, alongside enrichment in type I diabetes mellitus, allograft rejection, and infectious disease pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, hematopoietic stem and progenitor cells show up-regulation of RPL32 and RPS15 and down-regulation of SNCG, WFDC2, and BPIFB1 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:bd656bce6b94ea8c959a
claim_id: claim:bd656bce6b94ea8c959a
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Monocytes (Figure 7, C-D) show down-regulation of FLNB and HABP4 without significant upregulated genes, with enrichment in cytoskeleton and calcium signaling pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, monocytes show down-regulation of FLNB and HABP4 compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:31e3f05179edeb8cc2dd
claim_id: claim:31e3f05179edeb8cc2dd
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
B cells (Figure 8, C-D) show down-regulation of RAB28, AKT1 and EIF1AY without significant up-regulated genes, accompanied by extensive enrichment in VEGF signaling, longevity regulating pathway, and numerous signaling cascades.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, B cells show down-regulation of RAB28, AKT1, and EIF1AY compared to healthy controls.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:964a1b04b092d0ce5cfa
claim_id: claim:964a1b04b092d0ce5cfa
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Acinar cells show markedly increased expression of mitochondrial genes MT-CO1 and MT-CO2, indicating enhanced oxidative phosphorylation activity.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, acinar cells show increased expression of MT-CO1 and MT-CO2, indicating enhanced oxidative phosphorylation activity.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:15029327c65cc360eba5
claim_id: claim:15029327c65cc360eba5
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
We detect elevated levels of MIF, TMSB10, and S100A6, indicative of chronic inflammation and immune dys-regulation.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma tumor microenvironment, immune cells show elevated levels of MIF, TMSB10, and S100A6, indicative of chronic inflammation and immune dysregulation.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:10c56eb784a8ceb44224
claim_id: claim:10c56eb784a8ceb44224
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Effector molecules essential for tumor clearance, such as CX3CR1 in NK cells and TNFRSF25 in CD8 T cells, are downregulated, while the immunosuppressive regulator TSC22D3 is upregulated, consistent with terminal T cell exhaustion [26].

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, natural killer cells show down-regulation of CX3CR1, an effector molecule essential for tumor clearance.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:57ce09870a1e1a3871be
claim_id: claim:57ce09870a1e1a3871be
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Effector molecules essential for tumor clearance, such as CX3CR1 in NK cells and TNFRSF25 in CD8 T cells, are downregulated, while the immunosuppressive regulator TSC22D3 is upregulated, consistent with terminal T cell exhaustion [26].

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CD8 T cells show down-regulation of TNFRSF25 and up-regulation of the immunosuppressive regulator TSC22D3, consistent with terminal T cell exhaustion.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:b52131fd5bedb7d8e882
claim_id: claim:b52131fd5bedb7d8e882
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
CD4 T cells exhibit overactivation of the IL-17 pathway and downregulation of the homing receptor CCR7, indicating an inflammatory yet spatially disoriented immune state.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CD4 T cells show down-regulation of the homing receptor CCR7, indicating a spatially disoriented immune state.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:a0955c6d36d7d3292bf4
claim_id: claim:a0955c6d36d7d3292bf4
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Similarly, CD4 TCM cells display identity confusion and aberrant activation of cancer- and infection-related programs, coupled with reduced expression of transcriptional regulators (JUND, GNAS) and increased ribosomal activity—features characteristic of terminally differentiated and functionally exhausted memory T cells [27].

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, CD4 central memory T cells show reduced expression of transcriptional regulators JUND and GNAS, features characteristic of terminally differentiated and functionally exhausted memory T cells.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:2fbda7e464d65ce4d2fa
claim_id: claim:2fbda7e464d65ce4d2fa
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Hematopoietic stem and progenitor cells (HSPCs) show aberrant activation of autoimmune programs while suppressing key defense genes (SNCG, WFDC2, BPIFB1), suggesting defective myelopoiesis driven by chronic inflammation.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, hematopoietic stem and progenitor cells show suppression of key defense genes SNCG, WFDC2, and BPIFB1, suggesting defective myelopoiesis driven by chronic inflammation.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:aeaf972b80fd8086387d
claim_id: claim:aeaf972b80fd8086387d
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Circulating monocytes also exhibit structural (FLNB), communication (HABP4), and activation (KCNN3) defects, consistent with the paralyzed, immunosuppressive phenotype of tumor-associated monocytes reported in PDAC [29].

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, circulating monocytes exhibit defects in FLNB, HABP4, and KCNN3, consistent with the paralyzed, immunosuppressive phenotype of tumor-associated monocytes.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:d462109cfab687a4c87f
claim_id: claim:d462109cfab687a4c87f
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
One subset shows autoimmune activation with loss of the inhibitory receptor CD22, consistent with reports that B cell dysregulation contributes to tumor-associated autoimmunity and chronic inflammation in pancreatic cancer [30].

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, a B cell subset shows loss of the inhibitory receptor CD22, consistent with B cell dysregulation contributing to tumor-associated autoimmunity.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:debec75cba74254eed07
claim_id: claim:debec75cba74254eed07
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Conventional B cells display widespread downregulation of genes involved in survival (AKT1), trafficking (RAB28), and translation (EIF1AY), suggesting apoptosis and loss of antigen-presenting capacity, consistent with recent observations of B cell exhaustion across multiple solid tumors including PDAC.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, conventional B cells display widespread down-regulation of AKT1, RAB28, and EIF1AY, suggesting apoptosis and loss of antigen-presenting capacity.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:6d729b8cd2d2ba404b6f
claim_id: claim:6d729b8cd2d2ba404b6f
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Ductal cells also display elevated expression of survival and stress-response genes (TMBIM1, HSPB1), consistent with the adaptive epithelial states observed during oncogenic transformation [22].

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, ductal cells display elevated expression of survival and stress-response genes TMBIM1 and HSPB1, consistent with adaptive epithelial states during oncogenic transformation.


claim_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb:claim:767ae599a82d8f01fad0
claim_id: claim:767ae599a82d8f01fad0
paper_key: biorxiv:bb90a40e-70a1-1014-887a-db6e99ca95cb
span_literal:
Other unclassified cells (Figure 8, A-B) exhibit changes in CD22, SNCG and RPS15 expression, with enrichment in allograft rejection, type I diabetes mellitus, and various immune and metabolic pathways.

summary:
In Homo sapiens pancreatic ductal adenocarcinoma peripheral blood, other unclassified cells exhibit changes in CD22, SNCG, and RPS15 expression.


claim_key: biorxiv:bba3f638-6e9f-1014-acea-8b24d5cb22ff:claim:b3eb3093f1a10932e8bc
claim_id: claim:b3eb3093f1a10932e8bc
paper_key: biorxiv:bba3f638-6e9f-1014-acea-8b24d5cb22ff
summary: In Homo sapiens, activated monocytes are marked by positive expression of HLA-DR.
span_literal:
the responding phenotype observed after IFNa stimulation was also found at baseline (in the pre-stimulation condition) to positively associate with age in plasmacytoid dendritic cells (pDCs), conventional/myeloid DCs, activated monocytes (HLA-DR+), and CD38hi naive B-cells.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:f672144119ce20b6d2c2
claim_id: claim:f672144119ce20b6d2c2
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
summary: In Homo sapiens skin, basal cells are marked by COL17A1, KRT5, and KRT14.
span_literal:
we annotated each cell population based on their specific markers, including basal cells (COL17A1, KRT5, KRT14), spinous cells (KRT1, KRT10), granular cells (FLG, LOR), proliferating keratinocytes (Pro KCs) (MKI67, TOP2A), follicular cells (KRT6B, KRT17, SFRP1), Langerhans cells (CD207, CD1A), T cells (CD3D, PTPRC), melanocytes (PMEL, TYRP1) and fibroblasts (DCN, COL1A1)


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:d3224380698bab808c46
claim_id: claim:d3224380698bab808c46
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
Compared to Basal1, the expression levels of stemness markers (COL17A1, TP63, ITGB1, ITGA3) were decreased while inflammatory response genes (KRT16, S100A8, S100A9) were increased in Basal2

summary:
In Homo sapiens skin, the Basal2 subpopulation shows decreased expression of stemness markers COL17A1, TP63, ITGB1, and ITGA3 compared to the Basal1 subpopulation, while inflammatory response genes KRT16, S100A8, and S100A9 are increased.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:0a10ed4a78e3d9727695
claim_id: claim:0a10ed4a78e3d9727695
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
Compared with Spinous1, Spinous2 highly expressed small proline rich region proteins (SPRRs) encoding genes, such as SPRR1B, SPRR2D and SPRR2E

summary:
In Homo sapiens skin, the Spinous2 subpopulation highly expresses small proline rich region protein encoding genes SPRR1B, SPRR2D, and SPRR2E compared to the Spinous1 subpopulation.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:df2139d7cfb75976550e
claim_id: claim:df2139d7cfb75976550e
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
Meanwhile, Spinous2 also highly expressed the cysteine protease inhibitor M/E (CST6), suggesting that Spinous2 subgroup was a well-differentiated upper spinous layer

summary:
In Homo sapiens skin, the Spinous2 subpopulation highly expresses the cysteine protease inhibitor M/E CST6, suggesting it represents a well-differentiated upper spinous layer.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:0ddd27580aafdb8fa99e
claim_id: claim:0ddd27580aafdb8fa99e
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal: Follicular2 showed high levels of genes related to WNT signaling pathway (SFRP1, FRZB and DKK3)
summary:
In Homo sapiens skin, the Follicular2 subpopulation shows high expression of WNT signaling pathway related genes SFRP1, FRZB, and DKK3.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:b16c870a437948210a71
claim_id: claim:b16c870a437948210a71
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal: the stable monocyte derived DCs (Mo-DC) had characteristic high expression of CD14 and CLEC10A
summary:
In Homo sapiens cutaneous squamous cell carcinoma, monocyte derived dendritic cells have characteristic high expression of CD14 and CLEC10A.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:fdc253a028972466f072
claim_id: claim:fdc253a028972466f072
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal: The cluster with high expression of LAMP3 and CCR7 was identified as mature myeloid DCs (mmDC).
summary:
In Homo sapiens cutaneous squamous cell carcinoma, mature myeloid dendritic cells are identified by high expression of LAMP3 and CCR7.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:5be3680e1dc6db7b7b40
claim_id: claim:5be3680e1dc6db7b7b40
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal: Langerhans cells (LC) overexpressed CD1A, CD1C and CD207.
summary:
In Homo sapiens cutaneous squamous cell carcinoma, Langerhans cells overexpress CD1A, CD1C, and CD207.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:b11abb01acf5792ec8f3
claim_id: claim:b11abb01acf5792ec8f3
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
The immature conventional type I dendritic cells (cDC1) expressed unique C-type lectin receptor CLEC9A and chemokine receptor XCR

summary:
In Homo sapiens cutaneous squamous cell carcinoma, immature conventional type I dendritic cells express unique C-type lectin receptor CLEC9A and chemokine receptor XCR1.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:36d3c946927863ac845d
claim_id: claim:36d3c946927863ac845d
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal: The expression levels of PDGFRA in canonical_Fib were higher than those in other subgroups
summary:
In Homo sapiens cutaneous squamous cell carcinoma, canonical fibroblasts have higher expression of PDGFRA than other fibroblast subgroups.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:36dba8baf95042a9bebc
claim_id: claim:36dba8baf95042a9bebc
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
Vascular_Fib has a characteristic high expression of apolipoprotein APOE and COL18A1, which may be closely related to oxidative stress, inflammation and aging

summary:
In Homo sapiens cutaneous squamous cell carcinoma, vascular fibroblasts have characteristic high expression of APOE and COL18A1.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:16ba16726ea692242044
claim_id: claim:16ba16726ea692242044
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
Basal1 subgroup had high expression of the main components of hemidesmosomes COL17A1 and stem cell marker genes, suggesting that Basal1 might be stationary Basal cells attached to the basement membrane

summary:
In Homo sapiens skin, the Basal1 subgroup has high expression of COL17A1 and stem cell marker genes, suggesting they are stationary basal cells attached to the basement membrane.


claim_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8:claim:50623fea442504335e42
claim_id: claim:50623fea442504335e42
paper_key: biorxiv:bc260922-6c47-1014-a865-fe4e19bf3ea8
span_literal:
Follicular2 had higher expression of WNT pathway related suppressor genes such as SFRP1, FRZB, and DKK3 than that of Follicular1.

summary:
In Homo sapiens skin, the Follicular2 subpopulation has higher expression of WNT pathway related suppressor genes SFRP1, FRZB, and DKK3 compared to Follicular1.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:4a4d404dc6f63626291e
claim_id: claim:4a4d404dc6f63626291e
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
Using the acinar-specific UEA-1 lectin in combination with the duct cell marker CA19.9, we FACS-purified both cell populations (11, 12) (Figure 1a,b).

summary:
In Homo sapiens, UEA-1 lectin is an acinar cell-specific marker and CA19.9 is a duct cell marker used to purify pancreatic exocrine cell populations.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:15b18bc12ae541aea831
claim_id: claim:15b18bc12ae541aea831
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
Using the acinar-specific UEA-1 lectin in combination with the duct cell marker CA19.9, we FACS-purified both cell populations (11, 12) (Figure 1a,b).

summary:
In Homo sapiens, CA19.9 is a marker of duct cells used to distinguish them from acinar cells in the pancreas.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:df211e25bb47dc0ed2c6
claim_id: claim:df211e25bb47dc0ed2c6
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
We confirmed the mutually exclusive expression pattern of CD142, a progenitor marker (11) in the UEA1+ dedifferentiated acinar cells, and of CA19.9 in the UEA1-duct cells (Figure 1b).

summary:
In Homo sapiens, CD142 is a progenitor marker expressed in dedifferentiated acinar cells, while CA19.9 is expressed in duct cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:b81f6f2a2a9b66f9d4f4
claim_id: claim:b81f6f2a2a9b66f9d4f4
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
Conversely, duct cell-enriched genes included CFTR, SOX9, NKX6.1, HES1, HNF1B and ONECUT2 (HNF6B), established markers of duct cell differentiation.

summary:
In Homo sapiens, CFTR, SOX9, NKX6.1, HES1, HNF1B, and ONECUT2 are established markers of duct cell differentiation, enriched in duct cells compared to dedifferentiated acinar cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:65d2e38b05f03c09bc03
claim_id: claim:65d2e38b05f03c09bc03
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
The most significantly duct cell-enriched gene was DCDC2 (Doublecortin Domain Containing 2), demonstrated to bind tubulin and enhance microtubule polymerization (33) (Figure 1d).

summary:
In Homo sapiens, DCDC2 (Doublecortin Domain Containing 2) is the most significantly enriched gene in duct cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:d9a1e771f8fa42bfde63
claim_id: claim:d9a1e771f8fa42bfde63
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
Among the differentially expressed genes were 71 transcription factors. The most significantly enriched transcription factor in the dedifferentiated acinar cell fraction was MECOM (log2FC = −6,09; Adj. p = 1,04E-123) (Figure 1d, Supplementary Table 1).

summary:
In Homo sapiens, MECOM is the most significantly enriched transcription factor in the dedifferentiated acinar cell fraction compared to duct cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:c43fb06afd32032c5a3f
claim_id: claim:c43fb06afd32032c5a3f
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
RNA sequencing analysis showed that human dedifferentiated acinar cells expressed genes in ‘Pathways of cancer’ with prominence of the transcription factor MECOM (EVI-1) that was absent from duct cells.

summary:
In Homo sapiens, the transcription factor MECOM (EVI-1) is prominently expressed in dedifferentiated acinar cells and absent from duct cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:c0e8b2ecb8ccc6651837
claim_id: claim:c0e8b2ecb8ccc6651837
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
RNA sequencing analysis showed that human dedifferentiated acinar cells expressed genes in ‘Pathways of cancer’ with prominence of the transcription factor MECOM (EVI-1) that was absent from duct cells.

summary:
In Homo sapiens, the transcription factor MECOM (EVI-1) is absent from duct cells, in contrast to dedifferentiated acinar cells where it is expressed.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:a586ccf943cb0639e2c0
claim_id: claim:a586ccf943cb0639e2c0
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
Dedifferentiated acinar and duct cells did have equal expression of the embryonic precursor gene PDX1, confirming our previous work (13).

summary:
In Homo sapiens, both dedifferentiated acinar cells and duct cells express the embryonic precursor gene PDX1 at equal levels.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:4231bcbbf2f2e8167667
claim_id: claim:4231bcbbf2f2e8167667
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
Dedifferentiated acinar and duct cells did have equal expression of the embryonic precursor gene PDX1, confirming our previous work (13).

summary:
In Homo sapiens, duct cells express the embryonic precursor gene PDX1 at levels equal to dedifferentiated acinar cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:36306f523d925f7d0623
claim_id: claim:36306f523d925f7d0623
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
PTF1A, NR5A2, RBPJL, FOXA3 and GATA4 were expressed higher in the dedifferentiated acini reminiscent of their fully differentiated state.

summary:
In Homo sapiens, PTF1A, NR5A2, RBPJL, FOXA3, and GATA4 are expressed at higher levels in dedifferentiated acinar cells compared to duct cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:d8e7000abe5eaa5515d8
claim_id: claim:d8e7000abe5eaa5515d8
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
We uncovered that MECOM is uniquely expressed in dedifferentiated mouse and human acinar cells and absent from native duct cells, both in cell cultures and in tissue samples.

summary:
In Homo sapiens, MECOM is uniquely expressed in dedifferentiated acinar cells and absent from native duct cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:f28f0e6b11bb133e9c96
claim_id: claim:f28f0e6b11bb133e9c96
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
We uncovered that MECOM is uniquely expressed in dedifferentiated mouse and human acinar cells and absent from native duct cells, both in cell cultures and in tissue samples.

summary:
In Homo sapiens, MECOM is absent from native duct cells, in contrast to dedifferentiated acinar cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:15fd8a1b408a9b3662ef
claim_id: claim:15fd8a1b408a9b3662ef
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
span_literal:
while MECOM did not co-localize with the duct cell marker CK19 (5,69±2,32% MECOM+/CK19+ cells; N=5) (Figure 2d,e).

summary:
In Homo sapiens, CK19 is a duct cell marker that does not co-localize with MECOM in dedifferentiated acinar cells.


claim_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df:claim:e5b249dee1e295874c57
claim_id: claim:e5b249dee1e295874c57
paper_key: biorxiv:bc60e3db-6f3b-1014-9d48-bca06f1504df
summary: In Homo sapiens, SOX9 is an important marker of acinar cell dedifferentiation in the pancreas.
span_literal:
SOX9 is an important marker of acinar cell dedifferentiation and is indispensable for tumor formation in the pancreas (23).


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:831acef1cea762cc5a47
claim_id: claim:831acef1cea762cc5a47
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
As a result of cell type classification, it was observed that decorin (DCN) of FB and insulin-like growth factor binding protein 7 (IGFBP7) of SMC were the only markers specific to the sub-cell type of stromal cells reproduced in all groups.

summary:
In Homo sapiens non-small-cell lung cancer, decorin (DCN) is a marker of fibroblast and insulin-like growth factor-binding protein 7 (IGFBP7) is a marker of smooth muscle cell, both being sub-cell type markers of stromal cells.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:b0bed9c433d2e7e7581c
claim_id: claim:b0bed9c433d2e7e7581c
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
As a result of cell type classification, it was observed that decorin (DCN) of FB and insulin-like growth factor binding protein 7 (IGFBP7) of SMC were the only markers specific to the sub-cell type of stromal cells reproduced in all groups.

summary:
In Homo sapiens non-small-cell lung cancer, insulin-like growth factor-binding protein 7 (IGFBP7) is a marker of smooth muscle cell, a sub-cell type of stromal cells.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:43f2c2b5120880b0be96
claim_id: claim:43f2c2b5120880b0be96
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
In addition, DCN was used as a cell-type marker for fibroblast in the advanced NSCLC single-cell atlas and has been demonstrated as a marker significantly expressed in stromal cells in single-cell units of lung cancer

summary:
In Homo sapiens, DCN was used as a cell-type marker for fibroblast in the advanced non-small-cell lung cancer single-cell atlas and has been demonstrated as a marker significantly expressed in stromal cells in single-cell units of lung cancer.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:eb38ce246a84faac9600
claim_id: claim:eb38ce246a84faac9600
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
summary: In Homo sapiens, IGFBP7 is a cell type marker of smooth muscle cell.
span_literal:
According to previous studies, IGFBP7, a cell type marker of SMC, was also observed to be downregulated in various cancers such as breast, gastric, hepatocellular, and colorectal carcinoma


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:73d0ccc84810b3733781
claim_id: claim:73d0ccc84810b3733781
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
DCN and IGFBP7 were also expressed as stromal cell and SMC markers in brain cancer tissue that metastasized from lung cancer

summary:
In Homo sapiens, DCN is expressed as a stromal cell marker in brain cancer tissue that metastasized from lung cancer.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:02a0469971ba6738cfe6
claim_id: claim:02a0469971ba6738cfe6
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
DCN and IGFBP7 were also expressed as stromal cell and SMC markers in brain cancer tissue that metastasized from lung cancer

summary:
In Homo sapiens, IGFBP7 is expressed as a smooth muscle cell marker in brain cancer tissue that metastasized from lung cancer.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:0aa610ee664ef4689c24
claim_id: claim:0aa610ee664ef4689c24
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
DCN expressed in FB, a stromal cell sub-cell type of lung cancer patients, is different from the expression level known in the studies described above.

summary:
In Homo sapiens, DCN is expressed in fibroblast, a stromal cell sub-cell type of lung cancer patients.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:3782d36c66747e22e596
claim_id: claim:3782d36c66747e22e596
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
We detected decorin (DCN) and insulin-like growth factor-binding protein 7 (IGFBP7) as sub-cell type markers conserved in tumor and metastasis.

summary:
In Homo sapiens lung cancer, decorin (DCN) and insulin-like growth factor-binding protein 7 (IGFBP7) were detected as stromal cell sub-cell type markers conserved in tumor and metastasis.


claim_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53:claim:40b1b57474d8d8815eb2
claim_id: claim:40b1b57474d8d8815eb2
paper_key: biorxiv:bcbf54f0-6d06-1014-aea7-fa48d20f6b53
span_literal:
DCN and IGFBP7, which are markers specifically expressed in stromal cell sub-cell types of NSCLC and metastatic NSCLC, were found.

summary:
In Homo sapiens, DCN and IGFBP7 are markers specifically expressed in stromal cell sub-cell types of non-small-cell lung cancer and metastatic non-small-cell lung cancer.


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:93b7067341bb5a371f50
claim_id: claim:93b7067341bb5a371f50
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
span_literal:
DPT cells showed elevated expression of multiple genes encoding cytotoxic effector molecules, including GZMB, GZMH, GZMM, and GNLY, as well as genes involved in granule exocytosis and proteolytic activity such as NKG7, CST7, and CTSW.

summary:
In Homo sapiens, double-positive T cells show elevated expression of GZMB, GZMH, GZMM, GNLY, NKG7, CST7, and CTSW compared to single-positive T cells.


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:20663258c4cfd5ddbd77
claim_id: claim:20663258c4cfd5ddbd77
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
span_literal:
DPT cells expressed a distinct set of chemokines and receptors involved in immune cell trafficking and tissue surveillance, including CCL4, CCL5, XCL1, XCL2, and CX3CR1.

summary:
In Homo sapiens, double-positive T cells express CCL4, CCL5, XCL1, XCL2, and CX3CR1, which are involved in immune cell trafficking and tissue surveillance.


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:1bc1699c92460068cc4b
claim_id: claim:1bc1699c92460068cc4b
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
span_literal:
Feature importance analysis revealed that, in addition to canonical markers (CD4, CD8A, CD8B), the classifier relied heavily on genes associated with cytotoxic programs (CTSW, GNLY, GZMH, GZMK) [34,35] and transcriptional regulators (GATA3, FOXP3) [36–38], as well as genes involved in metabolic and structural processes (FTH1, PFN1, MALAT1, GABARAPL1) [39–41] (S4 Table).

summary:
In Homo sapiens, the machine learning classifier for double-positive T cells relied on canonical markers CD4, CD8A, CD8B, cytotoxic program genes CTSW, GNLY, GZMH, GZMK, transcriptional regulators GATA3 and FOXP3, and metabolic/structural genes FTH1, PFN1, MALAT1, and GABARAPL1.


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:7472390ac5ac9d02874a
claim_id: claim:7472390ac5ac9d02874a
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
span_literal:
While ThPOK expression remained low across all subsets, Runx3 expression was significantly elevated in both CD4⁺DPT and CD8⁺DPT cells relative to their single-positive counterparts (Fig. 4c, d).

summary:
In Homo sapiens, CD4-derived double-positive T cells show elevated Runx3 expression and low ThPOK expression relative to single-positive T cells.


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:22e61fdef8b50d929daa
claim_id: claim:22e61fdef8b50d929daa
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
span_literal:
While ThPOK expression remained low across all subsets, Runx3 expression was significantly elevated in both CD4⁺DPT and CD8⁺DPT cells relative to their single-positive counterparts (Fig. 4c, d).

summary:
In Homo sapiens, CD8-derived double-positive T cells show elevated Runx3 expression and low ThPOK expression relative to single-positive T cells.


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:f81836469c996cc5bb97
claim_id: claim:f81836469c996cc5bb97
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
summary: In Homo sapiens, CD4-derived double-positive T cells are enriched for TRAV35 and TRBV27.
span_literal:
Analysis of TCR gene usage revealed distinct patterns between DPT subsets, with CD4⁺DPT cells enriched for TRAV35 and TRBV27, and CD8⁺DPT cells preferentially expressing TRAV3 and TRBV4-2 (Fig. 4e).


claim_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7:claim:928a7704318d43945517
claim_id: claim:928a7704318d43945517
paper_key: biorxiv:bd0ff218-6c18-1014-ac36-a01faa0bb6b7
span_literal:
DPT cells were operationally defined as transcriptionally identified T cells exhibiting detectable expression of both CD4 and CD8A/CD8B transcripts after quality control and doublet filtering.

summary:
In Homo sapiens, double-positive T cells are defined by detectable expression of both CD4 and CD8A/CD8B transcripts.


claim_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757:claim:39c9e0f79e888a824bdd
claim_id: claim:39c9e0f79e888a824bdd
paper_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757
summary: In Homo sapiens retina, ganglion cells are marked by beta-3-tubulin (TUBB3) or HuC/D.
span_literal:
IBEX allowed precise simultaneous spatial visualisation of the major cell types in the retina (Figure 2A) and delineated its fine laminar organization including neuronal structures such as ganglion cells (via β3-tubulin or HuC/D), bipolar cells (PKCα or CHX10), amacrine or horizontal cells (Calretinin, Calbindin) and photoreceptors (ARR-C for cones and rhodopsin for rods).


claim_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757:claim:88feaa4e3a6385967b22
claim_id: claim:88feaa4e3a6385967b22
paper_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757
summary: In Homo sapiens retina, vascular endothelial cells are labeled by isolectin B4 (IB4).
span_literal:
To delineate the multilayered structure and interacting cells of the retinal blood vessel walls we used isolectin B4 (IB4) to label vascular endothelial cells, Collagen IV (COL IV) to outline the basement membrane, α-smooth muscle actin (α-SMA) to mark pericytes and smooth muscle cells of the vessel wall, and IBA1 to identify perivascular macrophages.


claim_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757:claim:5b733e5b69fa83d0ba81
claim_id: claim:5b733e5b69fa83d0ba81
paper_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757
span_literal:
To delineate the multilayered structure and interacting cells of the retinal blood vessel walls we used isolectin B4 (IB4) to label vascular endothelial cells, Collagen IV (COL IV) to outline the basement membrane, α-smooth muscle actin (α-SMA) to mark pericytes and smooth muscle cells of the vessel wall, and IBA1 to identify perivascular macrophages.

summary:
In Homo sapiens retina, pericytes and smooth muscle cells are marked by alpha-smooth muscle actin (α-SMA).


claim_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757:claim:2a55bbeec31a5b95192d
claim_id: claim:2a55bbeec31a5b95192d
paper_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757
span_literal:
For example, calbindin, as a canonical marker of horizontal cells, also exhibited transcriptional and protein expression within cone photoreceptors in the human retina (Supplementary Figure S2), but appears unexpressed within the mouse.

summary:
In Homo sapiens retina, calbindin is a canonical marker of horizontal cells and is also expressed in cone photoreceptors.


claim_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757:claim:2381482f5a0f5449098f
claim_id: claim:2381482f5a0f5449098f
paper_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757
span_literal:
For example, calbindin, as a canonical marker of horizontal cells, also exhibited transcriptional and protein expression within cone photoreceptors in the human retina (Supplementary Figure S2), but appears unexpressed within the mouse.

summary:
In Homo sapiens retina, cone photoreceptors express calbindin at both the transcriptional and protein level.


claim_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757:claim:8e8666bebcf721baed6c
claim_id: claim:8e8666bebcf721baed6c
paper_key: biorxiv:bee8bff4-6f5f-1014-bc4e-9548156f7757
summary: In Homo sapiens retina, CD44 is transcriptionally expressed on astrocytes and Müller glia.
span_literal:
Finally, we observed CD44 as a marker in both mouse and human retina that was transcriptionally expressed on astrocytes and Müller glia.


claim_key: biorxiv:c245f005-7ab6-1014-adbd-b49bd8bfffbc:claim:eeedd3366fc9eb73d20d
claim_id: claim:eeedd3366fc9eb73d20d
paper_key: biorxiv:c245f005-7ab6-1014-adbd-b49bd8bfffbc
summary: In Homo sapiens, T cells are marked by CD3D, CD3E, and TRAC.
span_literal:
T cells (CD3D, CD3E, TRAC), CD4+ T cells (CD4, IL7R), CD8+ T cells (CD8A, CD8B, GZMK), NK cells (GNLY, NKG7), B cells (MS4A1, CD79A), monocytes (CD14, LYZ, S100A9), and dendritic cells (FCER1A, CST3).


claim_key: biorxiv:c245f005-7ab6-1014-adbd-b49bd8bfffbc:claim:49cf043e5fffca4e5ef9
claim_id: claim:49cf043e5fffca4e5ef9
paper_key: biorxiv:c245f005-7ab6-1014-adbd-b49bd8bfffbc
span_literal: Heart markers included MYH6, MYH7, TNNT2, TNNI3, ACTC1, TPM1, MYL2, and MYL3.
summary:
In Homo sapiens, cardiac markers of heart tissue include MYH6, MYH7, TNNT2, TNNI3, ACTC1, TPM1, MYL2, and MYL3.


claim_key: biorxiv:c245f005-7ab6-1014-adbd-b49bd8bfffbc:claim:f68f4915ecdc3dfb99fb
claim_id: claim:f68f4915ecdc3dfb99fb
paper_key: biorxiv:c245f005-7ab6-1014-adbd-b49bd8bfffbc
summary: In Homo sapiens, neuronal cells in the brain are marked by NEUROD1, RBFOX3, SYT1, and MAP2.
span_literal:
Brain markers encompassed neuronal markers (NEUROD1, RBFOX3, SYT1, MAP2), astrocyte markers (GFAP, S100B, AQP4), oligodendrocyte markers (MBP, MOG, OLIG1, CNP), and microglial markers (CX3CR1, TMEM119)


claim_key: biorxiv:c3556304-707d-1014-b47e-8d7767eb41eb:claim:d4681733dbe78701d915
claim_id: claim:d4681733dbe78701d915
paper_key: biorxiv:c3556304-707d-1014-b47e-8d7767eb41eb
summary: In Homo sapiens, CD8-positive T cells are marked by GZMK, CD8A, and CD8B.
span_literal:
CD8+ T-cells (GZMK, CD8A, CD8B) (38), CD4+ T-cells (CD27, CCR7)(32), macrophages (C1QA) (38), monocytes (FCN1) (39), B-cells (MS4A1, CD79A) (40).


claim_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae:claim:8d2cc7e6e204613d1965
claim_id: claim:8d2cc7e6e204613d1965
paper_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae
summary: In Homo sapiens, amacrine cells are identified by the marker genes CALB2 and SLC6A9 in the retina.
span_literal:
Clusters corresponding to retinal cell types were identified using marker genes, including amacrine cells (AC; CALB2, SLC6A9), bipolar cells (BPC; TRPM1, GRIK1), cone photoreceptors (ARR3, OPN1SW, OPN1LW), horizontal cells (HC; ONECUT1), immune cells (IC; PTPRC), Müller glia (MG; SLC1A3, GLUL, VIM, CRABP1), RPE cells (RDH5, RLBP1, RPE65), and rod photoreceptors (NRL, NR2E3, PDE6B, AIF1)


claim_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae:claim:d0ed76f6facbc84e4c9c
claim_id: claim:d0ed76f6facbc84e4c9c
paper_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae
span_literal:
Clusters corresponding to retinal cell types were identified using marker genes, including amacrine cells (AC; CALB2, SLC6A9), bipolar cells (BPC; TRPM1, GRIK1), cone photoreceptors (ARR3, OPN1SW, OPN1LW), horizontal cells (HC; ONECUT1), immune cells (IC; PTPRC), Müller glia (MG; SLC1A3, GLUL, VIM, CRABP1), RPE cells (RDH5, RLBP1, RPE65), and rod photoreceptors (NRL, NR2E3, PDE6B, AIF1)

summary:
In Homo sapiens, cone photoreceptors are identified by the marker genes ARR3, OPN1SW, and OPN1LW in the retina.


claim_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae:claim:a1d5d7944d6053eb86f0
claim_id: claim:a1d5d7944d6053eb86f0
paper_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae
summary:
In Homo sapiens, Müller glia are identified by the marker genes SLC1A3, GLUL, VIM, and CRABP1 in the retina.


claim_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae:claim:66651ee43809eeeecb40
claim_id: claim:66651ee43809eeeecb40
paper_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae
summary:
In Homo sapiens, retinal pigment epithelium cells are identified by the marker genes RDH5, RLBP1, and RPE65 in the retina.


claim_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae:claim:bfb0ed51188731c1a903
claim_id: claim:bfb0ed51188731c1a903
paper_key: biorxiv:c401ab09-6e64-1014-b937-b2bead7f53ae
summary:
In Homo sapiens, rod photoreceptors are identified by the marker genes NRL, NR2E3, PDE6B, and AIF1 in the retina.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:7395b0a57d603fdcc15d
claim_id: claim:7395b0a57d603fdcc15d
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
four main cell types expressed ACE2 gene, including decidual stromal cells (dS) and decidual perivascular cells (dP) in decidua, and villous cytotrophoblast (VCT) and syncytiotrophoblast (SCT) in placenta

summary:
In Homo sapiens, decidual stromal cells express ACE2 (angiotensin-converting enzyme 2) in the decidua of the placenta.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:4187efc7a98e0c56b422
claim_id: claim:4187efc7a98e0c56b422
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
four main cell types expressed ACE2 gene, including decidual stromal cells (dS) and decidual perivascular cells (dP) in decidua, and villous cytotrophoblast (VCT) and syncytiotrophoblast (SCT) in placenta

summary:
In Homo sapiens, decidual perivascular cells express ACE2 (angiotensin-converting enzyme 2) in the decidua of the placenta.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:e70eb8f71b55c8df6401
claim_id: claim:e70eb8f71b55c8df6401
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
four main cell types expressed ACE2 gene, including decidual stromal cells (dS) and decidual perivascular cells (dP) in decidua, and villous cytotrophoblast (VCT) and syncytiotrophoblast (SCT) in placenta

summary:
In Homo sapiens, villous cytotrophoblast cells express ACE2 (angiotensin-converting enzyme 2) in the placenta.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:7fcf6726139c22c37d91
claim_id: claim:7fcf6726139c22c37d91
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
summary:
In Homo sapiens, syncytiotrophoblast cells express ACE2 (angiotensin-converting enzyme 2) in the placenta.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:871a50340976ade7e8e9
claim_id: claim:871a50340976ade7e8e9
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal: The extravillous trophoblast (EVT) did not express ACE2 at this time.
summary:
In Homo sapiens, extravillous trophoblast cells did not express ACE2 (angiotensin-converting enzyme 2) at the first trimester.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:4cf2e919d2e93ee8e82f
claim_id: claim:4cf2e919d2e93ee8e82f
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
summary: In Homo sapiens fetal heart, ACE2 (angiotensin-converting enzyme 2) is expressed in cardiomyocytes.
span_literal:
we observed that ACE2 was expressed in cardiomyocytes (CM), macrophages and smooth muscle cells and pericytes (SMC/Peri).


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:f806e46ffceb03a6630e
claim_id: claim:f806e46ffceb03a6630e
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
we observed that ACE2 was expressed in cardiomyocytes (CM), macrophages and smooth muscle cells and pericytes (SMC/Peri).

summary:
In Homo sapiens fetal heart, ACE2 (angiotensin-converting enzyme 2) is expressed in smooth muscle cells and pericytes.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:bcdafa3f67b46536ad85
claim_id: claim:bcdafa3f67b46536ad85
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal: ACE2 was detected in erythroid, fibroblast and hepatocyte (Figure 2B).
summary:
In Homo sapiens fetal liver, ACE2 (angiotensin-converting enzyme 2) is detected in fibroblast cells.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:8ebd1322ba450dc1ff69
claim_id: claim:8ebd1322ba450dc1ff69
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal: ACE2 was detected in erythroid, fibroblast and hepatocyte (Figure 2B).
summary:
In Homo sapiens fetal liver, ACE2 (angiotensin-converting enzyme 2) is detected in hepatocyte cells.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:a58125f78b578dca3e01
claim_id: claim:a58125f78b578dca3e01
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
we observed that ACE2 was highly expressed in airway epithelial cell and arterial endothelial cells (Figure 2F).

summary:
In Homo sapiens lung at post-natal day 1, ACE2 (angiotensin-converting enzyme 2) is highly expressed in airway epithelial cells.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:59ab89557348914609b9
claim_id: claim:59ab89557348914609b9
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
we observed that ACE2 was highly expressed in airway epithelial cell and arterial endothelial cells (Figure 2F).

summary:
In Homo sapiens lung at post-natal day 1, ACE2 (angiotensin-converting enzyme 2) is highly expressed in arterial endothelial cells.


claim_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f:claim:7e3a2f8f005de8d74649
claim_id: claim:7e3a2f8f005de8d74649
paper_key: biorxiv:c507fe4c-740e-1014-8455-8c072e8f204f
span_literal:
In a single cell study of fetal kidney at 7-9 week, we did not observe ACE2 expression in any cell type.

summary:
In Homo sapiens fetal kidney at 7-9 weeks, ACE2 (angiotensin-converting enzyme 2) expression was not observed in any cell type.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:b5fad6bf454af3461146
claim_id: claim:b5fad6bf454af3461146
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Figure 1C displays a heatmap of 15+ canonical cell-type markers (EPCAM, PECAM1, CD3D, etc.) with z-score normalized expression (blue-low to red-high) to validate annotation quality across all cells.

summary:
In Homo sapiens breast cancer tissues, EPCAM, PECAM1, and CD3D are used as canonical cell-type markers to validate cell type annotations across all cells.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:e6f9de8cf573c3e7a534
claim_id: claim:e6f9de8cf573c3e7a534
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Figure 1C displays a heatmap of 15+ canonical cell-type markers (EPCAM, PECAM1, CD3D, etc.) with z-score normalized expression (blue-low to red-high) to validate annotation quality across all cells.

summary:
In Homo sapiens breast cancer tissues, PECAM1 is used as a canonical cell-type marker for endothelial cells.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:0f34106084619ec42ec2
claim_id: claim:0f34106084619ec42ec2
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Expression of the metastasis-associated genes MAB21L1, F2RL2, and COL6A6 is cell-type-specific in both primary tumors and lymph node metastases (LNMs), as demonstrated by distinct expression patterns across diverse cell populations. Notably, fibroblasts exhibited robust enrichment for all three genes compared to other major cell types, showing consistently higher expression levels and a greater fraction of expressing cells in both tissue contexts.

summary:
In Homo sapiens breast cancer, fibroblasts exhibited robust enrichment for MAB21L1, F2RL2, and COL6A6 compared to other major cell types, showing consistently higher expression levels in both primary tumors and lymph node metastases.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:3d3dbacff90d29c261c5
claim_id: claim:3d3dbacff90d29c261c5
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
F2RL2+ fibroblasts mediated immune crosstalk (via CXCL14, C1S) and TGF-β balance; COL6A6+ fibroblasts reinforced ECM structure (COL6A6/COL6A3) and inhibited Wnt signaling (SFRP2); MAB21L1+ fibroblasts suppressed SMAD signaling (through NR2F1 upregulation) and blocked cell migration.

summary:
In Homo sapiens breast cancer, F2RL2-positive fibroblasts mediated immune crosstalk via CXCL14 and C1S expression.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:2f4a63e54b8927238242
claim_id: claim:2f4a63e54b8927238242
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
F2RL2+ fibroblasts mediated immune crosstalk (via CXCL14, C1S) and TGF-β balance; COL6A6+ fibroblasts reinforced ECM structure (COL6A6/COL6A3) and inhibited Wnt signaling (SFRP2); MAB21L1+ fibroblasts suppressed SMAD signaling (through NR2F1 upregulation) and blocked cell migration.

summary:
In Homo sapiens breast cancer, COL6A6-positive fibroblasts reinforced extracellular matrix structure via COL6A6 and COL6A3 and inhibited Wnt signaling via SFRP2.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:ed1fa0eaf655782eb7bb
claim_id: claim:ed1fa0eaf655782eb7bb
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
F2RL2+ fibroblasts mediated immune crosstalk (via CXCL14, C1S) and TGF-β balance; COL6A6+ fibroblasts reinforced ECM structure (COL6A6/COL6A3) and inhibited Wnt signaling (SFRP2); MAB21L1+ fibroblasts suppressed SMAD signaling (through NR2F1 upregulation) and blocked cell migration.

summary:
In Homo sapiens breast cancer, MAB21L1-positive fibroblasts suppressed SMAD signaling through NR2F1 upregulation.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:7bbbbed6a7a71fa86810
claim_id: claim:7bbbbed6a7a71fa86810
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
First, extracellular matrix reorganization is driven by structural regulators THBS4 (log2FC=4.85, padj=2.46e-31), CILP (log2FC=3.29, padj=9.64e-33), and COL6A3 (log2FC=2.06, padj=4.66e-21), which orchestrate collagen fibril assembly while MMP11 (log2FC=3.09, padj=8.71e-07) enables controlled matrix disassembly.

summary:
In Homo sapiens breast cancer, F2RL2-positive fibroblasts show upregulation of THBS4, CILP, COL6A3, and MMP11 driving extracellular matrix reorganization.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:c9c0185321f38f297183
claim_id: claim:c9c0185321f38f297183
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Second, TGF-β/BMP signaling modulation is evidenced by concurrent activation (INHBA↑, log2FC=1.88, padj=5.94e-07) and suppression (FSTL1↑, log2FC=1.42, padj=6.00e-12), creating a balanced signaling environment that limits EMT progression.

summary:
In Homo sapiens breast cancer, F2RL2-positive fibroblasts show upregulation of INHBA and FSTL1, modulating transforming growth factor beta/bone morphogenetic protein signaling.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:a40f70626c17b993d321
claim_id: claim:a40f70626c17b993d321
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Crucially, third, immune-metastasis crosstalk is mediated through CXCL14 (log2FC=3.26, padj=1.23e-17)-driven monocyte chemotaxis and C1S (log2FC=1.49, padj=2.34e-09)-initiated complement activation, recruiting tumor-suppressive leukocytes while TNFSF10 (log2FC=1.67, padj=3.62e-10) primes T-cell responses.

summary:
In Homo sapiens breast cancer, F2RL2-positive fibroblasts express CXCL14, C1S, and TNFSF10 to mediate immune-metastasis crosstalk including monocyte chemotaxis, complement activation, and T-cell priming.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:6ff3b2bfd07bdeafa7eb
claim_id: claim:6ff3b2bfd07bdeafa7eb
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
These processes are unified by potent metastasis suppression via SFRP2 (log2FC=2.18, padj=3.17e-31)-mediated Wnt inhibition and FSTL1-dependent BMP constraint, collectively establishing F2RL2+ fibroblasts as conductors of a multi-layered defense that integrates ECM fortification, immune recruitment, and pathway blockade to contain dissemination.

summary:
In Homo sapiens breast cancer, F2RL2-positive fibroblasts express SFRP2 for Wnt inhibition and FSTL1 for bone morphogenetic protein constraint as part of metastasis suppression.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:6bb154a7b82a75aaae61
claim_id: claim:6bb154a7b82a75aaae61
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Central to this defense is extracellular matrix fortification, driven by dominant upregulation of structural genes COL6A6 (log2FC=14.58), COL6A3 (log2FC=2.07), and LUM (log2FC=2.01), which collaboratively establish a physical barrier against invasion.

summary:
In Homo sapiens breast cancer, COL6A6-positive fibroblasts show dominant upregulation of COL6A6, COL6A3, and LUM for extracellular matrix fortification.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:3b78017c8a7ebac13643
claim_id: claim:3b78017c8a7ebac13643
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
This ECM reinforcement is coupled with potent migration suppression via SFRP2 (log2FC=1.72), a Wnt inhibitor that blocks pro-dissemination signals, and downregulation of motility drivers PDGFA (log2FC=-3.27) and ITGA1 (log2FC=-1.72).

summary:
In Homo sapiens breast cancer, COL6A6-positive fibroblasts show upregulation of SFRP2 and downregulation of PDGFA and ITGA1 for migration suppression.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:a5819d74e2ecb58b6594
claim_id: claim:a5819d74e2ecb58b6594
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Crucially, EMT constraint is mediated through TGFBR3 (log2FC=1.41), which sequesters TGF-β to limit epithelial-mesenchymal transition, while hypoxic adaptation is evidenced by suppression of HIF-1α targets NDUFA4L2 (log2FC=-5.37) and STEAP4 (log2FC=-6.16).

summary:
In Homo sapiens breast cancer, COL6A6-positive fibroblasts show upregulation of TGFBR3 and downregulation of NDUFA4L2 and STEAP4.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:7a1df0dcede0fba812f8
claim_id: claim:7a1df0dcede0fba812f8
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Further metastasis containment arises from Wnt pathway inhibition via SFRP1 (log2FC=2.00) and TGF-β/BMP modulation through FSTL1 (log2FC=1.47), with immune crosstalk facilitated by HLA-B/C downregulation (log2FC≈-1.70) attenuating antigen presentation.

summary:
In Homo sapiens breast cancer, COL6A6-positive fibroblasts show upregulation of SFRP1 and FSTL1 and downregulation of HLA-B and HLA-C.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:fcfb3d29da3aee014667
claim_id: claim:fcfb3d29da3aee014667
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Critically, we identified negative regulation of cell migration (padj < 0.05), validated by significant upregulation of motility inhibitors SFRP2 (log2FC=1.31, padj=5.27e-13) and DCN (log2FC=1.61, padj=7.76e-13).

summary:
In Homo sapiens breast cancer, MAB21L1-positive fibroblasts show significant upregulation of motility inhibitors SFRP2 and DCN, validating negative regulation of cell migration.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:553297de4392ab1a7fa0
claim_id: claim:553297de4392ab1a7fa0
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Equally compelling was the enrichment for negative regulation of SMAD protein signal transduction, mechanistically supported by overexpression of NR2F1 (log2FC=2.24, padj=2.88e-15), a known TGF-β pathway suppressor that inhibits epithelial-mesenchymal transition.

summary:
In Homo sapiens breast cancer, MAB21L1-positive fibroblasts show overexpression of NR2F1, a known transforming growth factor beta pathway suppressor, supporting negative regulation of SMAD protein signal transduction.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:2717946d829d21bcd76e
claim_id: claim:2717946d829d21bcd76e
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
The negative regulation of platelet-derived growth factor receptor signaling pathway was corroborated by concomitant upregulation of PDGFRA (log2FC=1.93, padj=8.76e-12) – which may act as a decoy receptor – paired with downregulation of its activator MDK (log2FC=1.02, padj=0.0001).

summary:
In Homo sapiens breast cancer, MAB21L1-positive fibroblasts show upregulation of PDGFRA and downregulation of MDK, corroborating negative regulation of platelet-derived growth factor receptor signaling.


claim_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e:claim:c3762a6c205e779e71f4
claim_id: claim:c3762a6c205e779e71f4
paper_key: biorxiv:c55f45c7-7001-1014-966f-865cda24634e
span_literal:
Furthermore, regulation of actin cytoskeleton organization was evidenced by elevated expression of cytoskeletal remodelers RND3 (log2FC=1.25, padj=8.12e-05) and reduced ACTA2 (log2FC=-1.28, padj=0.014), indicating *restricted* cellular motility.

summary:
In Homo sapiens breast cancer, MAB21L1-positive fibroblasts show elevated expression of RND3 and reduced expression of ACTA2, indicating restricted cellular motility.


claim_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab:claim:59c648baf0bd8b67ef92
claim_id: claim:59c648baf0bd8b67ef92
paper_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab
span_literal:
consistent with previous studies [9], an average of 72% cells were TRA-1-60(+) in the undifferentiated state (day0) and an average of 49% of cells were CXCR4(+) three days post differentiation (day3; Fig. S3).

summary:
In Homo sapiens, induced pluripotent stem cells in the undifferentiated state are marked by TRA-1-60 positivity.


claim_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab:claim:20490c700b6fbc54ca6c
claim_id: claim:20490c700b6fbc54ca6c
paper_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab
span_literal:
consistent with previous studies [9], an average of 72% cells were TRA-1-60(+) in the undifferentiated state (day0) and an average of 49% of cells were CXCR4(+) three days post differentiation (day3; Fig. S3).

summary:
In Homo sapiens, definitive endoderm cells three days post differentiation are marked by CXCR4 positivity.


claim_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab:claim:9d96249cc779e38d7855
claim_id: claim:9d96249cc779e38d7855
paper_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab
summary: In Homo sapiens, NANOG is a marker of the induced pluripotent stem cell stage.
span_literal:
Single cell expression (y axis) of selected markers for each developmental stage, spanning iPSC (NANOG), mesendo (T), and defendo (GATA6) stages, plotted along pseudotime (x axis).


claim_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab:claim:42690f18ed79cd7afd78
claim_id: claim:42690f18ed79cd7afd78
paper_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab
summary: In Homo sapiens, Brachyury (T) is a marker of mesendoderm cells.
span_literal:
Cells were assigned to the mesendo stage if they were collected at day1 or day2, and had pseudotime values between 0.15 and 0.5, corresponding to a pseudotime window around the peak expression of Brachyury (T), a marker of mesendoderm (Fig. S8A).


claim_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab:claim:09c1b5692202622f6163
claim_id: claim:09c1b5692202622f6163
paper_key: biorxiv:c6143e89-6c0b-1014-83d4-d632a03fd1ab
summary: In Homo sapiens, GATA6 is a marker of definitive endoderm cells.
span_literal:
Cells were assigned to the defendo stage if they were collected at day2 or day3, and had pseudotime values higher than 0.7, corresponding to a pseudotime window with maximal expression of GATA6, a marker of definitive endoderm (Fig. S8B).


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:2eb5b4e1460c91a673f3
claim_id: claim:2eb5b4e1460c91a673f3
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
summary: In Homo sapiens, CLU and SPARC are marker genes of astrocytes.
span_literal:
we observed a clear increase in expression over time for astrocyte marker genes (CLU, SPARC) when analyzing all cells per timepoint via pseudobulk


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:87a8783ddc20c73b2f50
claim_id: claim:87a8783ddc20c73b2f50
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
span_literal:
STMN2, a critical gene for neuron development and maintenance55, was most highly correlated with neuronal fate acquisition (r2=0.8789).

summary:
In Homo sapiens, STMN2 is a critical gene for neuron development and maintenance, most highly correlated with neuronal fate acquisition.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:5d415231c16508bc559f
claim_id: claim:5d415231c16508bc559f
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
span_literal:
Other genes highly correlated with neuronal fate acquisition included DCX (r2=0.6602), and two genes implicated in neuron-specific alternative splicing56, ELAVL4 (r2=0.7009) and ELAVL2 (r2=0.6452).

summary:
In Homo sapiens, DCX, ELAVL4, and ELAVL2 are genes highly correlated with neuronal fate acquisition in neurons.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:abe7a17be37ed646fa19
claim_id: claim:abe7a17be37ed646fa19
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
summary: In Homo sapiens, TTYH1 is the gene most correlated with the probability to become an astrocyte.
span_literal:
we first found that the gene most correlated with the probability to become an astrocyte was TTYH1 (r2=0.7104), visualized by marking cells with high TTYH1 expression on the astrocyte-fate log odds plot


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:086239ab704c74c7a071
claim_id: claim:086239ab704c74c7a071
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
span_literal:
Interestingly, both SPARC and SPARCL1 expression had similarly strong correlations with astrocyte fate acquisition probability (r2=0.6081 and 0.5509 respectively; Fig 1I).

summary:
In Homo sapiens, SPARC and SPARCL1 expression are strongly correlated with astrocyte fate acquisition probability.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:ad1c9e87b33b84adc160
claim_id: claim:ad1c9e87b33b84adc160
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
summary: In Homo sapiens, UGT8 and MBP are the genes most correlated with oligodendrocyte fate.
span_literal:
we examined acquisition of oligodendrocyte fate analysis, and identified UGT8 (r2=0.7794) and MBP (r2=0.7638) as the genes most correlated with oligodendrocyte fate.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:3761341766bcc6f389a6
claim_id: claim:3761341766bcc6f389a6
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
span_literal:
Published bulk RNAseq datasets on purified primary astrocytes report TTYH1 expression is restricted to astrocytes, and increases with age53.

summary:
In Homo sapiens, TTYH1 expression is restricted to astrocytes based on published bulk RNA sequencing datasets on purified primary astrocytes.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:b341c7063c94ef73c3de
claim_id: claim:b341c7063c94ef73c3de
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
summary: In Homo sapiens, ID1 is highly enriched in glial progenitor populations.
span_literal:
ID1 was highly enriched in two populations of glial progenitors, fitting with its recent identification as an astrocyte-subtype marker in mice65.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:5f09f25f5a5e52168adc
claim_id: claim:5f09f25f5a5e52168adc
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
span_literal:
BITFAM also detected ID3 activity specifically in the oligodendrocyte cluster, even though gene expression of this TF was higher in astrocytes, in line with observations from a recent scRNAseq analysis of human iPSC-derived oligodendrocytes66.

summary:
In Homo sapiens, ID3 transcription factor activity is detected specifically in the oligodendrocyte cluster from human induced pluripotent stem cell-derived oligodendrocytes.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:5a9f4fe5edafc951a86b
claim_id: claim:5a9f4fe5edafc951a86b
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
summary: In Homo sapiens, NFXL1 transcription factor activity is detected in the oligodendrocyte cluster.
span_literal:
We also note NFXL1 activity in the oligodendrocyte cluster, a TF recently associated with a familial speech disorder67 and localized to the brain68, that has not been previously implicated in oligodendrocyte development.


claim_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5:claim:39c6cae3c8164ca8612e
claim_id: claim:39c6cae3c8164ca8612e
paper_key: biorxiv:c6b2e62c-6bf8-1014-b389-a9824584e0b5
span_literal:
TFs detected with putative activity in astrocytes included POU2F2 in the cluster 2 astrocytes, which was recently identified as a potential driver of glioma formation from human astrocytes61, in addition to PAX2, which plays a key role in astrogenesis in mice62,63.

summary:
In Homo sapiens, POU2F2 has putative transcription factor activity in astrocytes and was identified as a potential driver of glioma formation from human astrocytes.


claim_key: biorxiv:c704e998-6f4b-1014-8cb1-c3d28b577fb8:claim:19b9ed58fb4d562e252e
claim_id: claim:19b9ed58fb4d562e252e
paper_key: biorxiv:c704e998-6f4b-1014-8cb1-c3d28b577fb8
summary: In Homo sapiens embryonic lung, SOX2, SOX9, and ASCL1 are markers of subsets of epithelial cells.
span_literal:
In the human embryonic lung sections, we used probes targeting transcripts encoding 3 transcription factors, SOX2, SOX9 and ASCL1 (Supplementary Figure 3), which have previously been detected by antibody staining in subsets of epithelial cells (40, 41).


claim_key: biorxiv:c704e998-6f4b-1014-8cb1-c3d28b577fb8:claim:e4b66bedb49943e5d717
claim_id: claim:e4b66bedb49943e5d717
paper_key: biorxiv:c704e998-6f4b-1014-8cb1-c3d28b577fb8
span_literal:
In agreement with the published results, the SCRINSHOT signal for SOX2 was confined mainly in the proximal part of the branching epithelium, whereas SOX9 was selectively expressed in the distal tips.

summary:
In Homo sapiens embryonic lung, SOX2 is a marker of proximal branching epithelial cells, whereas SOX9 is selectively expressed in distal tip epithelial cells.


claim_key: biorxiv:c704e998-6f4b-1014-8cb1-c3d28b577fb8:claim:5dce8da6bddad74efdca
claim_id: claim:5dce8da6bddad74efdca
paper_key: biorxiv:c704e998-6f4b-1014-8cb1-c3d28b577fb8
span_literal:
In agreement with the published results, the SCRINSHOT signal for SOX2 was confined mainly in the proximal part of the branching epithelium, whereas SOX9 was selectively expressed in the distal tips.

summary:
In Homo sapiens embryonic lung, SOX9 is selectively expressed in distal tip epithelial cells, whereas SOX2 is confined to the proximal branching epithelium.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:0df1cf3848ff057e195a
claim_id: claim:0df1cf3848ff057e195a
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal: all of which expressed CEC markers ALCAM (CD166), PRDX6, SLC4A11, PITX2, and ATP1A1,
summary:
In Homo sapiens, corneal endothelial cells express the markers ALCAM (CD166), PRDX6, SLC4A11, PITX2, and ATP1A1.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:479c380822de1e26bcc8
claim_id: claim:479c380822de1e26bcc8
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Clusters 0 and 5 presented increased differential gene expression of typical CEC markers, SLC4A11, COL4A3 (Van den Bogerd et al., 2019), CDH2 (He et al., 2016), and ALCAM, compared to the other sequenced cells, suggesting these clusters were composed of therapy-grade CECs

summary:
In Homo sapiens, therapy-grade corneal endothelial cells show increased expression of SLC4A11, COL4A3, CDH2, and ALCAM.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:6aaa4104b2bf696f18b5
claim_id: claim:6aaa4104b2bf696f18b5
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Cluster 1 was identified as CECs transitioning towards a senescent phenotype due to the high differential expression of senescence markers such as MT2A (Malavolta et al., 2017), CDKN2A (p16) (Enomoto et al., 2006), and TAGLN (Benadjaoud et al., 2022)

summary:
In Homo sapiens, corneal endothelial cells transitioning towards a senescent phenotype show high expression of MT2A, CDKN2A (p16), and TAGLN.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:88796691611b38af0722
claim_id: claim:88796691611b38af0722
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
summary: In Homo sapiens, highly proliferative corneal endothelial cells express MKI67, CENPF, and PTTG1.
span_literal:
Cluster 2 was composed of highly proliferative CECs expressing MKI67 (Sun and Kaufman, 2018), CENPF (Varis et al., 2006), and PTTG1 (Ersvær et al., 2020)


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:58a7875203af8a4cc055
claim_id: claim:58a7875203af8a4cc055
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Cluster 4 was composed of fibrotic CECs with increased differential expression of ACTA2 (α-smooth muscle actin (SMA)) (Rao et al., 2014), CD44 (Hamuro et al., 2016), and COL6A1 (Oouchi et al., 2021)

summary:
In Homo sapiens, fibrotic corneal endothelial cells show increased expression of ACTA2 (alpha-smooth muscle actin), CD44, and COL6A1.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:b7ad3c33c88dda095089
claim_id: claim:b7ad3c33c88dda095089
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Increased differential expression of typical CEC markers, such as COL4A6 (Van den Bogerd et al., 2019), SLC4A11, ATP1A1, COL4A3, and CDH2 suggested that clusters C0 and C1 were composed of therapy-grade CECs

summary:
In Homo sapiens, therapy-grade corneal endothelial cells show increased expression of COL4A6, SLC4A11, ATP1A1, COL4A3, and CDH2.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:73586a5d724e26847c71
claim_id: claim:73586a5d724e26847c71
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Cluster C3 was composed of proliferating CECs with differential high expression of MKI67 (KI-67), CENPF, and PTTG1

summary:
In Homo sapiens, proliferating corneal endothelial cells show high expression of MKI67 (KI-67), CENPF, and PTTG1.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:6faffdfef1429f1303d2
claim_id: claim:6faffdfef1429f1303d2
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Namely, CDKN2A (p16), TAGLN, and MT2A (Figure 3B and S7) in cluster C2 and CDKN1A (p21) (Matthaei et al., 2012), CDKN2A (p16), and TAGLN in cluster C4

summary:
In Homo sapiens, senescent corneal endothelial cells in cluster C2 express CDKN2A (p16), TAGLN, and MT2A, while senescent corneal endothelial cells in cluster C4 express CDKN1A (p21), CDKN2A (p16), and TAGLN.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:ef1543803344f4284b95
claim_id: claim:ef1543803344f4284b95
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Namely, CDKN2A (p16), TAGLN, and MT2A (Figure 3B and S7) in cluster C2 and CDKN1A (p21) (Matthaei et al., 2012), CDKN2A (p16), and TAGLN in cluster C4

summary:
In Homo sapiens, senescent corneal endothelial cells in cluster C4 express CDKN1A (p21), CDKN2A (p16), and TAGLN.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:5429134fa9bb3d434420
claim_id: claim:5429134fa9bb3d434420
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Cluster C4 had a high extracellular matrix production suggested by the differential high expression of COL4A1, COL4A2, COL5A1, and FBLN5 in cells that maintained the expression of endothelial markers such as SLC4A11, and COL4A3

summary:
In Homo sapiens, senescent corneal endothelial cells in cluster C4 show high expression of COL4A1, COL4A2, COL5A1, and FBLN5 while maintaining expression of SLC4A11 and COL4A3.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:15291518c0cecb27dd30
claim_id: claim:15291518c0cecb27dd30
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
In contrast, cells in cluster C2 presented a low expression of CEC markers such as ALCAM, SLC4A11, CDH2, and ATP1A1

summary:
In Homo sapiens, senescent corneal endothelial cells in cluster C2 show low expression of ALCAM, SLC4A11, CDH2, and ATP1A1.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:214e39078712cfb674f9
claim_id: claim:214e39078712cfb674f9
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Cluster C5 was composed of fibrotic cells differentially expressing the fibrosis-associated markers COL6A1, COL6A3, CD44, and ACTA2

summary:
In Homo sapiens, fibrotic corneal endothelial cells in cluster C5 differentially express the fibrosis-associated markers COL6A1, COL6A3, CD44, and ACTA2.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:41a2022ed808e52d760e
claim_id: claim:41a2022ed808e52d760e
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
The cells in cluster C5 had diminished expression of ALCAM (CD166) and lacked SLC4A11 expression, two CEC markers.

summary:
In Homo sapiens, fibrotic corneal endothelial cells in cluster C5 show diminished expression of ALCAM (CD166) and lack SLC4A11 expression.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:97baadb1da26f60ec951
claim_id: claim:97baadb1da26f60ec951
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Cluster C6 was composed of CECs with differential high expression of typical endothelial markers such as SLC4A11, COL4A3, and CDH2

summary:
In Homo sapiens, corneal endothelial cells in cluster C6 show high expression of SLC4A11, COL4A3, and CDH2.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:36b8e2dbb2fefbba18b3
claim_id: claim:36b8e2dbb2fefbba18b3
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
These cells differentially expressed higher GOLGA8A and GOLGA8B, suggesting a possible increase in secretory pathways.

summary:
In Homo sapiens, corneal endothelial cells in cluster C6 differentially express higher GOLGA8A and GOLGA8B.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:211a5992a75bf2422eb3
claim_id: claim:211a5992a75bf2422eb3
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
The expression of ALCAM (CD166), CGNL1 (cingulin-like protein 1), and NCAM1 (CD56) were higher in the clusters comprising therapy-grade CECs (clusters C0 and C1), and lower in the cells in clusters C2 and C5

summary:
In Homo sapiens, therapy-grade corneal endothelial cells (clusters C0 and C1) show higher expression of ALCAM (CD166), CGNL1 (cingulin-like protein 1), and NCAM1 (CD56) compared to senescent and fibrotic corneal endothelial cells (clusters C2 and C5).


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:bdc88c4738c241e10532
claim_id: claim:bdc88c4738c241e10532
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Additionally, the expression of CD44, MME (CD10), VMO1, and THBS2 were higher in the fibrotic cells in cluster C5 and lower in the cells in clusters C0, C1, and C6

summary:
In Homo sapiens, fibrotic corneal endothelial cells in cluster C5 show higher expression of CD44, MME (CD10), VMO1, and THBS2 compared to therapy-grade corneal endothelial cells in clusters C0, C1, and C6.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:f11b6f681dd5657f1cb8
claim_id: claim:f11b6f681dd5657f1cb8
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Immunofluorescence analysis confirmed that CGLN1, NCAM1 (CD56) and ALCAM (CD166) were exclusively expressed by good quality CECs and not expressed in the cultures containing CECs with an altered morphology

summary:
In Homo sapiens, good quality corneal endothelial cells exclusively express CGNL1, NCAM1 (CD56), and ALCAM (CD166), which are not expressed in lower quality corneal endothelial cells with altered morphology.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:bd8ceffbeaf191c41c73
claim_id: claim:bd8ceffbeaf191c41c73
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
Furthermore, immunofluorescence analysis also confirmed that CD44, MME (CD10), THBS2, and VMO1 were exclusively expressed by low quality CECs and not expressed in high quality CEC cultures

summary:
In Homo sapiens, low quality corneal endothelial cells exclusively express CD44, MME (CD10), THBS2, and VMO1, which are not expressed in high quality corneal endothelial cell cultures.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:07fc8710c7e8aab2e0af
claim_id: claim:07fc8710c7e8aab2e0af
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
therapy-grade CECs and on primary CEC cultures composed of cells with spindle shape morphology, a characteristic of cells undergoing an endothelial to mesenchymal transition, referred as low quality primary CECs (Figure 6B). Immunofluorescence analysis confirmed that CGLN1, NCAM1 (CD56) and ALCAM (CD166) were exclusively expressed by good quality CECs and not expressed in the cultures containing CECs with an altered morphology (Figure 6C). Furthermore, immunofluorescence analysis also confirmed that CD44, MME (CD10), THBS2, and VMO1 were exclusively expressed by low quality CECs and not expressed in high quality CEC cultures (Figure 6C).

## DISCUSSION

In this study, we present a single-cell roadmap of human CECs in culture, revealing the diverse trajectories of individual cells. Our scRNAseq census of 42,200 primary cultured CECs revealed the presence of 7 clusters in therapeutically relevant time points, including therapy- grade CECs expressing SLC4A11, ALCAM, and COL4A3

summary:
In Homo sapiens, therapy-grade corneal endothelial cells express SLC4A11, ALCAM, and COL4A3; highly proliferative corneal endothelial cells express MKI67 and CENPF; lower quality corneal endothelial cells entering senescence and endothelial-to-mesenchymal transition express CDKN1A, CDKN2A, and TAGLN; and fibrotic corneal endothelial cells express CD44 and ACTA2.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:48c9e04c1cce8e98a5fd
claim_id: claim:48c9e04c1cce8e98a5fd
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal: lower quality CECs entering senescence and EMT expressing CDKN1A, CDKN2A, and TAGLN
summary:
In Homo sapiens, lower quality corneal endothelial cells entering senescence and endothelial-to-mesenchymal transition express CDKN1A, CDKN2A, and TAGLN.


claim_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073:claim:cce4cb03f18e066fec96
claim_id: claim:cce4cb03f18e066fec96
paper_key: biorxiv:c78d9bda-6cc0-1014-aba5-dba9dd700073
span_literal:
we show that therapy-grade CEC should be identified by the expression of CD166 and NCAM1 membrane proteins together with CGNL1, a membrane-associated protein to cellular tight junctions; lack of expression of altered extracellular matrix, namely VMO1 and THBS2; and lack of expression of membrane proteins CD44 and CD10.

summary:
In Homo sapiens, therapy-grade corneal endothelial cells are identified by expression of CD166, NCAM1, and CGNL1, and by lack of expression of VMO1, THBS2, CD44, and CD10.


claim_key: biorxiv:c7fdc9c2-6d13-1014-a5fd-e51b1c35a4eb:claim:b2fa6cf263223aab97da
claim_id: claim:b2fa6cf263223aab97da
paper_key: biorxiv:c7fdc9c2-6d13-1014-a5fd-e51b1c35a4eb
summary: In Homo sapiens frontal cortex, glutamatergic neurons are marked by SLC17A7.
span_literal:
glutamatergic neurons are marked by SLC17A7, GABAergic interneurons are marked by GAD1, astrocytes are marked by GFAP, oligodendrocytes are marked by ST18, oligodendrocyte progenitor cell (OPC) is marked by VCAN, microglia are marked by CD74 and endothelial cells by CLDN5.


claim_key: biorxiv:c7fdc9c2-6d13-1014-a5fd-e51b1c35a4eb:claim:2fc549ebc0efb61b3a74
claim_id: claim:2fc549ebc0efb61b3a74
paper_key: biorxiv:c7fdc9c2-6d13-1014-a5fd-e51b1c35a4eb
span_literal: Neuronal cell types exhibited significantly higher expression of MEG3 PAS.
summary:
In Homo sapiens frontal cortex, neuronal cell types exhibited significantly higher expression of MEG3 poly(A) site transcripts compared to other neural cell types.


claim_key: biorxiv:c8264099-6fc3-1014-9d27-9ae05a0c1d33:claim:aafdae654a956c91b01a
claim_id: claim:aafdae654a956c91b01a
paper_key: biorxiv:c8264099-6fc3-1014-9d27-9ae05a0c1d33
span_literal: CD86, which is pivotal in B cell activation (39), emerged as top hub genes in the B cell CGN.
summary:
In Homo sapiens, CD86 is a top hub gene in the B cell cell type-specific gene network, pivotal in B cell activation.


claim_key: biorxiv:c8264099-6fc3-1014-9d27-9ae05a0c1d33:claim:ec8cd041f4af71205656
claim_id: claim:ec8cd041f4af71205656
paper_key: biorxiv:c8264099-6fc3-1014-9d27-9ae05a0c1d33
span_literal:
Similarly, genes essential for T cell identity like CD2, CD4, and CD28 were among the top 15 hub genes in the T cell CGN (40).

summary:
In Homo sapiens, CD2, CD4, and CD28 are essential hub genes for T cell identity in the T cell cell type-specific gene network.


claim_key: biorxiv:c8264099-6fc3-1014-9d27-9ae05a0c1d33:claim:d1546fdf7c1040d2dbcc
claim_id: claim:d1546fdf7c1040d2dbcc
paper_key: biorxiv:c8264099-6fc3-1014-9d27-9ae05a0c1d33
span_literal:
Additionally, S100A8, S100A9, CD14, markers for monocytic myeloid-derived suppressor cells were prominent hubs in the monocyte CGNs (41).

summary:
In Homo sapiens, S100A8, S100A9, and CD14 are markers for monocytic myeloid-derived suppressor cells and prominent hub genes in monocyte cell type-specific gene networks.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:e4f562d0267cc080f983
claim_id: claim:e4f562d0267cc080f983
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
ICE identified senescent fibro-adipogenic progenitors (FAPs) in muscle tissue, characterized by elevated expression of senescence-associated secretory phenotype (SASP) genes.

summary:
In Homo sapiens, senescent fibro-adipogenic progenitors in muscle tissue are characterized by elevated expression of senescence-associated secretory phenotype genes.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:af679ed269d673089f50
claim_id: claim:af679ed269d673089f50
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
ICE-identified cells exhibited highly expressed SASP genes, including IL6, CXCL8, and CXCL1 (Fig. 5d), which are strongly linked to muscle atrophy and fibrosis[33, 36].

summary:
In Homo sapiens, senescent fibro-adipogenic progenitors exhibit highly expressed senescence-associated secretory phenotype genes including IL6, CXCL8, and CXCL1, which are linked to muscle atrophy and fibrosis.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:197e7a97ea5f597fac6a
claim_id: claim:197e7a97ea5f597fac6a
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
In pancreatic β-cells, ICE identified a subpopulation with elevated ATF3 expression, which exhibited heightened unfolded protein response (UPR) pathway activity, marked by DDIT3 upregulation.

summary:
In Homo sapiens, a subpopulation of pancreatic beta cells exhibits elevated ATF3 expression and heightened unfolded protein response pathway activity marked by DDIT3 upregulation.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:b9c3fe82e73d322f4726
claim_id: claim:b9c3fe82e73d322f4726
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
These cells, characterized by high MX1 expression, displayed robust IFN-I signaling activity, which has been linked to AD progression.

summary:
In Homo sapiens, interferon-responsive microglia are characterized by high MX1 expression and robust type-I interferon signaling activity linked to Alzheimer's disease progression.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:14cf1269568f2524ad00
claim_id: claim:14cf1269568f2524ad00
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
Notably, MX1-associated microglia localized specifically to subcluster 5, while CDKN1A and CDKN2A were restricted to subclusters 2 and 4 (Fig. 7c).

summary:
In Homo sapiens, MX1-associated microglia localized to subcluster 5, while CDKN1A- and CDKN2A-associated microglia were restricted to subclusters 2 and 4 in Alzheimer's disease brains. In Homo sapiens, CDKN1A-associated microglia were restricted to subclusters 2 and 4 in Alzheimer's disease brains. In Homo sapiens, CDKN2A-associated microglia were restricted to subclusters 2 and 4 in Alzheimer's disease brains.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:58dd5f19421b51313c47
claim_id: claim:58dd5f19421b51313c47
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
These cells also showed upregulation of key regulators in IFN-I signaling genes, including STAT1, STAT2, OAS1, and OAS2 (Fig. 7f).

summary:
In Homo sapiens, MX1-associated microglia showed upregulation of type-I interferon signaling genes including STAT1, STAT2, OAS1, and OAS2.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:31c349691502ec6035cc
claim_id: claim:31c349691502ec6035cc
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
Specifically, DDIT3 (CHOP) functions as a key mediator of ER stress-induced apoptosis[39] and HSPA5 (GRP78/BiP) encodes a master regulator of the UPR[40].

summary:
In Homo sapiens, ATF3-associated beta cells exhibit upregulation of DDIT3, a key mediator of endoplasmic reticulum stress-induced apoptosis, and HSPA5, a master regulator of the unfolded protein response.


claim_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b:claim:c823e92b99cced9ef3a7
claim_id: claim:c823e92b99cced9ef3a7
paper_key: biorxiv:c94927bb-7bec-1014-9cd8-fedd121e156b
span_literal:
While CDKN1A, CDKN2A and MX1 displayed diffuse expression patterns, ATF3-associated cells were specifically enriched in subclusters 3 and 6 (Fig. 6b,c).

summary:
In Homo sapiens, ATF3-associated pancreatic beta cells were specifically enriched in subclusters 3 and 6, while CDKN1A, CDKN2A, and MX1 displayed diffuse expression patterns.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:33dbd921fceeaf35e6cb
claim_id: claim:33dbd921fceeaf35e6cb
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal: The NK cells were identified as CD16+CD56+CD3−, and purity was on average 91%.
summary:
In Homo sapiens, natural killer cells are identified by positive expression of CD16 and CD56 and negative expression of CD3.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:2797ccd660f62f0e70aa
claim_id: claim:2797ccd660f62f0e70aa
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal:
we assessed the phases of maturation and characterized them into three distinct phenotypical subsets: 1. Tolerant NK cells (CD56++CD16-CD27-CD11b-), 2. Regulatory NK cells (CD56++CD16-CD27+CD11b+), and 3. Cytotoxic NK cells (CD56+CD16++CD27-CD11b-)

summary:
In Homo sapiens, tolerant natural killer cells are characterized by high CD56 expression and negative expression of CD16, CD27, and CD11b.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:d56f983747c691322508
claim_id: claim:d56f983747c691322508
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal:
we assessed the phases of maturation and characterized them into three distinct phenotypical subsets: 1. Tolerant NK cells (CD56++CD16-CD27-CD11b-), 2. Regulatory NK cells (CD56++CD16-CD27+CD11b+), and 3. Cytotoxic NK cells (CD56+CD16++CD27-CD11b-)

summary:
In Homo sapiens, regulatory natural killer cells are characterized by high CD56 expression, negative CD16 expression, and positive expression of CD27 and CD11b.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:28d98ba0679b7f70cba1
claim_id: claim:28d98ba0679b7f70cba1
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal:
we assessed the phases of maturation and characterized them into three distinct phenotypical subsets: 1. Tolerant NK cells (CD56++CD16-CD27-CD11b-), 2. Regulatory NK cells (CD56++CD16-CD27+CD11b+), and 3. Cytotoxic NK cells (CD56+CD16++CD27-CD11b-)

summary:
In Homo sapiens, cytotoxic natural killer cells are characterized by positive CD56 expression, high CD16 expression, and negative expression of CD27 and CD11b.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:13a1c79eacb9fc06d800
claim_id: claim:13a1c79eacb9fc06d800
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal:
We also identified an intermediate stage that showed dim expression of both CD56 and CD16 (CD56+CD16+/- CD27-CD11b+), here described as pre-cytotoxic NK cells.

summary:
In Homo sapiens, pre-cytotoxic natural killer cells are characterized by dim expression of CD56 and CD16, negative CD27 expression, and positive CD11b expression.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:60837f7b1eeab9f2284b
claim_id: claim:60837f7b1eeab9f2284b
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal:
IFNγ and TNFα secretion were included as functional markers for immune regulation, CD107a (degranulation marker) as measure for cytotoxicity and NKG2A and NKp46 as maturation markers

summary:
In Homo sapiens, natural killer cell maturation is marked by NKG2A and NKp46, while CD107a serves as a degranulation marker for cytotoxicity, and IFNγ and TNFα are functional markers for immune regulation.


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:f748090928437be01a13
claim_id: claim:f748090928437be01a13
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
summary: In Homo sapiens, tolerant natural killer cells show higher expression of NKG2A.
span_literal:
As expected, the tolerant and regulatory phenotypes showed higher expression of NKG2A, while NKp46 was highly upregulated by more mature regulatory and cytotoxic phenotype


claim_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a:claim:d5e8406a8b658aa77116
claim_id: claim:d5e8406a8b658aa77116
paper_key: biorxiv:ca1bf343-7250-1014-ba36-aacb127d711a
span_literal:
As expected, the tolerant and regulatory phenotypes showed higher expression of NKG2A, while NKp46 was highly upregulated by more mature regulatory and cytotoxic phenotype

summary:
In Homo sapiens, regulatory natural killer cells show higher expression of NKG2A and highly upregulated NKp46.


claim_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3:claim:7c8091a405c109bd3a0e
claim_id: claim:7c8091a405c109bd3a0e
paper_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3
summary: In Homo sapiens melanoma, NGFR is a marker of the Neural Crest-like cell state.
span_literal:
Among the previously described marker genes NGFR was identified in the Neural-Crest-like state, VEGFA was highly expressed in Stress (hypoxia response) cells, and collagen genes (i.e. COL5A1) in MES cells


claim_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3:claim:fe40749a37f8f11f819e
claim_id: claim:fe40749a37f8f11f819e
paper_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3
span_literal:
HLA class I and II and other genes involved in antigen processing and presentation, such as TAP1, B2M and NLRC5, were identified as discriminative markers of the Antigen Presentation cell population

summary:
In Homo sapiens melanoma, TAP1, B2M, and NLRC5 as well as HLA class I and II genes are discriminative markers of the Antigen Presentation cell population.


claim_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3:claim:ebcfef475f6ff18214e9
claim_id: claim:ebcfef475f6ff18214e9
paper_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3
span_literal:
an Interferon Alpha/Beta Response state expressing interferon type I responsive genes (i.e. IFI6, IFI27, IRF7), but not genes involved in antigen processing and presentation

summary:
In Homo sapiens melanoma, the Interferon Alpha/Beta Response cell state expresses IFI6, IFI27, and IRF7.


claim_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3:claim:df91f8d293e2b56944d4
claim_id: claim:df91f8d293e2b56944d4
paper_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3
span_literal:
Several of these genes including CDH19 and S100A1, which we termed Minimal Lineage Genes (MLGs), were identified in both mouse and human MES signatures and were indeed highly and selectively expressed in MES cells

summary:
In Homo sapiens melanoma, CDH19 and S100A1, termed Minimal Lineage Genes, are highly and selectively expressed in Mesenchymal-like cells.


claim_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3:claim:c15c67f2d81de6371726
claim_id: claim:c15c67f2d81de6371726
paper_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3
span_literal:
whereas stromal genes like THY1, LUM and DCN were expressed at higher levels in CAFs than in MES cells, several markers including the basic helix-loop-helix TF TCF4 (also known as ITF2 or E2-2) were instead expressed at comparable levels in both cell types

summary:
In Homo sapiens melanoma, THY1, LUM, and DCN are expressed at higher levels in cancer-associated fibroblasts than in Mesenchymal-like cells, while TCF4 (also known as ITF2 or E2-2) is expressed at comparable levels in both cell types.


claim_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3:claim:5e90468103a84dc74af2
claim_id: claim:5e90468103a84dc74af2
paper_key: biorxiv:caef9c14-6e13-1014-bca1-ba3172fec7b3
span_literal:
Measuring expression of these genes in all melanoma states revealed that while CDH19 and S100A1 were expressed in all of them (including MES cells), TCF4 and other stromal genes were selectively expressed in melanoma MES cells

summary:
In Homo sapiens melanoma, TCF4 is selectively expressed in Mesenchymal-like cells, while CDH19 and S100A1 are expressed across all melanoma cell states.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:6b3760e8d28a671010bd
claim_id: claim:6b3760e8d28a671010bd
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal: well-characterized TE markers such as GATA2 and GATA3 were highly expressed in all TE-lineage cells
summary:
In Homo sapiens, GATA2 and GATA3 are positive markers of trophectoderm-lineage cells, being highly expressed in all trophectoderm-lineage cells.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:eba0765b13e89878a180
claim_id: claim:eba0765b13e89878a180
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal:
the expression of other TE markers such as DAB2, PTGES, TGFBR3 and PDGFA were significantly downregulated after implantation at day 7

summary:
In Homo sapiens, the trophectoderm markers DAB2, PTGES, TGFBR3, and PDGFA are significantly downregulated in trophoblasts after implantation at day 7.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:abb1230a4236f1846b10
claim_id: claim:abb1230a4236f1846b10
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal:
We found additional four TE markers, namely KRT19, KRT18, KRT8 and TFRC, that were consistently highly expressed in TE and trophoblasts from day6 through day 10 using our data

summary:
In Homo sapiens, KRT19, KRT18, KRT8, and TFRC are trophectoderm markers consistently highly expressed in trophectoderm and trophoblasts from day 6 through day 10.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:b860368a1a3f53a7295a
claim_id: claim:b860368a1a3f53a7295a
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal:
We found that many ST marker genes, such as HSD3B1, CYP19A1, SDC1, ERVW-1 (Syncytin-1), ERVV-1, CGA and CGB, were specifically highly expressed in Cluster 5.

summary:
In Homo sapiens, syncytiotrophoblast marker genes HSD3B1, CYP19A1, SDC1, ERVW-1 (Syncytin-1), ERVV-1, CGA, and CGB are specifically highly expressed in syncytiotrophoblast.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:8bbcb355cc2ff0ec181c
claim_id: claim:8bbcb355cc2ff0ec181c
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal: CT markers, such as ITGA6 and FZD5, were specifically expressed in Cluster 4.
summary:
In Homo sapiens, cytotrophoblast markers ITGA6 and FZD5 are specifically expressed in cytotrophoblast.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:9938e2a4f497f22937a2
claim_id: claim:9938e2a4f497f22937a2
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal: A few EVT marker genes such as MMP2 were specifically highly expressed in Cluster 2
summary:
In Homo sapiens, the extravillous cytotrophoblast marker gene MMP2 is specifically highly expressed in extravillous cytotrophoblast.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:5503ef3ca08e679bad7d
claim_id: claim:5503ef3ca08e679bad7d
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal:
Our scRNA-seq data revealed that DPPA3 (a.k.a STELLA and PGC7) expression is significantly downregulated in ST compared to CT and EVT

summary:
In Homo sapiens, DPPA3 expression is significantly downregulated in syncytiotrophoblast compared to cytotrophoblast and extravillous cytotrophoblast.


claim_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad:claim:a20bacc177599eb048e9
claim_id: claim:a20bacc177599eb048e9
paper_key: biorxiv:cc41b42e-6c00-1014-9887-9bb7d49b64ad
span_literal:
TBX3 knockdown also significantly reduced cell fusion (75±7% and 64±14% reduction in shTBX3-a and shTBX3-b cells, respectively) (Figure 5D) and downregulated ST markers transcription, including human chorionic gonadotropin subunits (CGA and CGB), Syncytin (ERVW-1) and other HERV-derived genes (ERVV-1 and ERVV-2)

summary:
In Homo sapiens, TBX3 knockdown downregulated syncytiotrophoblast markers including human chorionic gonadotropin subunits CGA and CGB, Syncytin ERVW-1, and human endogenous retrovirus-derived genes ERVV-1 and ERVV-2, demonstrating TBX3 is required for syncytiotrophoblast formation.


claim_key: biorxiv:ce0773ad-6e8e-1014-aef3-93ffcfb90238:claim:05101bf9770c773a3d7a
claim_id: claim:05101bf9770c773a3d7a
paper_key: biorxiv:ce0773ad-6e8e-1014-aef3-93ffcfb90238
span_literal:
In human blood, CD14hiCD16low cells are described as inflammatory classical monocytes/ macrophages which are trafficked to sites of inflammation and/or infection, and CD14lowCD16hi cells are the patrolling non-classical monocytes/macrophages, which adhere and crawl along the luminal surface of endothelial cells.

summary:
In Homo sapiens blood, CD14-high CD16-low inflammatory classical monocytes/macrophages are characterized by high expression of CD14 and low expression of CD16 (FCGR3), while CD14-low CD16-high patrolling non-classical monocytes/macrophages are characterized by low expression of CD14 and high expression of CD16 (FCGR3).


claim_key: biorxiv:ce0773ad-6e8e-1014-aef3-93ffcfb90238:claim:476aacf93ea1f55f52ba
claim_id: claim:476aacf93ea1f55f52ba
paper_key: biorxiv:ce0773ad-6e8e-1014-aef3-93ffcfb90238
span_literal:
In human blood, CD14hiCD16low cells are described as inflammatory classical monocytes/ macrophages which are trafficked to sites of inflammation and/or infection, and CD14lowCD16hi cells are the patrolling non-classical monocytes/macrophages, which adhere and crawl along the luminal surface of endothelial cells.

summary:
In Homo sapiens blood, CD14-low CD16-high patrolling non-classical monocytes/macrophages are characterized by low expression of CD14 and high expression of CD16 (FCGR3).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:e68d1cca7214d9ca5498
claim_id: claim:e68d1cca7214d9ca5498
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
We also identified suprabasal cells, characterized by low TP63 expression, decreasing gradients of KRT5 expression and increasing gradients of KRT19 and NOTCH3 expression (9–12) (Figure 1D).

summary:
In Homo sapiens, suprabasal cells are characterized by low TP63 expression, decreasing KRT5 expression, and increasing KRT19 and NOTCH3 expression.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:79ffc94004d70cc32861
claim_id: claim:79ffc94004d70cc32861
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, multiciliated cells express high levels of FOXJ1, TPPP3, and SNTN.
span_literal:
We detected clusters of multiciliated cells (expressing high levels of FOXJ1, TPPP3, and SNTN) and deuterosomal cells, which correspond to precursors of multiciliated cells and express several specific markers: CCDC67/DEUP1, FOXN4 and CDC20B (Figure 1C and 1D) (12, 13).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:ac55035048df17647666
claim_id: claim:ac55035048df17647666
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, serous cells of submucosal glands express high levels of LTF, LYZ, and PIP.
span_literal:
Two cell types were associated with submucosal glands: serous cells (expressing high levels of LTF, LYZ and PIP) and mucous cells (expressing high levels of MUC5B but no MUC5AC) (Figure 1C and 1D).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:c89510b7d81cbcfadf1e
claim_id: claim:c89510b7d81cbcfadf1e
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, alveolar type I pneumocytes express HOPX, AGER, and SPOCK2.
span_literal:
AT1 expressed HOPX, AGER, SPOCK2; AT2 expressed SFTPA, SFTPB, SFTPC and SFTPD (Figure 3B, Table E2, Figure E5).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:af36cf9da2309082e579
claim_id: claim:af36cf9da2309082e579
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
In the lymphoid lineage, we were able to discriminate B cells (expressing high levels of MS4A1 and LTB, and high PAX5 inferred activity) from plasma cells (expressing high levels of IGJ and MZBI, and high IRF4 inferred activity) (Figure 1D, Figure E6A, B).

summary:
In Homo sapiens, B cells express high levels of MS4A1 and LTB, with high PAX5 inferred activity, distinguishing them from plasma cells.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:e0421a171b02c2aa63ae
claim_id: claim:e0421a171b02c2aa63ae
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
In the lymphoid lineage, we were able to discriminate B cells (expressing high levels of MS4A1 and LTB, and high PAX5 inferred activity) from plasma cells (expressing high levels of IGJ and MZBI, and high IRF4 inferred activity) (Figure 1D, Figure E6A, B).

summary:
In Homo sapiens, plasma cells express high levels of IGJ and MZBI, with high IRF4 inferred activity, distinguishing them from B cells.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:997408f6bf702db4edc9
claim_id: claim:997408f6bf702db4edc9
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
T cells and related subtypes, that our analysis did not separate well, were characterized by a high and specific transcriptional activity of the XCL1 and CD3D regulatory units (Figure E6B, E6C and E6E).

summary:
In Homo sapiens, T cells are characterized by high and specific transcriptional activity of XCL1 and CD3D regulatory units.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:7d09417db37d63242a32
claim_id: claim:7d09417db37d63242a32
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, endothelial cells express high levels of DARC.
span_literal:
We annotated 4 stromal cell types (Figure 1C-1E) including endothelial cells, expressing high levels of DARC, fibroblasts, expressing high levels of FBLN1, as well as smooth muscle cells, characterized by high levels of desmin (DES) and high activity of the HOXA4 regulatory unit (Figure 1D, Figure E7C).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:ce4d31a8bc0c961594a1
claim_id: claim:ce4d31a8bc0c961594a1
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
We annotated 4 stromal cell types (Figure 1C-1E) including endothelial cells, expressing high levels of DARC, fibroblasts, expressing high levels of FBLN1, as well as smooth muscle cells, characterized by high levels of desmin (DES) and high activity of the HOXA4 regulatory unit (Figure 1D, Figure E7C).

summary:
In Homo sapiens, smooth muscle cells are characterized by high levels of desmin (DES) and high activity of the HOXA4 regulatory unit.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:5e0cca9779290a316081
claim_id: claim:5e0cca9779290a316081
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, pericytes are identified by specific expression of RERGL, MCAM, and PDGFRB.
span_literal:
Based on a specific expression of markers such as RERGL, MCAM and PDGFRB, we also identified pericytes, a population of peri-endothelial mesenchymal cells with contractile properties that are located on the vascular basement membrane of capillaries (15, 16).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:cb6b621078ae1a3af113
claim_id: claim:cb6b621078ae1a3af113
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, pericytes share expression of ACTA2 and MYL9 with smooth muscle cells.
span_literal:
Pericytes also share with smooth muscle cells markers such as ACTA2 and MYL9 (Figure 1D, Figure E7D).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:51d755814754ec4e2b33
claim_id: claim:51d755814754ec4e2b33
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, brush/tuft cells are identified by high expression of LRMP and RGS13.
span_literal:
We identified 13 brush/tuft cells according to their high expression of LRMP and RGS13 (12, 28, 29) (Figure 3A-3C).


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:2637031f432c36d3f7c6
claim_id: claim:2637031f432c36d3f7c6
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
PNECs expressed the neurotransmitter-associated genes PCSK1N, SCGN and NEB (Figure 3C) and we identified HOXB1, ASCL1, and FOXA2 as PNEC-specific regulatory units (Figure E10A).

summary:
In Homo sapiens, pulmonary neuroendocrine cells express the neurotransmitter-associated genes PCSK1N, SCGN, and NEB, and have HOXB1, ASCL1, and FOXA2 as specific regulatory units.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:b771a57fdfc6a20c524d
claim_id: claim:b771a57fdfc6a20c524d
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
Ionocytes were characterized by markers such as ASCL3 and CFTR (29) (Figure 3C), and we identified ASCL3, FOXI1 and DMRT2 as ionocyte-specific regulatory units (Figure E10A).

summary:
In Homo sapiens, ionocytes are characterized by markers ASCL3 and CFTR, and have ASCL3, FOXI1, and DMRT2 as ionocyte-specific regulatory units.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:070f23e3d61f8c62dadc
claim_id: claim:070f23e3d61f8c62dadc
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
span_literal:
Relative to the other rare populations, these cells expressed more specifically NREP, STMN1 and MDK (Figure 3C) but shared the expression of HEPACAM2, HES6, AZGP1, CRYM and LRMP with ionocytes, brush cells and PNECs.

summary:
In Homo sapiens, undefined rare cells express NREP, STMN1, and MDK more specifically relative to other rare populations.


claim_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d:claim:d931e8ffdda9b79d1390
claim_id: claim:d931e8ffdda9b79d1390
paper_key: biorxiv:cf0d429c-6c7f-1014-a5a8-f09b6915373d
summary: In Homo sapiens, cycling cells are defined by the expression of MKI67, TOP2A, and CDC20.
span_literal:
Before batch correction, we identified a cluster of cycling cells, defined by the expression of MKI67, TOP2A, CDC20 (Figure 4A).


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:1a2f14db9547b4f54c8a
claim_id: claim:1a2f14db9547b4f54c8a
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
In the human heart, IRX1 and IRX2 are specifically expressed in the apical region of the trabeculae, within cardiomyocytes destined to form the VCS (15).

summary:
In Homo sapiens, IRX1 and IRX2 are specifically expressed in cardiomyocytes of the apical trabecular region destined to form the ventricular conduction system.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:e3c8a2f071680ff0a6bc
claim_id: claim:e3c8a2f071680ff0a6bc
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
The broader trabecular myocardium is characterized by enriched expression of BMP10, IRX3, GJA5, and CGNL1 (Figure 1B).

summary:
In Homo sapiens, the trabecular myocardium cardiomyocyte is characterized by enriched expression of BMP10, IRX3, GJA5, and CGNL1.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:00b33d6806d18aa6b9aa
claim_id: claim:00b33d6806d18aa6b9aa
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
In contrast, the compact myocardium exhibits expression of HEY2 and PLK2, with PLK2 marking cardiomyocytes located closest to the epicardium (Figure 1B).

summary:
In Homo sapiens, the compact myocardium cardiomyocyte exhibits expression of HEY2 and PLK2, with PLK2 marking epicardial-proximal cardiomyocytes.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:b1273629883bc6cf0cd5
claim_id: claim:b1273629883bc6cf0cd5
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal: Markers like IRX1–3, GJA5, and CGNL1 identify regions fated for VCS development (15).
summary:
In Homo sapiens, IRX1, IRX2, IRX3, GJA5, and CGNL1 are markers of regions fated for ventricular conduction system development.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:792b6e94525b6483837d
claim_id: claim:792b6e94525b6483837d
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
In contrast, the compact myocardium expresses HEY2 and PLK2, linked to epicardial-proximal cardiomyocytes (15).

summary:
In Homo sapiens, the compact myocardium expresses HEY2 and PLK2, which are linked to epicardial-proximal cardiomyocytes.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:dcc00353db5d67f9202f
claim_id: claim:dcc00353db5d67f9202f
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
Farah et al. (2024) identified in the developing human heart a transient hybrid ventricular cardiomyocyte population co-expressing the trabecular marker IRX3 and the compact marker HEY2 (15).

summary:
In Homo sapiens, a transient hybrid ventricular cardiomyocyte population co-expresses the trabecular marker IRX3 and the compact marker HEY2.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:5834069fdd7f58d30f8d
claim_id: claim:5834069fdd7f58d30f8d
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
Etv1 is a conserved marker of trabecular myocardium in embryos and the VCS in postnatal hearts, in both mice and humans (15, 26).

summary:
In Homo sapiens, ETV1 is a conserved marker of trabecular myocardium cardiomyocyte in embryos and the ventricular conduction system in postnatal hearts.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:504e3943138b6bf7af1a
claim_id: claim:504e3943138b6bf7af1a
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
Etv1 is a conserved marker of trabecular myocardium in embryos and the VCS in postnatal hearts, in both mice and humans (15, 26).

summary:
In Homo sapiens, ETV1 is a conserved marker of the ventricular conduction system cell in postnatal hearts.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:99d0c72151ff7707bf36
claim_id: claim:99d0c72151ff7707bf36
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
summary: In Homo sapiens, CGNL1 and PLK2 show prominent expression in cardiomyocytes in the heart.
span_literal:
Although CGNL1 and PLK2 show prominent expression in cardiomyocytes in human hearts (15), they are only weakly expressed in cardiomyocytes of developing mouse hearts.


claim_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536:claim:9136d896272ea6d681a0
claim_id: claim:9136d896272ea6d681a0
paper_key: biorxiv:cfb3ce40-7a31-1014-ae9e-8efc9660d536
span_literal:
Furthermore, human ETV1 variants have been associated with conduction disease (31), highlighting the potential role of the Nrg1-Etv1 axis in the pathogenesis of LVNC and related cardiomyopathies.

summary:
In Homo sapiens, ETV1 variants have been associated with conduction disease, highlighting its role in ventricular conduction system cell function.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:fe9f85c6f1b02d177c9b
claim_id: claim:fe9f85c6f1b02d177c9b
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
YAP1 was high in PRAD/HGC but not NEPC (Figure 1C, P<1x10-4), while ASCL1 and other neuroendocrine–associated TFs were high in NEPC histologies but not PRAD/HGC

summary:
In Homo sapiens, YAP1 is highly expressed in prostate adenocarcinoma and high-grade carcinoma but not in neuroendocrine prostate cancer.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:aec9f4cfdb563fc65c5f
claim_id: claim:aec9f4cfdb563fc65c5f
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
YAP1 was high in PRAD/HGC but not NEPC (Figure 1C, P<1x10-4), while ASCL1 and other neuroendocrine–associated TFs were high in NEPC histologies but not PRAD/HGC

summary:
In Homo sapiens, YAP1 is highly expressed in high-grade carcinoma but not in neuroendocrine prostate cancer.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:fd879fb071c48fc130e9
claim_id: claim:fd879fb071c48fc130e9
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
YAP1 was high in PRAD/HGC but not NEPC (Figure 1C, P<1x10-4), while ASCL1 and other neuroendocrine–associated TFs were high in NEPC histologies but not PRAD/HGC

summary:
In Homo sapiens, ASCL1 is highly expressed in neuroendocrine prostate cancer but not in prostate adenocarcinoma or high-grade carcinoma.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:f9bf24832853e1ea806d
claim_id: claim:f9bf24832853e1ea806d
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal: Histologically defined NEPC tumors were enriched for expression of INSM1, SYP, FOXA2, and SOX2
summary:
In Homo sapiens, neuroendocrine prostate cancer tumors are enriched for expression of INSM1, SYP, FOXA2, and SOX2.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:3234678575ce85769bc2
claim_id: claim:3234678575ce85769bc2
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
TROP2, the target of an FDA–approved antibody–drug conjugate in breast and bladder cancers (33, 34), was expressed in all PRADs and HGCs but not in the majority of NEPC

summary:
In Homo sapiens, TROP2 is expressed in prostate adenocarcinoma and high-grade carcinoma but not in the majority of neuroendocrine prostate cancer samples.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:a46a9e68e3f2bdbe367f
claim_id: claim:a46a9e68e3f2bdbe367f
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
TROP2, the target of an FDA–approved antibody–drug conjugate in breast and bladder cancers (33, 34), was expressed in all PRADs and HGCs but not in the majority of NEPC

summary:
In Homo sapiens, TROP2 is expressed in high-grade carcinoma but not in the majority of neuroendocrine prostate cancer samples.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:3798e18ff3af5ef37e17
claim_id: claim:3798e18ff3af5ef37e17
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
summary: In Homo sapiens, DLL3 expression is restricted to neuroendocrine prostate cancer tumors.
span_literal:
expression of DLL3, the target of multiple agents currently under clinical investigation in SCLC (antibody drug conjugates, T cell engagers, CAR– T cells) (35, 36), was restricted to NEPC tumors


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:4717bbd8a36decc657db
claim_id: claim:4717bbd8a36decc657db
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
The single marker gene approach confirmed that both YAP1 and TROP2 are robust markers for PRAD and HGC histology, whereas DLL3 is an exclusively NEPC–specific cell surface antigen.

summary:
In Homo sapiens, YAP1 and TROP2 are robust markers for prostate adenocarcinoma and high-grade carcinoma, whereas DLL3 is an exclusively neuroendocrine prostate cancer-specific cell surface antigen.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:7d9ccb294a946507e279
claim_id: claim:7d9ccb294a946507e279
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
The single marker gene approach confirmed that both YAP1 and TROP2 are robust markers for PRAD and HGC histology, whereas DLL3 is an exclusively NEPC–specific cell surface antigen.

summary:
In Homo sapiens, YAP1 and TROP2 are robust markers for high-grade carcinoma, whereas DLL3 is an exclusively neuroendocrine prostate cancer-specific cell surface antigen.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:f55b0c067d18d2738387
claim_id: claim:f55b0c067d18d2738387
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
The single marker gene approach confirmed that both YAP1 and TROP2 are robust markers for PRAD and HGC histology, whereas DLL3 is an exclusively NEPC–specific cell surface antigen.

summary:
In Homo sapiens, DLL3 is an exclusively neuroendocrine prostate cancer-specific cell surface antigen.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:ab1fb4fbc4fcebedc42a
claim_id: claim:ab1fb4fbc4fcebedc42a
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
both ASCL1 and INSM1 are highly specific markers of NEPC and tend to lose expression of YAP1 expression, providing a strong dichotomy between PRAD and NEPC states.

summary:
In Homo sapiens, both ASCL1 and INSM1 are highly specific markers of neuroendocrine prostate cancer, which tends to lose YAP1 expression, providing a strong dichotomy between prostate adenocarcinoma and neuroendocrine prostate cancer states.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:cdcb1227c2d98101d9e4
claim_id: claim:cdcb1227c2d98101d9e4
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
TROP2 expression was enriched across all adenocarcinomas regardless of AR status, indicative of a broader lineage profile

summary:
In Homo sapiens, TROP2 expression is enriched across all prostate adenocarcinoma regardless of AR status.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:57baa299e9916907e9b3
claim_id: claim:57baa299e9916907e9b3
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
In contrast to TROP2, CEACAM5 displayed a negative correlation with AR in CRPC–adenocarcinoma and was expressed in all NEPC clusters, suggesting that CEACAM5 is an actionable target for non–AR–driven disease

summary:
In Homo sapiens, CEACAM5 is expressed in all neuroendocrine prostate cancer clusters and displays a negative correlation with AR in castrate-resistant prostate adenocarcinoma.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:68f2c7a10a2b8a172e28
claim_id: claim:68f2c7a10a2b8a172e28
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
While DLL3 was expressed in all NEPC regulons, NEPC–N regulons displayed lower expression compared with NEPC–A

summary:
In Homo sapiens, DLL3 is expressed in all neuroendocrine prostate cancer regulons, but the NEUROD1-positive neuroendocrine prostate cancer subtype displays lower DLL3 expression compared with the ASCL1-positive neuroendocrine prostate cancer subtype.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:84e1173bfd4da4e1af76
claim_id: claim:84e1173bfd4da4e1af76
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal:
PRADs showed high immunohistochemical scores for CK8, along with the prostate luminal markers AR (Supplementary Figure 1A) and NKX3.1

summary:
In Homo sapiens, prostate adenocarcinoma shows high immunohistochemical scores for CK8, along with the prostate luminal markers AR and NKX3.1.


claim_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4:claim:44cc062053c65d0e00fd
claim_id: claim:44cc062053c65d0e00fd
paper_key: biorxiv:d00e7bca-700f-1014-91f0-ae4c53ddfbf4
span_literal: The basal lineage marker P63 was absent in all tumors
summary:
In Homo sapiens, the basal lineage marker P63 was absent in all castrate-resistant prostate cancer tumors.


claim_key: biorxiv:d138bac9-6d67-1014-914f-c022dd616f62:claim:b46bf03a3db71dbc0d5f
claim_id: claim:b46bf03a3db71dbc0d5f
paper_key: biorxiv:d138bac9-6d67-1014-914f-c022dd616f62
span_literal:
Mg-TAMs and DAM appear to activate similar programs including decreased homeostatic genes, classical activation markers (e.g. Spp1, Il1b), the phagocytic (e.g. Apoe, Trem2, Tyrobp) and APC (e.g. Itgax and Igf1) signatures.

summary:
In Homo sapiens, microglia-derived tumor-associated macrophages and disease-associated microglia activate similar programs including SPP1, IL1B as classical activation markers, APOE, TREM2, TYROBP as phagocytic markers, and ITGAX and IGF1 as antigen-presenting cell markers.


claim_key: biorxiv:d138bac9-6d67-1014-914f-c022dd616f62:claim:c544f9738cdbf2cc16f4
claim_id: claim:c544f9738cdbf2cc16f4
paper_key: biorxiv:d138bac9-6d67-1014-914f-c022dd616f62
span_literal:
Mg-TAMs and DAM appear to activate similar programs including decreased homeostatic genes, classical activation markers (e.g. Spp1, Il1b), the phagocytic (e.g. Apoe, Trem2, Tyrobp) and APC (e.g. Itgax and Igf1) signatures.

summary:
In Homo sapiens, disease-associated microglia activate similar programs including SPP1, IL1B as classical activation markers, APOE, TREM2, TYROBP as phagocytic markers, and ITGAX and IGF1 as antigen-presenting cell markers.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:874ff22a59d884c09cc7
claim_id: claim:874ff22a59d884c09cc7
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: T cells (50,365 cells; CD3D+and CD3E+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, T cells are marked by positive expression of CD3D and CD3E.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:8555093e435f2f9f1217
claim_id: claim:8555093e435f2f9f1217
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: bile duct cells (25,837 cells; EPCAM+, KRT19+, and KRT7+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, bile duct cells are marked by positive expression of EPCAM, KRT19, and KRT7.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:c20acc0a90ca6846084a
claim_id: claim:c20acc0a90ca6846084a
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: endothelial cells (10,841 cells; PTPRB+, CLDN5+, and CDH5+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, endothelial cells are marked by positive expression of PTPRB, CLDN5, and CDH5.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:a48678e03425add0e3ad
claim_id: claim:a48678e03425add0e3ad
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: monocytes (6,843 cells; FCN1+, S100A8+, and S100A9+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, monocytes are marked by positive expression of FCN1, S100A8, and S100A9.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:0191fee940e84c8972f9
claim_id: claim:0191fee940e84c8972f9
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: NK cells (5,854 cells; NCAM1+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, natural killer cells are marked by positive expression of NCAM1.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:8343726502d06a6b9c9d
claim_id: claim:8343726502d06a6b9c9d
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: macrophages (5,243 cells; C1QA+ and C1QB+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, macrophages are marked by positive expression of C1QA and C1QB.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:fdccbe8d429e76131235
claim_id: claim:fdccbe8d429e76131235
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: fibroblasts (4,998 cells; ACTA2+ and COL1A2+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, fibroblasts are marked by positive expression of ACTA2 and COL1A2.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:7e0f8f19a5dde333e709
claim_id: claim:7e0f8f19a5dde333e709
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: B cells (2,847 cells; MS4A1+ and CD79A+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, B cells are marked by positive expression of MS4A1 and CD79A.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:06810ec671aecdaf72d4
claim_id: claim:06810ec671aecdaf72d4
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: cDC2 (2,177 cells; CD1A+, CD1C+, and CD1E+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, conventional dendritic cell type 2 is marked by positive expression of CD1A, CD1C, and CD1E.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:adb4ea57cac14340c119
claim_id: claim:adb4ea57cac14340c119
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: hepatocytes (1,550 cells; APOA1+, APOC3+, and FABP1+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, hepatocytes are marked by positive expression of APOA1, APOC3, and FABP1.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:d9ae8b070005aae809c3
claim_id: claim:d9ae8b070005aae809c3
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: plasma cells (1,183 cells; MZB1+, IGKC+, and JCHAIN+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, plasma cells are marked by positive expression of MZB1, IGKC, and JCHAIN.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:ce0f14de568a63c5ad55
claim_id: claim:ce0f14de568a63c5ad55
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: cDC1 (1,122 cells; CLEC9A+, XCR1+, and BATF3+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, conventional dendritic cell type 1 is marked by positive expression of CLEC9A, XCR1, and BATF3.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:9eed45c4fc7c9c9a8095
claim_id: claim:9eed45c4fc7c9c9a8095
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: pDC (493 cells; LILRA4+ and CLEC4C+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, plasmacytoid dendritic cells are marked by positive expression of LILRA4 and CLEC4C.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:0b9a7c0a01ec9ea31f5b
claim_id: claim:0b9a7c0a01ec9ea31f5b
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal: mast cells (265 cells; TPSAB1+ and TPSB2+)
summary:
In Homo sapiens intrahepatic cholangiocarcinoma, mast cells are marked by positive expression of TPSAB1 and TPSB2.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:aebc483b3a6eccbaaa7a
claim_id: claim:aebc483b3a6eccbaaa7a
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
Expression patterns of PTPRC, MGP, and EPCAM delineated the major immune, stromal, and epithelial populations in ICC tissues

summary:
In Homo sapiens intrahepatic cholangiocarcinoma tissues, PTPRC marks immune cells, MGP marks stromal cells, and EPCAM marks epithelial cells.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:28f62fe0f44c86fa39f1
claim_id: claim:28f62fe0f44c86fa39f1
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
characterized by pronounced expression of immunosuppressive markers such as TIGIT, TNFRSF4, CTLA4, IL2RA, and TNFRSF18

summary:
In Homo sapiens intrahepatic cholangiocarcinoma, regulatory T cells are characterized by pronounced expression of TIGIT, TNFRSF4, CTLA4, IL2RA, and TNFRSF18.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:efcd06299d284577fe2f
claim_id: claim:efcd06299d284577fe2f
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
we observed an increasing trend in CD8+ proliferating T cells (Figure 3B, C, Supplementary Figure 5B), which expressed a number of exhaustion markers, including LAG3, TIGIT, HAVCR2, and SIRPG, indicating an exhaustion state for these cells

summary:
In Homo sapiens intrahepatic cholangiocarcinoma, CD8+ proliferating T cells express exhaustion markers LAG3, TIGIT, HAVCR2, and SIRPG.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:2ead3a3e67a693838cf5
claim_id: claim:2ead3a3e67a693838cf5
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
IFI30+ macrophages emerge as the predominant macrophage subpopulation within tumor tissues (Figure 5B), exhibiting high expression of the lysosomal thiol reductase (IFI30), steopontin-encoding gene (SPP1) and Fibronectin 1 (FN1)

summary:
In Homo sapiens intrahepatic cholangiocarcinoma, IFI30+ macrophages exhibit high expression of IFI30, SPP1, and FN1.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:97165c3e86629b6261b6
claim_id: claim:97165c3e86629b6261b6
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
FOLR2+ macrophages, abundant in normal and adjacent tissues (Figure 5B), represent a type of tissue-resident macophage, expressing non-canonical myeloid markers (LYVE1 and SELENOP) alongside heightened levels of complement genes (C1QA and C1QC) and scavenger receptors (MACRO and SEPP1)

summary:
In Homo sapiens intrahepatic cholangiocarcinoma, FOLR2+ macrophages express LYVE1, SELENOP, C1QA, C1QC, MACRO, and SEPP1.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:b1dcf8c4c82e30073159
claim_id: claim:b1dcf8c4c82e30073159
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
CD3E+ macrophages highly express immune regulatory molecules (CD3E and CD7), chemokines (CCL5 and IL32), and calcium-binding proteins (S100A8, S100A9, and S100A12), potentially orchestrating inflammatory and immune response.

summary:
In Homo sapiens intrahepatic cholangiocarcinoma, CD3E+ macrophages highly express CD3E, CD7, CCL5, IL32, S100A8, S100A9, and S100A12.


claim_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173:claim:2ecc2ccf3e1d205fe7b8
claim_id: claim:2ecc2ccf3e1d205fe7b8
paper_key: biorxiv:d2042444-7138-1014-94ac-a1f590fd3173
span_literal:
Within KRTs+ macrophages, keratin-encoding genes (KRT8, KRT18, and KRT19) are significantly expressed

summary:
In Homo sapiens intrahepatic cholangiocarcinoma, KRTs+ macrophages significantly express KRT8, KRT18, and KRT19.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:d5ad16afed77fd82d631
claim_id: claim:d5ad16afed77fd82d631
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
CD8 TEMRA were distributed across multiple clusters including cluster 1, which was enriched for mTOR-LE genes and expressed genes controlling terminal effector fate HOPX,34 GZMH,35 and the transcription factor ZEB2

summary:
In Homo sapiens, CD8+ terminally differentiated effector memory T cells re-expressing CD45RA express HOPX, GZMH, and ZEB2, which are genes controlling terminal effector fate.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:c8afa28d43ea2f534668
claim_id: claim:c8afa28d43ea2f534668
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
Upregulation of GZMA, OAS1, IFITM2, LCK, MKI67, and PDCD1 in this subset driven by elevated activation protein CD38 was consistent with a proliferating effector phenotype

summary:
In Homo sapiens, CD38++ CD8+ effector T cells show upregulation of GZMA, OAS1, IFITM2, LCK, MKI67, and PDCD1, consistent with a proliferating effector phenotype.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:eeae59df0e9b5a9f9288
claim_id: claim:eeae59df0e9b5a9f9288
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
IL15 and interferon-simulated genes (ISGs) B2M, CD38 and STAT1 were oppositely regulated between groups from baseline to post-treatment (upregulated in the irAE group and downregulated in the non irAE group).

summary:
In Homo sapiens, classical monocytes in the immune-related adverse event group show upregulation of IL15, B2M, CD38, and STAT1 post-treatment with avelumab.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:f07b0c70d486912a417b
claim_id: claim:f07b0c70d486912a417b
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
mTOR-LE genes such as SLC2A1, GAPDH, FADS1, FADS2, LDLR, and ADIPOR2 (Fig. 2a) suggested this enrichment may reflect a metabolic state downstream of mTOR, since these genes are involved in glucose and lipid metabolism.

summary:
In Homo sapiens, CD8+ terminally differentiated effector memory T cells re-expressing CD45RA in the immune-related adverse event group show elevated expression of mTOR leading-edge genes SLC2A1, GAPDH, FADS1, FADS2, LDLR, and ADIPOR2, reflecting a metabolic state downstream of mTOR.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:746ba8a67f3e82e41a14
claim_id: claim:746ba8a67f3e82e41a14
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
They also displayed potential enhanced tissue migratory capacity given the enrichment of epithelial-to-mesenchymal transition genes, including CD44, VIM, VCAN, THBS1, and SDC4

summary:
In Homo sapiens, CD1c-high dendritic cells in the immune-related adverse event group display enrichment of epithelial-to-mesenchymal transition genes including CD44, VIM, VCAN, THBS1, and SDC4, suggesting enhanced tissue migratory capacity.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:a00c4118c9929aa9310a
claim_id: claim:a00c4118c9929aa9310a
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
In the CD38++ subset, upregulation of T-cell activation and cell cycle signals included genes CDC25B, CDC27, MCM3, and CSK2

summary:
In Homo sapiens, CD38++ CD8+ effector T cells show upregulation of T-cell activation and cell cycle genes CDC25B, CDC27, MCM3, and CSK2 post-avelumab treatment.


claim_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0:claim:0f028f36c26531e83f30
claim_id: claim:0f028f36c26531e83f30
paper_key: biorxiv:d249a77b-6c97-1014-8df4-e171a53e6bf0
span_literal:
Interestingly, BHLHE40, a member of our mTOR-LE signature, is the gene with the most significant differential expression between ICI-induced colitis vs. non-colitis in cluster 10 (effector cluster 2).

summary:
In Homo sapiens, BHLHE40 is the most significantly differentially expressed gene in effector CD8+ T-cell cluster 10 between immune checkpoint inhibitor-induced colitis and non-colitis.


claim_key: biorxiv:d30d2651-6c1b-1014-8313-dcecc093f4ce:claim:d48b8f84c72ce6aab465
claim_id: claim:d48b8f84c72ce6aab465
paper_key: biorxiv:d30d2651-6c1b-1014-8313-dcecc093f4ce
span_literal:
SNAP25 expression was used to broadly define neuronal cells, while GAD1 expression defined inhibitory interneurons.

summary:
In Homo sapiens, SNAP25 expression is used to broadly define neuronal cells, while GAD1 expression defines inhibitory interneurons.


claim_key: biorxiv:d30d2651-6c1b-1014-8313-dcecc093f4ce:claim:ac9ecdc969733212b4d4
claim_id: claim:ac9ecdc969733212b4d4
paper_key: biorxiv:d30d2651-6c1b-1014-8313-dcecc093f4ce
span_literal:
T cells with activation-independent exhaustion profiles, characterized by expression of co-inhibitory receptors (e.g. PD1 and TIM3), could be distinguished from cytotoxic T cell profiles.

summary:
In Homo sapiens, exhausted T cells are characterized by expression of PD1 and TIM3, distinguishing them from cytotoxic T cells.


claim_key: biorxiv:d30d2651-6c1b-1014-8313-dcecc093f4ce:claim:c87ed8f7d01b9a39d2e2
claim_id: claim:c87ed8f7d01b9a39d2e2
paper_key: biorxiv:d30d2651-6c1b-1014-8313-dcecc093f4ce
span_literal:
A human middle temporal gyrus cortical layer 1 GABAergic interneuron that selectively expresses KIT, NTNG1, and POU6F2 mRNAs

summary:
In Homo sapiens, the rosehip neuron, a middle temporal gyrus cortical layer 1 GABAergic interneuron, selectively expresses KIT, NTNG1, and POU6F2.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:af30e07b2fc16e3d0891
claim_id: claim:af30e07b2fc16e3d0891
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
We detected immunostaining for TBR1 and PAX6, which are markers of ventricular zone (VZ) and subventricular zone (SVZ) of the developing neocortex (respectively), as dorsal forebrain markers.

summary:
In Homo sapiens, TBR1 is a marker of the ventricular zone of the developing neocortex, and PAX6 is a marker of the subventricular zone of the developing neocortex, both serving as dorsal forebrain markers.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:82dd73d665801b3d473c
claim_id: claim:82dd73d665801b3d473c
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
We detected immunostaining for TBR1 and PAX6, which are markers of ventricular zone (VZ) and subventricular zone (SVZ) of the developing neocortex (respectively), as dorsal forebrain markers.

summary:
In Homo sapiens, PAX6 is a marker of the subventricular zone of the developing neocortex, serving as a dorsal forebrain marker.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:c990703c50ee2c46df3a
claim_id: claim:c990703c50ee2c46df3a
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
For examining ventral organoid parts, we detected the immunofluorescence staining of DLX2 and NKX2.1, markers of medial ganglionic eminence (MGE), and GSX2, marker of lateral ganglionic eminence (LGE).

summary:
In Homo sapiens, DLX2 and NKX2.1 are markers of the medial ganglionic eminence, and GSX2 is a marker of the lateral ganglionic eminence.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:bc1030985e9b208e84ae
claim_id: claim:bc1030985e9b208e84ae
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
In the developing brain, there is an expression of the PAX6 marker, which indicates the presence of a population of early progenitors, and the expression of the TBR1 marker, which indicates the presence of a population of early-born neurons.

summary:
In Homo sapiens, PAX6 is a marker of early progenitors, and TBR1 is a marker of early-born neurons in the developing brain.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:f8d59b14df5d764bbb17
claim_id: claim:f8d59b14df5d764bbb17
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
The panels of representative micrographs are designated by HD (71D/71V, 77D/77V), control (17D/17V, 21D/21V), and mosaic organoid (21D/71V, 71D/21V) types. The panels contain a co-staining experiment with PAX6 (green) and TBR1 (red) and a merged image of both stainings for each organoid. The micrographs revealed the occurrence of a large number of PAX6-positive neural rosettes lying close to each other and the occurrence of the separate layers of TBR1 expression in HD fused organoids (71D/71V & 77D/77V) while in control fused organoids (17D/17V & 21D/21V) only several scattered rosettes and lower expression of PAX6 and TBR1 is present, indicating less neural stem cells therefore less proliferative profile.

summary:
In Homo sapiens, PAX6 is a positive marker of neural stem cells in neural rosettes of brain organoids.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:c7c2b5593cc23ca15c1f
claim_id: claim:c7c2b5593cc23ca15c1f
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
DARPP-32, encoded by the PPP1R1B gene, plays a pivotal role in integrating signal transduction in dopaminoceptive neurons and has a regulatory role in the central nervous system (CNS) (Lin et al., 2021).

summary:
In Homo sapiens, DARPP-32, encoded by the PPP1R1B gene, is a marker of dopaminoceptive neurons in the central nervous system.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:038382229c101f4026dd
claim_id: claim:038382229c101f4026dd
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
The expression of ATOX1, a marker of neuronal progenitors, and HS3ST4, a marker of excitatory neurons, was also increased in 71Q HD lines in comparison to 21Q and 33Q control organoids (ANOVA pval = 0.0033 and 0.0086, respectively).

summary:
In Homo sapiens, ATOX1 is a marker of neuronal progenitors, and HS3ST4 is a marker of excitatory neurons.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:7a132ba854bd1188cb4a
claim_id: claim:7a132ba854bd1188cb4a
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
span_literal:
We have detected that HD organoids were highly populated by TTR-positive choroid plexus cells, also characterized in our scRNAseq data by the expression of TJP1 (pval = ∼ 2,54E-08; log(FC) = ∼ 7.59) and GATA3 transcription factor (pval = ∼ 1,93E-05; log(FC) = ∼ 4.71), which is prominently active in the development and the S100B (pval = ∼ 0.00048; log(FC) = ∼ 3.13).

summary:
In Homo sapiens, choroid plexus cells are marked by TTR, TJP1, GATA3, and S100B expression in HD organoids.


claim_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b:claim:42d6f2d43e9a67402d39
claim_id: claim:42d6f2d43e9a67402d39
paper_key: biorxiv:d5d99202-6f97-1014-84ab-c6b2cf40b34b
summary: In Homo sapiens, NOS1 is a marker of nitrergic neurons.
span_literal:
The opposite result was established for NOS1, a marker of nitrergic neurons, which showed upregulation in 71Q and 77Q organoids and downregulation in the 109Q line (ANOVA < 0.0008).


claim_key: biorxiv:d5e0a81d-6e24-1014-b5a4-ca20bf0dc632:claim:e3fe60daceb5209058de
claim_id: claim:e3fe60daceb5209058de
paper_key: biorxiv:d5e0a81d-6e24-1014-b5a4-ca20bf0dc632
span_literal:
OCT4 is a pluripotency TF widely used as a marker of pluripotency, whose expression is both necessary to establish and maintain the pluripotent state and lost when cells exit pluripotency

summary:
In Homo sapiens, OCT4 is a marker of pluripotent stem cells, whose expression is necessary to establish and maintain the pluripotent state and is lost when cells exit pluripotency.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:83ea60f848346a24632e
claim_id: claim:83ea60f848346a24632e
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Fibrosis in MASH is linked to a profibrogenic macrophage population expressing the "Fab5" gene signature: TREM2, CD9, FABP5, osteopontin (SPP1), and GPNMB.

summary:
In Homo sapiens, profibrogenic macrophages express the Fab5 gene signature including TREM2, CD9, FABP5, SPP1, and GPNMB.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:4dbb55beb1fc495b48c7
claim_id: claim:4dbb55beb1fc495b48c7
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Upon activation, naïve CD4+ T cells differentiate into various subsets defined by specific cytokine profiles and transcription factor expression, including Th1 (IFNγ, T-bet), Th2 (IL-4, GATA3), Th17 (IL-17, RORγT), and regulatory T (Treg; IL-10/TGFβ, FoxP3) cells.

summary:
In Homo sapiens, T helper 1 cells are defined by expression of interferon gamma and T-bet, T helper 2 cells by interleukin 4 and GATA3, T helper 17 cells by interleukin 17 and RORγT, and regulatory T cells by interleukin 10/transforming growth factor beta and FoxP3.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:95fbf7be3125916ac307
claim_id: claim:95fbf7be3125916ac307
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
summary:
In Homo sapiens, regulatory T cells are defined by expression of interleukin 10, transforming growth factor beta, and FoxP3.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:d95e93523f8387897f0a
claim_id: claim:d95e93523f8387897f0a
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Liver sections from patients with isolated steatosis or MASH were stained with a panel of antibodies against select T-cell markers, including T-bet, Eomes, FoxP3, and RORγt.

summary:
In Homo sapiens, liver sections from patients were stained for T-cell markers including T-bet for T helper 1 cells, Eomes for cytotoxic CD4+ T cells, FoxP3 for regulatory T cells, and RORγt for T helper 17 cells.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:ad012107959205f1d112
claim_id: claim:ad012107959205f1d112
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Liver sections from patients with isolated steatosis or MASH were stained with a panel of antibodies against select T-cell markers, including T-bet, Eomes, FoxP3, and RORγt.

summary:
In Homo sapiens, liver sections from patients were stained for Eomes as a marker of cytotoxic CD4+ T cells.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:02212075e52580ba3d24
claim_id: claim:02212075e52580ba3d24
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Liver sections from patients with isolated steatosis or MASH were stained with a panel of antibodies against select T-cell markers, including T-bet, Eomes, FoxP3, and RORγt.

summary:
In Homo sapiens, liver sections from patients were stained for FoxP3 as a marker of regulatory T cells.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:6c49f6f08c0d05acb355
claim_id: claim:6c49f6f08c0d05acb355
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
summary:
In Homo sapiens, liver sections from patients were stained for RORγt as a marker of T helper 17 cells.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:0e9e0fa8ab3eab40a9c5
claim_id: claim:0e9e0fa8ab3eab40a9c5
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Tnfrsf4 (TNF receptor superfamily member 4), encoding the OX40 costimulatory receptor on antigen-experienced T cells, was also specifically expressed by subsets enriched in MASH livers, such as Th1 and Treg cells, including some cytotoxic cells, both in murine and human MASH (Fig.6B, Fig. S6A).

summary:
In Homo sapiens, TNFRSF4 (TNF receptor superfamily member 4), encoding the OX40 costimulatory receptor, is specifically expressed by T helper 1 cells in metabolic dysfunction-associated steatohepatitis livers.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:beb3d3db09387ed8a738
claim_id: claim:beb3d3db09387ed8a738
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Tnfrsf4 (TNF receptor superfamily member 4), encoding the OX40 costimulatory receptor on antigen-experienced T cells, was also specifically expressed by subsets enriched in MASH livers, such as Th1 and Treg cells, including some cytotoxic cells, both in murine and human MASH (Fig.6B, Fig. S6A).

summary:
In Homo sapiens, TNFRSF4 (TNF receptor superfamily member 4), encoding the OX40 costimulatory receptor, is specifically expressed by regulatory T cells in metabolic dysfunction-associated steatohepatitis livers.


claim_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2:claim:418eb00cae4383782b3f
claim_id: claim:418eb00cae4383782b3f
paper_key: biorxiv:d830f4b7-6ce4-1014-9599-d1774896c1b2
span_literal:
Tnfrsf4 (TNF receptor superfamily member 4), encoding the OX40 costimulatory receptor on antigen-experienced T cells, was also specifically expressed by subsets enriched in MASH livers, such as Th1 and Treg cells, including some cytotoxic cells, both in murine and human MASH (Fig.6B, Fig. S6A).

summary:
In Homo sapiens, TNFRSF4 (TNF receptor superfamily member 4), encoding the OX40 costimulatory receptor, is expressed by some cytotoxic CD4+ T cells in metabolic dysfunction-associated steatohepatitis livers.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:797db27fa7b2caace535
claim_id: claim:797db27fa7b2caace535
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal: we found DEGs for established ovarian cancer biomarkers, including WFDC2 and SLPI
summary:
In Homo sapiens, WFDC2 and SLPI are established ovarian cancer biomarkers found as differentially expressed genes in ovarian high-grade serous carcinoma epithelial cells.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:9539e7339bdef0dd80f3
claim_id: claim:9539e7339bdef0dd80f3
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
NMF cluster 3, which primarily comprised spots from sample 2B with smaller representation from 3C and 4D, showed upregulation in genes associated with B-cell or plasmablast activity, such as IGKC, IGHG3, IGHG4, and JCHAIN.

summary:
In Homo sapiens, IGKC, IGHG3, IGHG4, and JCHAIN are upregulated in B cell or plasmablast populations in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:c9773dcad8f905e21c7c
claim_id: claim:c9773dcad8f905e21c7c
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
In NMF cluster 6, VEGFA, known to be associated with endothelial activity and vasculature development, and S100A10, a hallmark gene for cancer migration

summary:
In Homo sapiens, VEGFA is a marker associated with endothelial cell activity and vasculature development in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:1f66f1867d966f8e38f3
claim_id: claim:1f66f1867d966f8e38f3
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
In NMF cluster 7, we found SPP1, which is known to be expressed by cancer cells and tumor-associated macrophages

summary:
In Homo sapiens, SPP1 is expressed by tumor-associated macrophages in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:0da84777000e540cedb4
claim_id: claim:0da84777000e540cedb4
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
We found that 5 spatial domains (0, 2, 7, 9, 10) had a high expression for a known marker for ovarian cancer WFDC2

summary:
In Homo sapiens, WFDC2 is a known marker for ovarian cancer epithelial cell-dominant spatial domains.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:a014882a481c5221be55
claim_id: claim:a014882a481c5221be55
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Domain 4 displayed DE gene sets associated with cytokine-mediated signaling pathways, antigen processing and presentation, innate immune responses, and several macrophage markers (LYZ, CD68) and was potentially representative of a mixture of infiltrating immune cells and tumor associated macrophages.

summary:
In Homo sapiens, LYZ and CD68 are macrophage markers in the ovarian high-grade serous carcinoma tumor microenvironment.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:af201242d82b62b49de0
claim_id: claim:af201242d82b62b49de0
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Four of the 19 leiden clusters (cluster 5, 6, 8, 9) were identified as tumor/epithelial cells due to their expression of canonical epithelial ovarian cancer markers including WFDC2, and ELF3

summary:
In Homo sapiens, WFDC2 and ELF3 are canonical epithelial ovarian cancer markers used to identify epithelial cells.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:b367aac62a3a10fbd323
claim_id: claim:b367aac62a3a10fbd323
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Clusters 12 and 16 were identified as mesothelial cells by marker gene expression of CALB2, KRT8, KRT18 and WT1

summary:
In Homo sapiens, mesothelial cells are identified by marker gene expression of CALB2, KRT8, KRT18, and WT1.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:495a5b8e04a4847bcd4d
claim_id: claim:495a5b8e04a4847bcd4d
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Cluster 7 was identified as endothelial cells by expression of canonical marker genes CLDN5, VWF and CLEC14A

summary:
In Homo sapiens, endothelial cells are identified by expression of canonical marker genes CLDN5, VWF, and CLEC14A.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:1dd59e3e53ba937d1684
claim_id: claim:1dd59e3e53ba937d1684
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal: First, a T/NK cell cluster (2) expressing NKG7 and CD3D was detected
summary:
In Homo sapiens, T/natural killer cells are identified by expression of NKG7 and CD3D in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:9fe4f2add505dd3fe7e8
claim_id: claim:9fe4f2add505dd3fe7e8
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal: Another cluster (10) expressing FKBP51 and RHOH appeared as an additional T lymphocyte cluster
summary:
In Homo sapiens, an additional T lymphocyte cluster is identified by expression of FKBP51 and RHOH in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:702a2ccc3779ec6229d0
claim_id: claim:702a2ccc3779ec6229d0
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal: Cluster 15 expressed IGHG1 and IGHG4 and was denoted B/Plasmablast.
summary:
In Homo sapiens, B cell/plasmablast is identified by expression of IGHG1 and IGHG4 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:b2a31debbd276d5ac73d
claim_id: claim:b2a31debbd276d5ac73d
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal: Cluster 3 showed expression of CD68, MSR1 and MRC1 and was hence identified as macrophage.
summary:
In Homo sapiens, macrophages are identified by expression of CD68, MSR1, and MRC1 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:49a05189c2c014c7c67d
claim_id: claim:49a05189c2c014c7c67d
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Cluster 17 expressed considerably less macrophage marker CD83 and showed high expression of CD14 hence we denoted it as a separate monocyte population.

summary:
In Homo sapiens, a monocyte population is identified by high expression of CD14 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:ebcbd0a200742d22b54e
claim_id: claim:ebcbd0a200742d22b54e
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Cluster 18 lacked CD68 but expressed high levels of CD83 as well as pDC markers LILRA4 and CXCR3 and hence was identified as a pDC population

summary:
In Homo sapiens, plasmacytoid dendritic cells are identified by expression of CD83, LILRA4, and CXCR3 and lack of CD68 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:8e09a133ebe85bc2b190
claim_id: claim:8e09a133ebe85bc2b190
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Cluster 13 showed high expression of LUM, DCN, and DPT and was denoted as Fibroblast (DPT) population.

summary:
In Homo sapiens, fibroblast (DPT) population is identified by high expression of LUM, DCN, and DPT in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:7b4a4df85550aea8c59c
claim_id: claim:7b4a4df85550aea8c59c
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Clusters 11 and 16 showed expression of college subunits including COL1A1, COL1A2 and COL3A1, with cluster 16 additionally expressing FN1 and EBF1, and hence were classified as Fibroblast (COL1A1) and Fibroblast (FN1), respectively.

summary:
In Homo sapiens, fibroblast (COL1A1) is identified by expression of COL1A1, COL1A2, and COL3A1 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:7521b7dcf56dc9b72893
claim_id: claim:7521b7dcf56dc9b72893
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Clusters 11 and 16 showed expression of college subunits including COL1A1, COL1A2 and COL3A1, with cluster 16 additionally expressing FN1 and EBF1, and hence were classified as Fibroblast (COL1A1) and Fibroblast (FN1), respectively.

summary:
In Homo sapiens, fibroblast (FN1) is identified by expression of COL1A1, COL1A2, COL3A1, FN1, and EBF1 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:3c86af6316bd1bcdf99e
claim_id: claim:3c86af6316bd1bcdf99e
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Clusters 0 and 1 had moderate expression of DCN and expressed moderate to high amounts of STAR and FOXL2 gene and were identified as two Fibroblast (STAR) populations.

summary:
In Homo sapiens, fibroblast (STAR) populations are identified by expression of DCN, STAR, and FOXL2 in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4:claim:938eb3c99a941cfc7ab1
claim_id: claim:938eb3c99a941cfc7ab1
paper_key: biorxiv:d8ee72e2-7047-1014-a159-a9ef37bce7a4
span_literal:
Lastly, cluster 4 expressed canonical myofibroblast marker genes ACTA2 and TAGLN, hence was denoted as Myofibroblasts

summary:
In Homo sapiens, myofibroblasts are identified by expression of canonical marker genes ACTA2 and TAGLN in ovarian high-grade serous carcinoma.


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:2776befbbc959c3eff4a
claim_id: claim:2776befbbc959c3eff4a
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
span_literal:
Stem cell markers associated with the colon as well as other tissue-specific stem cells including BMI1, MEX3A, and SMOC2 were upregulated in LGR5(+) cells, while known markers of colonic differentiation, including MUC2, TFF3, and KRT20 were down-regulated (Figure 5D).

summary:
In Homo sapiens, LGR5-positive adenoma stem cells show upregulation of stem cell markers BMI1, MEX3A, and SMOC2, and downregulation of colonic differentiation markers MUC2, TFF3, and KRT20.


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:208602d42f0c34690bd0
claim_id: claim:208602d42f0c34690bd0
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
summary: In Homo sapiens adult duodenum, Paneth cells are marked by defensin alpha 5 (DEFA5).
span_literal:
duodenum showed weak punctate LGR5 expression, while adjacent cells stained with the paneth cell marker DefensinA5 (DEFA5)


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:bc590f3e5542b3a851aa
claim_id: claim:bc590f3e5542b3a851aa
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
summary: In Homo sapiens, OLFM4 is a marker of intestinal stem cells, expressed in normal colon and adenoma.
span_literal:
LGR5(+) cells were collected and subsequently analyzed by qPCR for LGR5 and the intestinal stem cell marker OLFM4, which was recently shown to be expressed in normal human colon, and in adenoma (Jang et al. 2016).


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:1b78d89d5fdf8854217b
claim_id: claim:1b78d89d5fdf8854217b
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
span_literal:
The intestine is maintained by stem cells, marked by LGR5 expression, located at the base of crypts.

summary:
In Homo sapiens, intestinal stem cells are marked by leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5) expression.


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:da9525b9bb4673ac6ed0
claim_id: claim:da9525b9bb4673ac6ed0
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
span_literal:
A comparison between these 33 genes in the “human adenoma LGR5(+) cell gene signature” and the previously published “murine intestinal stem cell signature,” generated from isolated Lgr5HI ISCs (Munoz et al. 2012), identified 4 overlapping genes that were enriched in both populations, including the canonical ISC markers LGR5, SMOC2, and CDCA7 (Figure 6B).

summary:
In Homo sapiens, the canonical intestinal stem cell markers LGR5, SMOC2, and CDCA7 are enriched in LGR5-positive adenoma cells.


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:4a792a36e2ccb06fda82
claim_id: claim:4a792a36e2ccb06fda82
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
summary: In Homo sapiens normal colon, LGR5 protein expression is localized to crypt base columnar cells.
span_literal:
LGR5 immunohistochemical (IHC) expression was localized with clone STE-1-89-11.5 to the crypt base columnar (CBC) cells, with rare staining in the stromal lamina propria in normal formalin fixed paraffin embedded (FFPE) colon (Figure 1a1).


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:a8c360d80e46e7aa047e
claim_id: claim:a8c360d80e46e7aa047e
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
span_literal:
We identified an average of 7.5-fold increase in LGR5 expression and 2.3-fold increase in OLFM4 mRNA expression in the sorted LGR5(+) normal colon cells relative to the LGR5(−) cells (Figure 8B).

summary:
In Homo sapiens normal colon, sorted LGR5-positive cells show increased LGR5 and OLFM4 expression relative to LGR5-negative cells.


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:00b236063c6bbe196f19
claim_id: claim:00b236063c6bbe196f19
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
span_literal:
two of the most over-expressed genes by overall fold change in LGR5(+) adenoma cells compared to normal colon were the Wnt pathway inhibitor DKK4 (dickkopf WNT signaling pathway inhibitor 4) and FGF20 (fibroblast growth factor 20).

summary:
In Homo sapiens, LGR5-positive adenoma cells show overexpression of dickkopf WNT signaling pathway inhibitor 4 (DKK4) and fibroblast growth factor 20 (FGF20) compared to normal colon.


claim_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e:claim:7a0f609896e6c1c749c4
claim_id: claim:7a0f609896e6c1c749c4
paper_key: biorxiv:d95d7dc6-6c35-1014-b1f0-b4af8a20948e
summary: In Homo sapiens, DKK4 could be a novel biomarker of colon adenoma stem cells.
span_literal:
the association with LGR5 expression suggests that DKK4 could be a novel biomarker of colon adenoma stem cells or cells with high Wnt activity, and may prove useful for colon cancer prevention or treatment efforts.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:9fdaae488daf6c51792c
claim_id: claim:9fdaae488daf6c51792c
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Clusters with neuronal identity were initially identified as either tumor cells or Schwann cells (based on expression of SOX10 and S100B; data not shown)

summary:
In Homo sapiens neuroblastoma samples, Schwann cells were identified based on expression of SOX10 and S100B.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:2f3f991e6e083608530b
claim_id: claim:2f3f991e6e083608530b
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Tumor cell identity was confirmed based on copy number variation (CNV) analysis using the inferCNV algorithm (Fig. S1H) and expression of the NB-specific markers PHOX2B, HAND2, and GATA3 (Fig. 1E), which are part of the ADRN core regulatory circuit (12, 25).

summary:
In Homo sapiens, neuroblastoma tumor cell identity was confirmed by expression of the neuroblastoma-specific markers PHOX2B, HAND2, and GATA3, which are part of the adrenergic core regulatory circuit.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:2342103669a5c34feaad
claim_id: claim:2342103669a5c34feaad
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Consistent with this finding, the gene encoding the proliferation marker MKI67 and genes involved in cell cycle regulation such as TOP2A and MYBL2 (encoding DNA topoisomerase II alpha and MYB proto-oncogene like 2, respectively) were expressed at higher levels in the DTCs

summary:
In Homo sapiens, bone marrow-disseminated tumor cells express higher levels of the proliferation marker MKI67, TOP2A (DNA topoisomerase II alpha), and MYBL2 (MYB proto-oncogene like 2) compared to primary tumor cells.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:f799ac04518ab2974528
claim_id: claim:f799ac04518ab2974528
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
In fact, genes expressing markers for ADRN NB cells such as PHOX2B (paired like homeobox 2B), DBH (dopamine beta-hydroxylase), and GAP43 (growth-associated protein 43) were among the higher expressed genes in DTCs

summary:
In Homo sapiens, adrenergic neuroblastoma cells are marked by PHOX2B (paired like homeobox 2B), DBH (dopamine beta-hydroxylase), and GAP43 (growth-associated protein 43), which were among the higher expressed genes in disseminated tumor cells.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:3690bf9d580b47300af3
claim_id: claim:3690bf9d580b47300af3
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
We found that NGFR, which encodes the nerve growth factor receptor (also known as p75NTR or CD271), was among the genes that were expressed at high levels in GD2-low DTCs (Fig. 5C).

summary:
In Homo sapiens, NGFR (nerve growth factor receptor, also known as p75NTR or CD271) was expressed at high levels in GD2-low disseminated tumor cells.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:91e7c3538e9d67d39c91
claim_id: claim:91e7c3538e9d67d39c91
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Dormant subpopulations of DTCs, which exhibited reduced predicted sensitivity to chemotherapy, contained cells expressing GD2 at low levels and showed increased surface expression of NGFR

summary:
In Homo sapiens, dormant disseminated tumor cells contained cells expressing low levels of GD2 and increased NGFR (nerve growth factor receptor) expression.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:de9185db8f42f1397d67
claim_id: claim:de9185db8f42f1397d67
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Our characterization of the transcriptome in GD2-low versus GD2-high DTCs confirmed a more MES-like phenotype, as suggested previously (55) based on increased expression of ELN/CALD1/LGALS1, genes which have been linked—either directly or indirectly—to the induction of EMT (60–62).

summary:
In Homo sapiens, GD2-low disseminated tumor cells showed a more mesenchymal-like phenotype with increased expression of ELN, CALD1, and LGALS1 compared to GD2-high disseminated tumor cells.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:1fe64cca38d533f1fef1
claim_id: claim:1fe64cca38d533f1fef1
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Here, we identified NGFR as a potential additional surface marker for detecting a subset of MES-like GD2-low DTCs, as well as a subpopulation of dormant DTCs.

summary:
In Homo sapiens, NGFR (nerve growth factor receptor) was identified as a potential surface marker for mesenchymal-like GD2-low disseminated tumor cells and dormant disseminated tumor cells.


claim_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45:claim:24fe354c953afb66de28
claim_id: claim:24fe354c953afb66de28
paper_key: biorxiv:d95eb71e-714d-1014-9dc7-c3da2c2efb45
span_literal:
Here, we identified NGFR as a potential additional surface marker for detecting a subset of MES-like GD2-low DTCs, as well as a subpopulation of dormant DTCs.

summary:
In Homo sapiens, NGFR (nerve growth factor receptor) was identified as a potential surface marker for dormant disseminated tumor cells.


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:73e4987d1e83e25b0a9d
claim_id: claim:73e4987d1e83e25b0a9d
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal: ~ 7% NK cells (enrichment of NKG7 in cluster 9)
summary:
In Homo sapiens, natural killer cells are marked by enrichment of NKG7 in peripheral blood mononuclear cells.


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:ff79846cf975a8aeada8
claim_id: claim:ff79846cf975a8aeada8
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal: ~ 27% myeloid cells (enrichment of S100A8 in clusters 1and 5)
summary:
In Homo sapiens, myeloid cells are marked by enrichment of S100A8 in peripheral blood mononuclear cells.


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:66df8866dd4523e90341
claim_id: claim:66df8866dd4523e90341
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal:
clusters 2, 3, 4 and 8 were CD4+ T cells (IL7R-enriched), whereas cluster 6 was CD8+ T cells (CD8A-enriched)

summary:
In Homo sapiens, CD4-positive T cells are marked by enrichment of IL7R, whereas CD8-positive T cells are marked by enrichment of CD8A in peripheral blood mononuclear cells.


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:d19e2a59f4a41da97701
claim_id: claim:d19e2a59f4a41da97701
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal:
clusters 2, 3, 4 and 8 were CD4+ T cells (IL7R-enriched), whereas cluster 6 was CD8+ T cells (CD8A-enriched)

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


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:a7e3e6ecbcd8c315a74d
claim_id: claim:a7e3e6ecbcd8c315a74d
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal:
Three subtypes were found: CD14+ monocyte (CD14-enriched), CD16+ monocyte (FCGR3A-enriched) and dendritic cells (FCER1A-enriched).

summary:
In Homo sapiens, CD14-positive monocytes are marked by enrichment of CD14 in peripheral blood mononuclear cells.


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:22fb1d6b2a4858a5e2df
claim_id: claim:22fb1d6b2a4858a5e2df
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal:
Three subtypes were found: CD14+ monocyte (CD14-enriched), CD16+ monocyte (FCGR3A-enriched) and dendritic cells (FCER1A-enriched).

summary:
In Homo sapiens, CD16-positive monocytes are marked by enrichment of FCGR3A in peripheral blood mononuclear cells.


claim_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e:claim:7a2d5ad4db681a2c2e39
claim_id: claim:7a2d5ad4db681a2c2e39
paper_key: biorxiv:db2dac46-6bff-1014-9770-df4e9ca7485e
span_literal:
Three subtypes were found: CD14+ monocyte (CD14-enriched), CD16+ monocyte (FCGR3A-enriched) and dendritic cells (FCER1A-enriched).

summary:
In Homo sapiens, dendritic cells are marked by enrichment of FCER1A in peripheral blood mononuclear cells.


claim_key: biorxiv:db8af155-6c8b-1014-b5f3-cedb7b3b1723:claim:3a68bcb755f4e355472f
claim_id: claim:3a68bcb755f4e355472f
paper_key: biorxiv:db8af155-6c8b-1014-b5f3-cedb7b3b1723
summary: In Homo sapiens, mast cells are marked by TPSAB1, TPSB2, and CPA3.
span_literal:
We used the markers proposed in the (Lambrechts et al., 2018) study, but also added a few markers for mast cell (TPSAB1, TPSB2 and CPA3; (Dwyer et al., 2016) Table 1)


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:3d23e504e3fd928bd3e0
claim_id: claim:3d23e504e3fd928bd3e0
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
span_literal:
CD52, ICAM3 and CLCN5 were widely expressed in granulocytes, monocytes, T lymphocytes, B lymphocytes, dendritic cells and NK cells, whereas ADAMTS3 was rarely expressed in those cells.

summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in granulocytes, monocytes, T lymphocytes, B lymphocytes, dendritic cells and natural killer cells. In Homo sapiens acute myeloid leukemia, ICAM3 is widely expressed in granulocytes. In Homo sapiens acute myeloid leukemia, CLCN5 is widely expressed in granulocytes. In Homo sapiens acute myeloid leukemia, ADAMTS3 is rarely expressed in granulocytes, monocytes, T lymphocytes, B lymphocytes, dendritic cells and natural killer cells.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:e58168130454a176ec01
claim_id: claim:e58168130454a176ec01
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
span_literal:
CD52, ICAM3 and CLCN5 were widely expressed in granulocytes, monocytes, T lymphocytes, B lymphocytes, dendritic cells and NK cells, whereas ADAMTS3 was rarely expressed in those cells.

summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in monocytes. In Homo sapiens acute myeloid leukemia, ICAM3 is widely expressed in monocytes. In Homo sapiens acute myeloid leukemia, CLCN5 is widely expressed in monocytes. In Homo sapiens acute myeloid leukemia, ADAMTS3 is rarely expressed in monocytes.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:b0fedf23294dc5408e11
claim_id: claim:b0fedf23294dc5408e11
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
span_literal:
CD52, ICAM3 and CLCN5 were widely expressed in granulocytes, monocytes, T lymphocytes, B lymphocytes, dendritic cells and NK cells, whereas ADAMTS3 was rarely expressed in those cells.

summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in T lymphocytes. In Homo sapiens acute myeloid leukemia, ICAM3 is widely expressed in T lymphocytes. In Homo sapiens acute myeloid leukemia, CLCN5 is widely expressed in T lymphocytes. In Homo sapiens acute myeloid leukemia, ADAMTS3 is rarely expressed in T lymphocytes.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:7108ffcb51cace8ce652
claim_id: claim:7108ffcb51cace8ce652
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in B lymphocytes. In Homo sapiens acute myeloid leukemia, ICAM3 is widely expressed in B lymphocytes. In Homo sapiens acute myeloid leukemia, CLCN5 is widely expressed in B lymphocytes. In Homo sapiens acute myeloid leukemia, ADAMTS3 is rarely expressed in B lymphocytes.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:56545bed37768b7dc2f2
claim_id: claim:56545bed37768b7dc2f2
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in dendritic cells. In Homo sapiens acute myeloid leukemia, ICAM3 is widely expressed in dendritic cells. In Homo sapiens acute myeloid leukemia, CLCN5 is widely expressed in dendritic cells. In Homo sapiens acute myeloid leukemia, ADAMTS3 is rarely expressed in dendritic cells.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:931853355133f8ac247f
claim_id: claim:931853355133f8ac247f
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in natural killer cells. In Homo sapiens acute myeloid leukemia, ICAM3 is widely expressed in natural killer cells. In Homo sapiens acute myeloid leukemia, CLCN5 is widely expressed in natural killer cells. In Homo sapiens acute myeloid leukemia, ADAMTS3 is rarely expressed in natural killer cells.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:fb8e22e2142b87cb177c
claim_id: claim:fb8e22e2142b87cb177c
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
span_literal: HAL is highly expressed in granulocytes and monocytes but rarely expressed in other immune cells.
summary:
In Homo sapiens acute myeloid leukemia, histidine ammonia lyase (HAL) is highly expressed in granulocytes but rarely expressed in other immune cells.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:2de3f07f6dd7600cc921
claim_id: claim:2de3f07f6dd7600cc921
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
span_literal: HAL is highly expressed in granulocytes and monocytes but rarely expressed in other immune cells.
summary:
In Homo sapiens acute myeloid leukemia, histidine ammonia lyase (HAL) is highly expressed in monocytes but rarely expressed in other immune cells.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:39fffc78586a8f5426cc
claim_id: claim:39fffc78586a8f5426cc
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
summary: In Homo sapiens, ADAMTS3 is expressed in mast cells.
span_literal:
Previous studies demonstrated that ADAMTS3 is expressed in mast cells(Charoentong et al., 2017), and mast cells have both tumor-promoting and tumor-inhibiting effects(Oldford & Marshall, 2015), thus leading to different prognoses in different tumors(Fleischmann et al., 2009; Groot Kormelink, Abudukelimu, & Redegeld, 2009; Rajput et al., 2008).


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:d1d4dbd89ba957a5ccb1
claim_id: claim:d1d4dbd89ba957a5ccb1
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
span_literal: Our study found that CD52 was widely expressed in leukemia cells and all types of immune cells.
summary:
In Homo sapiens acute myeloid leukemia, CD52 is widely expressed in leukemia cells and all types of immune cells.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:bea050369e498011dd94
claim_id: claim:bea050369e498011dd94
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
summary: In Homo sapiens acute myeloid leukemia (5q-), CD52 is highly expressed in CD34-positive stem cells.
span_literal:
Evidence has revealed the high expression of CD52 in CD34+ stem cells of AML (5q-) patients and a significantly negative correlation between the CD52 expression value and the prognosis of AML (Blatt et al., 2014), which is consistent with our results.


claim_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013:claim:c8be4c2fd8f0ce18b97b
claim_id: claim:c8be4c2fd8f0ce18b97b
paper_key: biorxiv:dbf486c9-6c54-1014-9bc5-bf4d8f303013
summary: In Homo sapiens, intercellular adhesion molecule 3 (ICAM-3) is expressed in granulocytes.
span_literal:
Consistent with our scRNA sequencing results, ICAM-3 is expressed in granulocytes, monocytes and lymphocytes(de Fougerolles & Springer, 1992).


claim_key: biorxiv:dcc4f18b-6c19-1014-8ffb-d4dccdf6774b:claim:363655fc20dbba448ea4
claim_id: claim:363655fc20dbba448ea4
paper_key: biorxiv:dcc4f18b-6c19-1014-8ffb-d4dccdf6774b
span_literal:
the tumor cells were readily distinguishable from the remaining cells through the expression of the basal marker Keratin 5, or expression of either the luminal marker GATA3 or other keratin proteins

summary:
In Homo sapiens upper tract urothelial carcinoma, tumor cells are distinguished from non-tumor cells by expression of the basal marker Keratin 5 or the luminal marker GATA3.


claim_key: biorxiv:dcc4f18b-6c19-1014-8ffb-d4dccdf6774b:claim:5347778fa964a9798919
claim_id: claim:5347778fa964a9798919
paper_key: biorxiv:dcc4f18b-6c19-1014-8ffb-d4dccdf6774b
span_literal:
In total, from 14 samples of 6 patients, we generated 58 images containing the spatial distribution of 27 distinct molecular biomarkers, which included markers of tumor cells (pan-Keratin, Keratin 5, GATA3, E-cadherin), immune cells (CD3, CD16, CD68), among others such as functional or stromal markers present in various cell types

summary:
In Homo sapiens upper tract urothelial carcinoma, tumor cells are marked by pan-Keratin, Keratin 5, GATA3, and E-cadherin.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:c17e4a1169e00e4e2a8a
claim_id: claim:c17e4a1169e00e4e2a8a
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
We inferred the cell type of each cluster by checking their expression of HSC specific genes and hematopoietic lineage specific genes, including HSC (MEG3+, AVP+, CRHBP+, Lin-), multipotent progenitor (MPP) (AVP+, CRHBP+, CSF3R+), lymphoid-primed multi-potential progenitor (LMPP) (CSF3R+, CRHBP+), myeloid (My) progenitor (MPO+, LYZ+ and IRF8+), common lymphoid progenitor (CLP) (CCR7+, NKG7+), B progenitor (VPRE+, EBF1+), T progenitor (ETP, Thy #1, Thy #2, Thy #3) (CD3D+, CD7+, RAG2+, CD1A+), megakaryocytic (Mk) progenitor (GATA2+, PF4+, PPBP+) and erythroid (Ery) progenitor (GATA2+, CD36+)

summary:
In Homo sapiens, hematopoietic stem cells are marked by positive expression of MEG3, AVP, and CRHBP.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:69f84b4866f366569b74
claim_id: claim:69f84b4866f366569b74
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
We inferred the cell type of each cluster by checking their expression of HSC specific genes and hematopoietic lineage specific genes, including HSC (MEG3+, AVP+, CRHBP+, Lin-), multipotent progenitor (MPP) (AVP+, CRHBP+, CSF3R+), lymphoid-primed multi-potential progenitor (LMPP) (CSF3R+, CRHBP+), myeloid (My) progenitor (MPO+, LYZ+ and IRF8+), common lymphoid progenitor (CLP) (CCR7+, NKG7+), B progenitor (VPRE+, EBF1+), T progenitor (ETP, Thy #1, Thy #2, Thy #3) (CD3D+, CD7+, RAG2+, CD1A+), megakaryocytic (Mk) progenitor (GATA2+, PF4+, PPBP+) and erythroid (Ery) progenitor (GATA2+, CD36+)

summary:
In Homo sapiens, multipotent progenitor cells are marked by positive expression of AVP, CRHBP, and CSF3R.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:c6815defa5d70b7acbb0
claim_id: claim:c6815defa5d70b7acbb0
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
We inferred the cell type of each cluster by checking their expression of HSC specific genes and hematopoietic lineage specific genes, including HSC (MEG3+, AVP+, CRHBP+, Lin-), multipotent progenitor (MPP) (AVP+, CRHBP+, CSF3R+), lymphoid-primed multi-potential progenitor (LMPP) (CSF3R+, CRHBP+), myeloid (My) progenitor (MPO+, LYZ+ and IRF8+), common lymphoid progenitor (CLP) (CCR7+, NKG7+), B progenitor (VPRE+, EBF1+), T progenitor (ETP, Thy #1, Thy #2, Thy #3) (CD3D+, CD7+, RAG2+, CD1A+), megakaryocytic (Mk) progenitor (GATA2+, PF4+, PPBP+) and erythroid (Ery) progenitor (GATA2+, CD36+)

summary:
In Homo sapiens, lymphoid-primed multi-potential progenitor cells are marked by positive expression of CSF3R and CRHBP.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:7a021017ddcfdda4d472
claim_id: claim:7a021017ddcfdda4d472
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
summary:
In Homo sapiens, common lymphoid progenitor cells are marked by positive expression of CCR7 and NKG7.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:1af12afa43f326854d05
claim_id: claim:1af12afa43f326854d05
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
summary:
In Homo sapiens, megakaryocytic progenitor cells are marked by positive expression of GATA2, PF4, and PPBP.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:122d105a43697cd42cb0
claim_id: claim:122d105a43697cd42cb0
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
summary: In Homo sapiens, B progenitor cells highly express CXCR4 for anchoring in bone marrow.
span_literal:
We found B progenitors highly expressed CXCR4 for anchoring in BM, while cells with low expression of CXCR4 facilitate their migration out of BM.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:41efda47ce5a854c9216
claim_id: claim:41efda47ce5a854c9216
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
Interaction analysis of CXCR4-CXCL12 axis showed that BM_SC was the strongest signaling sender through CXCL12, and pre-B was the strongest signaling receiver through CXCR4 among all the cell subsets in BM (Fig 3d).

summary:
In Homo sapiens, pre-B cells are the strongest receiver of CXCR4 signaling among all hematopoietic stem and progenitor cell subsets in bone marrow, indicating high CXCR4 expression.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:816c106d83a312a1500a
claim_id: claim:816c106d83a312a1500a
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
Indeed, pre-B expressed the highest level of CXCR4 and BM_SC expressed the highest level of CXCL12 among all cell subsets in BM (Fig 3e, f).

summary:
In Homo sapiens, pre-B cells express the highest level of CXCR4 among all cell subsets in bone marrow.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:18610e3ec88309449580
claim_id: claim:18610e3ec88309449580
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
The most pronounced ETP specific genes, including thymocyte determination genes (CD7, CD3D) (Fig 4d).

summary:
In Homo sapiens, earliest thymic progenitor cells specifically express thymocyte determination genes CD7 and CD3D.


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:fade3746bb3b11ad0e9c
claim_id: claim:fade3746bb3b11ad0e9c
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
summary: In Homo sapiens, thymus-seeding progenitor cells specifically express RPL4, RPL12, and AREG.
span_literal:
The most pronounced TSP specific genes include ribosomal genes (RPL4 and RPL12) and stem cell associated genes (AREG) (Fig 4d).


claim_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4:claim:f78d729bc3dee2c7dbbe
claim_id: claim:f78d729bc3dee2c7dbbe
paper_key: biorxiv:dd32f357-70c5-1014-bad0-ccf1b5b647f4
span_literal:
In particular, pre-B has the highest expression of CXCR4 among all HSPC subsets and almost exclusively locates in BM.

summary:
In Homo sapiens, pre-B cells have the highest expression of CXCR4 among all hematopoietic stem and progenitor cell subsets and are almost exclusively located in bone marrow.


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:d850eada0d8532402bd7
claim_id: claim:d850eada0d8532402bd7
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
summary: In Homo sapiens, T cells upregulate CD44 upon antigen stimulation, indicating antigen experience.
span_literal:
Upon antigen stimulation, T cells upregulate CD44 and exist along a spectrum of diverse differentiation states with varying functionalities (9-11).


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:5086a6b0b5f0dcda12f9
claim_id: claim:5086a6b0b5f0dcda12f9
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
span_literal:
On one end of the spectrum, T cells possess stem-cell-like plasticity, accompanied by memory, proliferative and cytotoxic capabilities, and are identified by expression of T-BET, and/or TCF-1 (12, 13).

summary:
In Homo sapiens, stem-cell-like T cells with memory, proliferative, and cytotoxic capabilities are identified by expression of T-BET and/or TCF-1.


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:67f2d4ccb72098f830e7
claim_id: claim:67f2d4ccb72098f830e7
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
summary: In Homo sapiens, exhausted T cells canonically express TOX1 and/or EOMES.
span_literal:
On the other end of the spectrum, T cells are exhausted and/or dysfunctional and canonically express TOX1 and/or EOMES (14, 15).


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:e30f8213a799ab380098
claim_id: claim:e30f8213a799ab380098
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
span_literal:
Along the spectrum, expressed in varying combinations, are T cells expressing immune checkpoint molecules such as PD-1, LAG- 3 and TIM3, with increased numbers of immune checkpoint molecules correlating with more exhausted T cells (16).

summary:
In Homo sapiens, partially exhausted T cells express immune checkpoint molecules PD-1, LAG-3, and TIM3, with increased numbers of these molecules correlating with greater exhaustion.


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:d29af18044b2ae4b45d8
claim_id: claim:d29af18044b2ae4b45d8
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
span_literal:
However, terminally differentiated T cells expressing TOX1 or EOMES are resistant to rescue by ICB and cannot proliferate or exert cytotoxic activity (19).

summary:
In Homo sapiens, terminally differentiated T cells express TOX1 or EOMES and are resistant to rescue by immune checkpoint blockade.


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:0b9b6dbe96f41792db2d
claim_id: claim:0b9b6dbe96f41792db2d
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
span_literal:
First, 423,317 T cells were identified by CD3 expression and then subsequently stratified by CD8α expression.

summary:
In Homo sapiens, T cells were identified by CD3 expression and further stratified by CD8α expression.


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:35b57af92ea79d84abca
claim_id: claim:35b57af92ea79d84abca
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
summary: In Homo sapiens, CD4+ T helper 1 cells were defined by T-BET expression.
span_literal:
CD4+ Th1 cells were defined by T-BET+ expression, and further classified as one of three cell states (TEFF, TEM, or TEMRA) (Fig. 1F).


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:bd62f6fc24f7d776430d
claim_id: claim:bd62f6fc24f7d776430d
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
summary: In Homo sapiens, regulatory T cells were identified as CD3+ CD8- FOXP3+ cells.
span_literal:
Finally, the remaining CD3+ CD8- T cells were FOXP3+ TREG cells, and classified into three cell states (Naive TREG, mTREG, and T-BET+ TREG) (Fig. 1F).


claim_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab:claim:0947591f8add0f39e221
claim_id: claim:0947591f8add0f39e221
paper_key: biorxiv:de5904ff-71b0-1014-b1f7-fe7935302eab
span_literal:
TOX1+ T cells are at the far end of the exhausted T cell spectrum (14, 79), and TOX1 expression correlates with PD-1 on T cells and impaired immunotherapy response in hepatocellular carcinoma (80).

summary:
In Homo sapiens, TOX1-positive T cells represent the far end of the exhausted T cell spectrum, and TOX1 expression correlates with PD-1 expression on T cells.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:322f8f49b3aab49a0a52
claim_id: claim:322f8f49b3aab49a0a52
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
We found that a specific CD8+ CAR-T cell subpopulation was predominantly derived from solid tumor datasets rather than blood cancer datasets (blue in Figure 3H, S3F-S3H). Notably, several T cell exhaustion markers, such as TIM3 (HAVCR2), TIGIT, and CTLA4, were highly expressed in this cluster, although a typical marker, PDCD1 (PD-1), was not enriched

summary:
In Homo sapiens, exhaustion-like CD8+ chimeric antigen receptor T cells stimulated by solid tumors highly express HAVCR2, TIGIT, and CTLA4, while PDCD1 is not enriched.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:75315a0c4b4cbe61f861
claim_id: claim:75315a0c4b4cbe61f861
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
This cluster was characterized by high expression of TNFRSF9 and CCL3, which were other exhaustion-related genes

summary:
In Homo sapiens, the exhaustion-like CD8+ chimeric antigen receptor T cell subpopulation is characterized by high expression of TNFRSF9 and CCL3.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:2c2b17fcf22a68a799d4
claim_id: claim:2c2b17fcf22a68a799d4
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
Since monocytic markers, such as CD14 and CD16, were highly expressed in CD3- fraction (Figure S2A), we interpreted CD3- fraction as CD4+ monocytes.

summary:
In Homo sapiens, CD4+ monocytes are characterized by high expression of CD14 and CD16 and absence of CD3.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:88bb525c7e5dc712873f
claim_id: claim:88bb525c7e5dc712873f
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
We found that these cytokine-encoding genes (e.g. IL1B, TNFSF13) were highly expressed in CD4+ monocytes but mostly diminished in CD4+CD3+ T cells

summary:
In Homo sapiens, IL1B and TNFSF13 are highly expressed in CD4+ monocytes but mostly diminished in CD4+CD3+ T cells.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:ed1879512ee6367bd9dd
claim_id: claim:ed1879512ee6367bd9dd
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
We found that these cytokine-encoding genes (e.g. IL1B, TNFSF13) were highly expressed in CD4+ monocytes but mostly diminished in CD4+CD3+ T cells

summary:
In Homo sapiens, IL1B and TNFSF13 are mostly diminished in CD4+CD3+ T cells compared to CD4+ monocytes.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:3730616034ef8b9e07b8
claim_id: claim:3730616034ef8b9e07b8
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
summary: In Homo sapiens, PFKFB4 is highly expressed in CD4+ monocytes.
span_literal:
PFKFB4, which is a potential prognostic marker of cytokine release syndrome grade [19], was also highly expressed in CD4+ monocytes.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:c99ea2361ac2f6365e52
claim_id: claim:c99ea2361ac2f6365e52
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
In fact, the CD28-hinge domain-specific clusters highly expressed genes related to T cell activation (e.g. AQP3, LINC00861, LEF1, TCF7)

summary:
In Homo sapiens, CD28-hinge domain-specific CD4+ chimeric antigen receptor T cell clusters highly express AQP3, LINC00861, LEF1, and TCF7, which are related to T cell activation.


claim_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65:claim:3e062a9f9b4929d9958d
claim_id: claim:3e062a9f9b4929d9958d
paper_key: biorxiv:de6d33dd-734f-1014-a302-e21bedf0ba65
span_literal:
Interestingly, this cluster highly expressed alarmins (S100A8 and S100A9) that negatively impact on CAR-T cell anti-tumor activity

summary:
In Homo sapiens, the granule secretion CD8+ chimeric antigen receptor T cell cluster associated with relapse highly expresses alarmins S100A8 and S100A9.


claim_key: biorxiv:e23331bf-7510-1014-82e6-fe697c7128c1:claim:0bf7ffe14d84e5fbee89
claim_id: claim:0bf7ffe14d84e5fbee89
paper_key: biorxiv:e23331bf-7510-1014-82e6-fe697c7128c1
span_literal:
For KLF4, we observed that as the predicted expression increases, the appearance of cells changes from differentiated-like to undifferentiated-like. This observation agrees with the known biology of KLF4, as it has previously been established that KLF4 is a key gene for iPSC reprogramming and de-differentiation process in somatic cells, and that this process can be paused by manipulating the KLF4 expression (25–26.

summary:
In Homo sapiens, KLF4 is a key gene for induced pluripotent stem cell reprogramming, with higher expression associated with undifferentiated-like morphology in human induced pluripotent stem cells.


claim_key: biorxiv:e23331bf-7510-1014-82e6-fe697c7128c1:claim:b99b5ac19d2e5572cea9
claim_id: claim:b99b5ac19d2e5572cea9
paper_key: biorxiv:e23331bf-7510-1014-82e6-fe697c7128c1
span_literal:
We measured expression levels for 980 genes related to stemness and pluripotency. Out of those 980 genes, we filtered the genes by their average (mean) and coefficient of variation values (CV) across all the samples to identify genes with sufficient expression levels and significant variance, as those suggest predictive power needed for robust model building. The final list contained 218 genes, including three Yamanaka factor genes: KLF4, SOX2, and POU5F1 (Figure 1).

summary:
In Homo sapiens, KLF4, SOX2, and POU5F1 are Yamanaka factor genes related to stemness and pluripotency in human induced pluripotent stem cells.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:a398155096d5fbd9c313
claim_id: claim:a398155096d5fbd9c313
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
Clusters CD8.3 and CD8.5 with increased expression of cytotoxic markers (GNLY, PRF1, FGFBP2, FCGR3A/CD16, and NKG7; Supplementary Fig. 3.1b and 3.2a), and a high cytotoxicity score

summary:
In Homo sapiens, cytotoxic CD8 T cell clusters CD8.3 and CD8.5 are marked by increased expression of GNLY, PRF1, FGFBP2, FCGR3A, and NKG7.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:7e73be737976b3e9f7a0
claim_id: claim:7e73be737976b3e9f7a0
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
CD8.8 (CXCL13high) expressing exhaustion markers (CTLA4, ENTPD1/CD39, HAVCR2/TIM3, LAG3, TOX and PDCD1; Supplementary Fig. 3.1b, 3. 2a) and exhibiting the highest exhaustion score

summary:
In Homo sapiens, exhausted CD8 T cell cluster CD8.8 is marked by expression of CXCL13, CTLA4, ENTPD1, HAVCR2, LAG3, TOX, and PDCD1.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:d28ed58ed2e1b60709da
claim_id: claim:d28ed58ed2e1b60709da
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal: CD8.2 that expressed naive cell markers including CCR7, TCF7, LEF1, and SELL, and also GZMK
summary:
In Homo sapiens, naive/transition CD8 T cell cluster CD8.2 expresses naive cell markers CCR7, TCF7, LEF1, and SELL, as well as GZMK.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:c2fb9990f19214c9d62f
claim_id: claim:c2fb9990f19214c9d62f
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
summary: In Homo sapiens, pre-exhausted CD8 T cell cluster CD8.1 expresses GZMK and RGS1.
span_literal:
CD8.1 expressing pre-exhausted and exhausted markers (GZMK, RGS1), was enriched on the naïve/transition branch


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:a9f2fddb5c930ebda910
claim_id: claim:a9f2fddb5c930ebda910
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
both the CD8.8 (exhausted) and CD8.4 (pre-exhausted) clusters expressed tissue-resident memory (TRM) markers including ITGAE/CD103, ITGA1/CD49a, CD69 and CXCR6

summary:
In Homo sapiens, exhausted CD8 T cell cluster CD8.8 expresses tissue-resident memory markers ITGAE, ITGA1, CD69, and CXCR6.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:e6d7057a84fef4733b83
claim_id: claim:e6d7057a84fef4733b83
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
both the CD8.8 (exhausted) and CD8.4 (pre-exhausted) clusters expressed tissue-resident memory (TRM) markers including ITGAE/CD103, ITGA1/CD49a, CD69 and CXCR6

summary:
In Homo sapiens, pre-exhausted CD8 T cell cluster CD8.4 expresses tissue-resident memory markers ITGAE, ITGA1, CD69, and CXCR6.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:428b6689380e292d4284
claim_id: claim:428b6689380e292d4284
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
CD4.10 showed increased expression of exhaustion markers (TIGIT, CTLA4, TOX, LAG3, PDCD1), elevated exhaustion score

summary:
In Homo sapiens, exhausted CD4 T cell cluster CD4.10 expresses exhaustion markers TIGIT, CTLA4, TOX, LAG3, and PDCD1.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:eb1e44f63f1182885096
claim_id: claim:eb1e44f63f1182885096
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal: and also expressed CXCL13 characteristic of human TFH cell42 (Supplementary Fig 3.1c and 3.5)
summary:
In Homo sapiens, exhausted CD4 T cell cluster CD4.10 expresses CXCL13, characteristic of T follicular helper cells.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:2300147a4b1b1a599ec5
claim_id: claim:2300147a4b1b1a599ec5
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
CD4.9 expressed both inhibitory markers (TIGIT, TOX, PDCD1) and naïve/TCM markers (LEF1, CCR7, TCF7, SELL; Supplementary Fig. 3.1c, 3.5, and 3.6a), representing a transitioning population between naïve and exhausted CD4 T cells

summary:
In Homo sapiens, transitioning CD4 T cell cluster CD4.9 expresses inhibitory markers TIGIT, TOX, and PDCD1 as well as naive/central memory markers LEF1, CCR7, TCF7, and SELL.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:2b681e7b39cb5a45e306
claim_id: claim:2b681e7b39cb5a45e306
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
Cluster CD4.4 expressing characteristic markers of regulatory T cells (Tregs: FOXP3, IKZF2/HELIOS, IL2RA/CD25, CTLA4; Supplementary Fig. 3.1c, 3.5)

summary:
In Homo sapiens, regulatory T cell cluster CD4.4 expresses characteristic markers FOXP3, IKZF2, IL2RA, and CTLA4.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:32cbecd0f310e40066ed
claim_id: claim:32cbecd0f310e40066ed
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
Treg.1 showed elevated expression of naïve markers (LEF1, SELL, CCR7, and TCF7), Treg.2 showed elevated expression of suppressive markers (FOXP3, CTLA4, TIGIT, PDCD1/PD1, HAVCR2/TIM3, ICOS, LAG3), and Treg.3 displayed an intermediate phenotype

summary:
In Homo sapiens, naive regulatory T cell subcluster Treg.1 expresses LEF1, SELL, CCR7, and TCF7, while suppressive regulatory T cell subcluster Treg.2 expresses FOXP3, CTLA4, TIGIT, PDCD1, HAVCR2, ICOS, and LAG3.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:20cf646a940105c8fee2
claim_id: claim:20cf646a940105c8fee2
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
Treg.1 showed elevated expression of naïve markers (LEF1, SELL, CCR7, and TCF7), Treg.2 showed elevated expression of suppressive markers (FOXP3, CTLA4, TIGIT, PDCD1/PD1, HAVCR2/TIM3, ICOS, LAG3), and Treg.3 displayed an intermediate phenotype

summary:
In Homo sapiens, suppressive regulatory T cell subcluster Treg.2 expresses FOXP3, CTLA4, TIGIT, PDCD1, HAVCR2, ICOS, and LAG3.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:6a43e05affc92b5daeaa
claim_id: claim:6a43e05affc92b5daeaa
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
Compared to Treg.1, Treg.2 showed significantly up-regulated genes (TNFRSF4/OX40, TNFRSF18/GITR, TNFRSF9/4-1BB, TNFRSF1B/TNFR2 and LAIR2) associated with suppressive functions of tumor-infiltrating Tregs

summary:
In Homo sapiens, suppressive regulatory T cell subcluster Treg.2 shows upregulated expression of TNFRSF4, TNFRSF18, TNFRSF9, TNFRSF1B, and LAIR2 compared to naive regulatory T cell subcluster Treg.1.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:c8712614b78ac84f3c63
claim_id: claim:c8712614b78ac84f3c63
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
NK.6 showed increased expression of GZMK, which was shown to be upregulated in NK cells in melanoma59, as well as ITGA1/CD49a, CD69, and CXCR6, which serve as markers for tissue-resident NK (trNK) cells

summary:
In Homo sapiens, tissue-resident natural killer cell cluster NK.6 expresses GZMK, ITGA1, CD69, and CXCR6.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:192424d6993fb9435aa0
claim_id: claim:192424d6993fb9435aa0
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
summary: In Homo sapiens, natural killer cell clusters NK.5 and NK.6 express the chemokines XCL1 and XCL2.
span_literal:
NK.5 and NK.6 also showed increased expression of the chemokines XCL1 and XCL2 (Supplementary Fig 3.8b), which are known to recruit XCR1high cross-presenting cDC1 cells into tumors


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:c475fedb6c928d22f007
claim_id: claim:c475fedb6c928d22f007
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal: Cluster NK.2 showed increased expression of chemokines CCL4, CCL4L2, CCL3, and CCL3L1
summary:
In Homo sapiens, natural killer cell cluster NK.2 expresses chemokines CCL4, CCL4L2, CCL3, and CCL3L1.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:718ee0fa9242264946ff
claim_id: claim:718ee0fa9242264946ff
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
Mac.5 showed increased expression of proinflammatory genes (CXCL9, CXCL10 and CXCL11), associated with increased pro-inflammatory (M1) score

summary:
In Homo sapiens, proinflammatory monocyte-derived macrophage cluster Mac.5 expresses CXCL9, CXCL10, and CXCL11.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:efb98b47306238a2aa8a
claim_id: claim:efb98b47306238a2aa8a
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
We observed expression of SELENOP in Mac.2 and SPP1 in Mac.6 (Supplementary Fig. 4.1b and 4.2a), which have been shown to contribute to macrophage polarization from pro-inflammatory (M1-like) to anti-inflammatory (M2-like)

summary:
In Homo sapiens, anti-inflammatory monocyte-derived macrophage cluster Mac.2 expresses SELENOP, contributing to M2-like polarization.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:8b6396a2e173795902dc
claim_id: claim:8b6396a2e173795902dc
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
We observed expression of SELENOP in Mac.2 and SPP1 in Mac.6 (Supplementary Fig. 4.1b and 4.2a), which have been shown to contribute to macrophage polarization from pro-inflammatory (M1-like) to anti-inflammatory (M2-like)

summary:
In Homo sapiens, anti-inflammatory monocyte-derived macrophage cluster Mac.6 expresses SPP1, contributing to M2-like polarization.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:5f902b0c551d4bbeb83e
claim_id: claim:5f902b0c551d4bbeb83e
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
The Mac.2 and Mac.6 clusters also showed increased expression of TREM2 (triggering receptor expressed on myeloid cells 2; Supplementary Fig. 4.2f)

summary:
In Homo sapiens, anti-inflammatory monocyte-derived macrophage clusters Mac.2 and Mac.6 express TREM2 (triggering receptor expressed on myeloid cells 2).


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:1f4d1ae923174a154a94
claim_id: claim:1f4d1ae923174a154a94
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
we reclustered DCs and identified discrete subsets including type 1 conventional DC (cDC1) expressing XCR1 and CLEC9A, type 2 conventional DC (cDC2) expressing CLEC10A and AREG, mature-regulatory DCs (mregDC) and Langerhans cells (LCs)

summary:
In Homo sapiens, type 1 conventional dendritic cell expresses XCR1 and CLEC9A, while type 2 conventional dendritic cell expresses CLEC10A and AREG.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:57897fe6689c398fc1cc
claim_id: claim:57897fe6689c398fc1cc
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
mregDCs expressing immunoregulatory genes CD274 (PD-L1), PDCD1LG2 (PD-L2), IDO1, IL4I, CD200, and EBI3 (IL27B) were associated with the highest immunosuppressive score

summary:
In Homo sapiens, mature-regulatory dendritic cells express immunoregulatory genes CD274, PDCD1LG2, IDO1, IL4I1, CD200, and EBI3.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:c3e554d66f643f5ac80e
claim_id: claim:c3e554d66f643f5ac80e
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
summary: In Homo sapiens, mature-regulatory dendritic cells express CCR7, CCL19, and CCL22.
span_literal:
mregDCs expressed CCR7 which facilitates their migration to lymph nodes for antigen presentation79, and chemokines CCL19 and CCL22 which facilitate the recruitment of CCR4+ Tregs


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:76f7c0af4a5e0022cd4a
claim_id: claim:76f7c0af4a5e0022cd4a
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
EP.6 and EP.11, were discretely located between normal club cells and AT2 cells (Fig. 2b, Supplementary Fig. 2.1a) and expressed markers of transitional club-AT2 cells (SCGB3A1, SCGB3A2, SFTPD, NAPSA; Supplementary Fig. 2.2c)

summary:
In Homo sapiens, tumor transition epithelial cell clusters EP.6 and EP.11 express markers of transitional club-alveolar type 2 cells including SCGB3A1, SCGB3A2, SFTPD, and NAPSA.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:6ef649cb22938b069ffb
claim_id: claim:6ef649cb22938b069ffb
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
summary: In Homo sapiens, pericytes/smooth muscle cells express ACTA2, COL4A1, and MYH11.
span_literal:
Pericytes/smooth muscle cells, important regulators of angiogenesis and vascular integrity expressed ACTA2/α-SMA, COL4A1, and MYH11


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:a2787eb4d61a84898e5e
claim_id: claim:a2787eb4d61a84898e5e
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
cDC2.4 showed marked expression of complement pathway genes including classical C1Q (C1QA, C1QB, and C1QC), and alternative C3

summary:
In Homo sapiens, type 2 conventional dendritic cell subcluster cDC2.4 expresses complement pathway genes C1QA, C1QB, C1QC, and C3.


claim_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d:claim:5e6af3796a7c4eb856a3
claim_id: claim:5e6af3796a7c4eb856a3
paper_key: biorxiv:e2efdcad-73c4-1014-9c6c-8a89f519fd2d
span_literal:
CD4.7 (CCL4high) with increased expression of effector/memory markers and chemokines (GZMA, GZMH, IFNG, PRF1, CCL3, CCL4 and CCL5

summary:
In Homo sapiens, effector/memory CD4 T cell cluster CD4.7 expresses GZMA, GZMH, IFNG, PRF1, CCL3, CCL4, and CCL5.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:aeba4dfe5acd684d5452
claim_id: claim:aeba4dfe5acd684d5452
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Expression of markers CD14 and CD16 (FCGR3A) separated monocytes and macrophages within the myeloid group, while markers CD4, CD8A, and CD160 clearly separated CD4, CD8 and NK cells within the T/NK cell cluster

summary:
In Homo sapiens head and neck squamous cell carcinoma, CD14 and FCGR3A separate monocytes and macrophages within the myeloid group.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:6c493296b8729728480e
claim_id: claim:6c493296b8729728480e
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Expression of markers CD14 and CD16 (FCGR3A) separated monocytes and macrophages within the myeloid group, while markers CD4, CD8A, and CD160 clearly separated CD4, CD8 and NK cells within the T/NK cell cluster

summary:
In Homo sapiens head and neck squamous cell carcinoma, FCGR3A separates macrophages from monocytes within the myeloid group.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:5fb0bff5aaebbfa1b4af
claim_id: claim:5fb0bff5aaebbfa1b4af
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
summary: In Homo sapiens head and neck squamous cell carcinoma, plasma cells are positive for IGHG1.
span_literal:
We also identified plasma cells (IGHG1-positive), B cells (CD20/MS4A1-positive), and Mast cells (TSAB1-positive).


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:a2cb00bf06a357393426
claim_id: claim:a2cb00bf06a357393426
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
the naïve population has been referred to by a variety of names: naïve (Choi[23]), CD4 (Kurten[25]), naïve-like (Quah[27]), conventional T-helper (Puram[15], Cillo[24]), and TCF7+ cells (Peng[26]), despite expressing a consistent set of genes (IL7R, LTB, CCR7, SELL, TCF7).

summary:
In Homo sapiens head and neck squamous cell carcinoma, naïve CD4 T cells express a consistent set of genes including IL7R, LTB, CCR7, SELL, and TCF7.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:77829c0315041a721514
claim_id: claim:77829c0315041a721514
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
summary: In Homo sapiens, natural killer cells display up-regulation of CD160 in peripheral blood.
span_literal:
Clusters 13 and 16 displayed up-regulation of CD160, previously shown to be expressed in peripheral blood NK cells[29], and enrichment of the NK cell signature


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:bcab6848f200d9c294db
claim_id: claim:bcab6848f200d9c294db
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Clusters 5 and 7 were identified as potential macrophages due to the expression of C1QB and macrophage cell type signatures and a lack of enrichment for classical monocyte signatures

summary:
In Homo sapiens head and neck squamous cell carcinoma, macrophages are identified by expression of C1QB.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:7f32e86d083e6fbb4b1c
claim_id: claim:7f32e86d083e6fbb4b1c
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Interrogation of the top genes enriched for each cluster revealed two clusters, SPP1-positive and CXCL9-positive macrophages, showing high expression of macrophage marker genes C1QB, CD4, and CD163

summary:
In Homo sapiens head and neck squamous cell carcinoma, SPP1-positive macrophages show high expression of macrophage marker genes C1QB, CD4, and CD163.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:b48b3fb7c47579e537bb
claim_id: claim:b48b3fb7c47579e537bb
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Interrogation of the top genes enriched for each cluster revealed two clusters, SPP1-positive and CXCL9-positive macrophages, showing high expression of macrophage marker genes C1QB, CD4, and CD163

summary:
In Homo sapiens head and neck squamous cell carcinoma, CXCL9-positive macrophages show high expression of macrophage marker genes C1QB, CD4, and CD163.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:a0052664e1276b4b737f
claim_id: claim:a0052664e1276b4b737f
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
The CXCL9 cluster was further uniquely defined by high expression of CXCL9 and enriched for antigen presenting-related genes

summary:
In Homo sapiens head and neck squamous cell carcinoma, the CXCL9-positive macrophage cluster is uniquely defined by high expression of CXCL9.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:55f6045525b8cd3d38b8
claim_id: claim:55f6045525b8cd3d38b8
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
The SPP1 cluster was defined by high expression of SPP1 and enriched for metalloproteinases (MMPs), coincident with a relative dearth of Kegg or Hallmark terms

summary:
In Homo sapiens head and neck squamous cell carcinoma, the SPP1-positive macrophage cluster is defined by high expression of SPP1.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:de42b44e50953c2cb58f
claim_id: claim:de42b44e50953c2cb58f
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal: The remaining four clusters were negative for macrophage marker genes C1QB, CD4, APOE and CD163
summary:
In Homo sapiens head and neck squamous cell carcinoma, the CXCL10-positive myeloid cluster, IL1B-positive myeloid cluster, neutrophil cluster, and HCAR3-positive cluster are negative for macrophage marker genes C1QB, CD4, APOE, and CD163.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:69d85bde8fc00a2e44d3
claim_id: claim:69d85bde8fc00a2e44d3
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
We identified a CXCL10-positive cluster that also over-expressed IFIT genes and CCL2 and was enriched for interferon alpha and gamma responses

summary:
In Homo sapiens head and neck squamous cell carcinoma, the CXCL10-positive myeloid cluster over-expresses CXCL10 and CCL2.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:fc081d1f93d4ee3437e6
claim_id: claim:fc081d1f93d4ee3437e6
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
we identified a cluster not previously described in HNSCC with characteristics of myeloid-derived suppressor cells (MDSCs), particularly characterized by high expression of inflammatory cytokines including IL1β, but negative for the macrophage markers SPP1 and CXCL9

summary:
In Homo sapiens head and neck squamous cell carcinoma, a myeloid-derived suppressor cell cluster is characterized by high expression of IL1B but is negative for SPP1 and CXCL9.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:49cbc5e0b37b4ec9cb46
claim_id: claim:49cbc5e0b37b4ec9cb46
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
The Neutrophil cluster appeared to be neutrophil-like due to its lack of HLA-DRA, HLA-DRB1, and CD74 expression, and its expression of IFITM2, S100A8, PROK2, HCAR3, CMTM2, and CSF3R, among others.

summary:
In Homo sapiens head and neck squamous cell carcinoma, the neutrophil cluster lacks HLA-DRA, HLA-DRB1, and CD74 expression, and expresses IFITM2, S100A8, PROK2, HCAR3, CMTM2, and CSF3R.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:4ae3bc6ecc1d68568c77
claim_id: claim:4ae3bc6ecc1d68568c77
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Epi1 was enriched for CD44, a marker of CSCs[44], and KRT18, expressed in progenitor cells and malignant epithelial cells[45].

summary:
In Homo sapiens head and neck squamous cell carcinoma, the least differentiated epithelial cluster Epi1 is enriched for CD44, a marker of cancer stem cells, and KRT18.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:12c6acdd865404e172b5
claim_id: claim:12c6acdd865404e172b5
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Epi6 showed high expression of KRT5 and KRT14, characteristically co-expressed in basal cells[46], indicating that this cluster was at an early stage of the differentiation trajectory.

summary:
In Homo sapiens head and neck squamous cell carcinoma, basal cells characteristically co-express KRT5 and KRT14.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:37c51e77cd26f0be658a
claim_id: claim:37c51e77cd26f0be658a
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal: Epi4 showed high expression of KRT13, KRT4, and SPRR3, genes characteristic of suprabasal cells.
summary:
In Homo sapiens head and neck squamous cell carcinoma, suprabasal cells are characterized by KRT13, KRT4, and SPRR3.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:7b663f24514edeac2646
claim_id: claim:7b663f24514edeac2646
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Cluster 16 was also enriched for the ECM signature but also expressed immune-related genes such as CXCL12 and CXCL14.

summary:
In Homo sapiens head and neck squamous cell carcinoma, CXCL12-positive cancer-associated fibroblasts express immune-related genes CXCL12 and CXCL14.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:ece66967021b5cbd77e3
claim_id: claim:ece66967021b5cbd77e3
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Clusters 10, 14, 22, and 32 were identified as myofibroblast-like pericytes, as they showed high expression of smooth muscle actin (ACTA2, a myofibroblast marker) and pericyte marker genes

summary:
In Homo sapiens head and neck squamous cell carcinoma, myofibroblast-like pericytes show high expression of ACTA2, a myofibroblast marker.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:7e7e842dea0dcf215c55
claim_id: claim:7e7e842dea0dcf215c55
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
Cluster 0 expressed a separate set of immune related genes, including CXCL8, CXCL1, MMPs and IL24, and was enriched for inflammation

summary:
In Homo sapiens head and neck squamous cell carcinoma, CXCL8-positive cancer-associated fibroblasts express CXCL8, CXCL1, and IL24.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:2162f4fc43217a8e9de0
claim_id: claim:2162f4fc43217a8e9de0
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
IL1β, but negative for the macrophage markers SPP1 and CXCL9. Finally, a cluster of Neutrophils was also identified.

The IL1β cluster showed similarity with VCAN– and EREG-expressing tumor-associated macrophages (TAMs) associated with angiogenesis identified in a pan-cancer macrophage atlas.[36] This cluster was also found to be enriched for inflammatory genes, including the aforementioned IL1β, which has been shown to promote drug resistance through induction of ICAM1 on tumor cells[37], IL6 and IL10

summary:
In Homo sapiens head and neck squamous cell carcinoma, the IL1B-positive myeloid cluster is enriched for IL1B, IL6, and IL10.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:3e939896ea81360fa867
claim_id: claim:3e939896ea81360fa867
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
However, we observed key differences in the expression of several key M2 markers such as a lack of CD163 expression, the absence of complement gene expression, and the lack of ARG1 expression.

summary:
In Homo sapiens head and neck squamous cell carcinoma, the IL1B-positive myeloid cluster lacks CD163 and ARG1 expression, distinguishing it from M2 macrophages.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:f77ecaad34011cb5e579
claim_id: claim:f77ecaad34011cb5e579
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
ACKR1, an alternative receptor for these ligands[62] was expressed solely on the vascular endothelial cells

summary:
In Homo sapiens head and neck squamous cell carcinoma, ACKR1 is expressed solely on vascular endothelial cells.


claim_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1:claim:db19d0a4bf808c072fdd
claim_id: claim:db19d0a4bf808c072fdd
paper_key: biorxiv:e3312584-7421-1014-b0a7-823d4471ccf1
span_literal:
CD8 T cells can become dysfunctional, also known as “exhausted”, a state associated with loss of cytokine production and effector killer function that is characterized by expression of immune checkpoint markers such as LAG3, TIGIT, CTLA4, and PD-L1.

summary:
In Homo sapiens, dysfunctional CD8 T cells are characterized by expression of immune checkpoint markers LAG3, TIGIT, CTLA4, and PD-L1 (CD274).


claim_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19:claim:b50f60d7e1dc4eb10c14
claim_id: claim:b50f60d7e1dc4eb10c14
paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
span_literal:
This resolved key cytotoxic subsets; γδ T cells (TRDC+; cluster 6 and 7), CD8 T cells (CD8A+; cluster 10) and Natural Killer (NK) cells (XCL1+; cluster 9)

summary:
In Homo sapiens small cell lung cancer biopsies, gamma delta T cells are marked by positive expression of TRDC.


claim_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19:claim:f324d291831515640ab7
claim_id: claim:f324d291831515640ab7
paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
span_literal:
This resolved key cytotoxic subsets; γδ T cells (TRDC+; cluster 6 and 7), CD8 T cells (CD8A+; cluster 10) and Natural Killer (NK) cells (XCL1+; cluster 9)

summary:
In Homo sapiens small cell lung cancer biopsies, CD8 T cells are marked by positive expression of CD8A.


claim_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19:claim:f40018f8c4646c4e5388
claim_id: claim:f40018f8c4646c4e5388
paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
span_literal:
This resolved key cytotoxic subsets; γδ T cells (TRDC+; cluster 6 and 7), CD8 T cells (CD8A+; cluster 10) and Natural Killer (NK) cells (XCL1+; cluster 9)

summary:
In Homo sapiens small cell lung cancer biopsies, natural killer cells are marked by positive expression of XCL1.


claim_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19:claim:bcf6bd34444c0da8b59d
claim_id: claim:bcf6bd34444c0da8b59d
paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
span_literal:
Using mRNA expression of the δ TCR chain TRDC as a proxy for γδ T cell infiltration, we found that TRDC-high SCLC tumors were associated with significantly longer OS following atezolizumab plus EP (15.4 months) compared to TRDC-low tumors treated with EP alone (9.4 months)

summary:
In Homo sapiens, mRNA expression of TRDC serves as a proxy for gamma delta T cell infiltration in small cell lung cancer tumors.


claim_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19:claim:48278fa37bebcf968912
claim_id: claim:48278fa37bebcf968912
paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
span_literal:
Similarly, atezolizumab plus EP-treated tumors with high expression of TRGC2 (encoding the γ TCR chain), showed the highest OS benefit (14.5 months) compared to TRGC2-low tumors treated with EP only (9.4 months; HR=0.51, 95% CI:0.31-0.85)

summary:
In Homo sapiens, high expression of TRGC2, encoding the gamma T cell receptor chain, is associated with gamma delta T cell infiltration in small cell lung cancer tumors.


claim_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19:claim:94abe3fc22764bc1ff76
claim_id: claim:94abe3fc22764bc1ff76
paper_key: biorxiv:e3425dcb-7964-1014-bf63-abb2012bdd19
span_literal:
Moreover, EpCAM+ tumor cells present in the ex vivo propagated LN biopsy sample expressed NCAM (CD56), a clinical marker of SCLC55

summary:
In Homo sapiens, small cell lung cancer tumor cells are marked by positive expression of EPCAM and NCAM (CD56).


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:b8357b8ca2561cc53270
claim_id: claim:b8357b8ca2561cc53270
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
One subtype, known as cytokine secreting/inflammatory CAFs (iCAFs), is characterized by the upregulation of the fibroblast activation protein (FAP) and interleukin 6 (IL-6) along with downregulation of the alpha smooth muscle actin (aSMA).

summary:
In Homo sapiens, inflammatory cancer-associated fibroblasts are characterized by upregulation of fibroblast activation protein and interleukin 6 along with downregulation of alpha smooth muscle actin.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:7ec5bf5801991bfc8430
claim_id: claim:7ec5bf5801991bfc8430
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
Another subtype, myofibroblastic CAFs (myCAF, FAP+, aSMAhigh, IL-6low), are in close proximity to the neoplastic cells, forming a periglandular ring surrounding cancer cell clusters.

summary:
In Homo sapiens, myofibroblastic cancer-associated fibroblasts are positive for fibroblast activation protein, high for alpha smooth muscle actin, and low for interleukin 6.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:05458581dbc89ee5d3ae
claim_id: claim:05458581dbc89ee5d3ae
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
We identified robust canonical PDAC cell markers including KRT19, SOX9, EPCAM, CD44, CD9, and BPIFBI (Fig. 7C).

summary:
In Homo sapiens, pancreatic ductal adenocarcinoma cells are marked by KRT19, SOX9, EPCAM, CD44, CD9, and BPIFB1.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:2b125121485f3358d33b
claim_id: claim:2b125121485f3358d33b
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
We identified five strong marker genes in control HPSCs, COL1A1, TAGLN, MYL9, CXCL1 and -8 (Fig. 7F).

summary:
In Homo sapiens, human pancreatic stellate cells are marked by COL1A1, TAGLN, MYL9, CXCL1, and CXCL8.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:49e06db130e0a7874eef
claim_id: claim:49e06db130e0a7874eef
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
Violin plots of CAF marker gene expression - vimentin, FAP, and α-SMA (encoded by ACTA2 gene) - show upregulation of vimentin and FAP expression in starved cells compared to the non-starved controls (Fig. 5F).

summary:
In Homo sapiens, inflammatory cancer-associated fibroblast-like cells show upregulation of vimentin and fibroblast activation protein compared to non-starved human pancreatic stellate cells, while alpha smooth muscle actin (encoded by ACTA2) is a marker of cancer-associated fibroblasts.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:8ecbf56f22c12f28d5fa
claim_id: claim:8ecbf56f22c12f28d5fa
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
The two main categories include αSMAhigh peri-glandular myCAFs located close to the tumor cells, and the more distantly located, α-SMAlow iCAFs.

summary:
In Homo sapiens, myofibroblastic cancer-associated fibroblasts are characterized by high alpha smooth muscle actin expression, while inflammatory cancer-associated fibroblasts show low alpha smooth muscle actin expression.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:ef49501c43e2c0039d32
claim_id: claim:ef49501c43e2c0039d32
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
The two main categories include αSMAhigh peri-glandular myCAFs located close to the tumor cells, and the more distantly located, α-SMAlow iCAFs.

summary:
In Homo sapiens, inflammatory cancer-associated fibroblasts are characterized by low alpha smooth muscle actin expression compared to myofibroblastic cancer-associated fibroblasts.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:519dbabbedd7be980f07
claim_id: claim:519dbabbedd7be980f07
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
Expression of KRT19, SOX9, CDH1 and EPCAM is consistent in ductal but undetectable in stellate cells, regardless of stellate cell activation by serum-starvation (Activ.) or clemastine treatment (Clem.).

summary:
In Homo sapiens, pancreatic ductal tumor cells consistently express KRT19, SOX9, CDH1, and EPCAM, which are undetectable in pancreatic stellate cells.


claim_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b:claim:0e9701f578e9421bd979
claim_id: claim:0e9701f578e9421bd979
paper_key: biorxiv:e3c88c7c-7fe3-1014-8c3f-f97dd191bd5b
span_literal:
Expression of KRT19, SOX9, CDH1 and EPCAM is consistent in ductal but undetectable in stellate cells, regardless of stellate cell activation by serum-starvation (Activ.) or clemastine treatment (Clem.).

summary:
In Homo sapiens, pancreatic stellate cells do not express KRT19, SOX9, CDH1, or EPCAM, which are markers of pancreatic ductal tumor cells.


claim_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d:claim:e54e076f189c89b214b7
claim_id: claim:e54e076f189c89b214b7
paper_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d
span_literal:
we spot-checked some existing HMC3 RNAseq datasets from Gene Expression Omnibus to validate the expression of common myeloid cell markers including ITGAM (CD11b), PTPRC, SYK, TYROBP, CX3CR1, and Fc receptors.

summary:
In Homo sapiens, myeloid cells are expected to express common markers including ITGAM, PTPRC, SYK, TYROBP, and CX3CR1.


claim_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d:claim:41de2f903403904a473f
claim_id: claim:41de2f903403904a473f
paper_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d
span_literal:
In their study, HMC3 cells failed to express canonical microglia markers (Iba1, CD45, PU.1) and instead stained positive for mural cell markers such as PDGFRβ and NG2.

summary:
In Homo sapiens, Human Microglia Clone 3 (HMC3) cells failed to express canonical microglia markers Iba1, CD45, and PU.1, and instead expressed mural cell markers PDGFRβ and NG2.


claim_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d:claim:ae2e1f30309706a80bbc
claim_id: claim:ae2e1f30309706a80bbc
paper_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d
span_literal:
In their study, HMC3 cells failed to express canonical microglia markers (Iba1, CD45, PU.1) and instead stained positive for mural cell markers such as PDGFRβ and NG2.

summary:
In Homo sapiens, Human Microglia Clone 3 (HMC3) cells stained positive for mural cell markers PDGFRβ and NG2, indicating these genes mark mural cells.


claim_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d:claim:614cba975b107eaa3abf
claim_id: claim:614cba975b107eaa3abf
paper_key: biorxiv:e3c9e28c-70c5-1014-9616-aa7d906f9d5d
span_literal:
In their study, HMC3 cells failed to express canonical microglia markers (Iba1, CD45, PU.1) and instead stained positive for mural cell markers such as PDGFRβ and NG2.

summary:
In Homo sapiens, Human Microglia Clone 3 (HMC3) cells failed to express Iba1, CD45, and PU.1, and instead expressed PDGFRβ and NG2, indicating HMC3 cells lack microglia markers and express mural cell markers.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:84e445aa96cad496e085
claim_id: claim:84e445aa96cad496e085
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
span_literal:
These cells expressed key Tr1-associated genes (IL10, LAG3, CTLA4, PDCD1, MAF, PRDM1, GZMA, GZMK); they were distinct from FOXP3-expressing Tregs; and, they demonstrated long-term memory with clonal fidelity (maintaining their Tr1 identity) upon recall6.

summary:
In Homo sapiens, type 1 regulatory T cells express IL10, LAG3, CTLA4, PDCD1, MAF, PRDM1, GZMA, and GZMK, and are distinct from FOXP3-expressing regulatory T cells.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:0fbe0293ade40f2a1e27
claim_id: claim:0fbe0293ade40f2a1e27
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
span_literal:
These Tr1 cells expressed CXCR6 and had low to no expression of IL7R—a pattern that appeared relatively unique among memory CD4+ T cells (Fig. 1B).

summary:
In Homo sapiens, type 1 regulatory T cells express CXCR6 and have low to no expression of IL7R, distinguishing them from other memory CD4+ T cells.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:d3e8cbcc8ba4e1282549
claim_id: claim:d3e8cbcc8ba4e1282549
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
span_literal: Tr1 cells (CXCR6+ CD127-
summary:
In Homo sapiens, type 1 regulatory T cells are identified by positive expression of CXCR6 and negative expression of CD127 (IL7R).


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:866f70806813bf21ac17
claim_id: claim:866f70806813bf21ac17
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
span_literal:
We utilized a large multiparameter phenotyping panel to simultaneously detect Tr1 (CXCR6+ CD127-), Th1 (CCR4-CCR6-CXCR3+), Th2 (CCR4+ CCR6-CXCR3-), Th17 (CCR4+ CCR6+ CXCR3-), Treg (CD25+ FOXP3+), and circulating T follicular helper (cTfh) cells (CXCR5+ PD-1+) cells using conventional gating strategies (Fig. S4A).

summary:
In Homo sapiens, type 1 regulatory T cells are identified as CXCR6-positive CD127-negative, T helper 1 cells as CCR4-negative CCR6-negative CXCR3-positive, T helper 2 cells as CCR4-positive CCR6-negative CXCR3-negative, T helper 17 cells as CCR4-positive CCR6-positive CXCR3-negative, regulatory T cells as CD25-positive FOXP3-positive, and circulating T follicular helper cells as CXCR5-positive PD-1-positive.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:945a2b1214bda9c94f66
claim_id: claim:945a2b1214bda9c94f66
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
summary:
In Homo sapiens, circulating T follicular helper cells are identified as CXCR5-positive PD-1-positive.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:a73b43133c711fc053cd
claim_id: claim:a73b43133c711fc053cd
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
summary: In Homo sapiens, regulatory T cells typically lack or lowly express CD127 (IL7R).
span_literal:
The largest contaminating population among CXCR6+ CD127-memory CD4+ T cells (<10%) was FOXP3-expressing Tregs (Fig. S2A), consistent with conventional Tregs also typically lacking or lowly expressing CD12712.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:c9ebfe8cdb4f7084e2df
claim_id: claim:c9ebfe8cdb4f7084e2df
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
summary: In Homo sapiens, type 1 regulatory T cells lack FOXP3 but express IL-10.
span_literal:
a subset of memory CD4+ T cells that lack FOXP3 but regulate immune responses through expression of IL-10 and coinhibitory receptors7.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:080b73fcb324cde397ed
claim_id: claim:080b73fcb324cde397ed
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
span_literal:
The cell surface markers CD49b and lymphocyte activation gene 3 (LAG-3) were transcriptionally enriched among IL-10 producing expanded human T cell clones.

summary:
In Homo sapiens, CD49b and lymphocyte activation gene 3 (LAG-3) are transcriptionally enriched among IL-10-producing expanded T cell clones.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:c5f7f3697ddf536ab358
claim_id: claim:c5f7f3697ddf536ab358
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
summary: In Homo sapiens, CCR5-positive PD-1-positive CD4+ T cells co-express IL-10 and IFNγ in the gut.
span_literal:
More recently, CCR5+ PD-1+ was shown to enrich for CD4+ T cells that suppress colitis in mice and that co-express IL-10 and IFNγ in the human gut11.


claim_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab:claim:73f8301d670a57ee7ca3
claim_id: claim:73f8301d670a57ee7ca3
paper_key: biorxiv:e41f3b4d-7312-1014-8c3d-9c868a469aab
summary: In Homo sapiens, activated type 1 regulatory T cells downregulate CXCR6.
span_literal:
However, activated Tr1 cells (and some memory Tr1 cells) downregulate CXCR6 (Fig. S2E), suggesting that CXCR6+ CD127-may not capture all Tr1 cell subsets with the same efficacy.


claim_key: biorxiv:e568b53a-6d0f-1014-b567-f89875467104:claim:ec945f3d0f1d22ca6316
claim_id: claim:ec945f3d0f1d22ca6316
paper_key: biorxiv:e568b53a-6d0f-1014-b567-f89875467104
span_literal:
Furthermore, we recently identified that NTRK2 is highly upregulated in MECs of irradiated human SGs along with other neurotrophin receptors and stimulation of neurotrophin signaling in vitro promoted myoepithelial differentiation47.

summary:
In Homo sapiens, NTRK2 is highly upregulated in myoepithelial cells of irradiated salivary glands along with other neurotrophin receptors.


claim_key: biorxiv:e6391442-6c81-1014-9943-822578d46439:claim:4082017b4ea529be6571
claim_id: claim:4082017b4ea529be6571
paper_key: biorxiv:e6391442-6c81-1014-9943-822578d46439
span_literal:
Our differential testing found that while Prph2, Rs1, and Gngt1 had expression differences matching that the findings Yan et al. and Peng et al. published, they failed to replicate in our test with pvalue and padj being above 0.1 for all three.

summary:
In Homo sapiens, PRPH2, RS1, and GNGT1 were previously proposed as markers distinguishing macula from peripheral cones but failed to replicate significantly in the scEiaD differential test.


claim_key: biorxiv:e6391442-6c81-1014-9943-822578d46439:claim:f57f52cfe64d83fb6313
claim_id: claim:f57f52cfe64d83fb6313
paper_key: biorxiv:e6391442-6c81-1014-9943-822578d46439
span_literal:
In contrast Calb1 did replicate strongly with the sixth lowest padj (0.00721) across our entire test and a log2 fold change of 2.87.

summary:
In Homo sapiens, CALB1 is a positive marker of macula-derived cones, replicating strongly as a cone region marker.


claim_key: biorxiv:e6391442-6c81-1014-9943-822578d46439:claim:3d869a7dcf5977061ed0
claim_id: claim:3d869a7dcf5977061ed0
paper_key: biorxiv:e6391442-6c81-1014-9943-822578d46439
span_literal:
We find six more genes with a padj < 0.01: Pde6g, Akap12, Hspb1, Gadd45b, Cc2d2a, and RP1l1 (Figure 6 and Supplemental Table 5).

summary:
In Homo sapiens, PDE6G, AKAP12, HSPB1, GADD45B, CC2D2A, and RP1L1 are proposed as new cone region markers distinguishing macula from peripheral cones.


claim_key: biorxiv:e6391442-6c81-1014-9943-822578d46439:claim:88effbb9df1b22e72e75
claim_id: claim:88effbb9df1b22e72e75
paper_key: biorxiv:e6391442-6c81-1014-9943-822578d46439
span_literal:
We find one gene, Zbtb38, that meets this criteria and drops in expression when comparing RPC to neurogenic.

summary:
In Homo sapiens, ZBTB38 drops in expression in neurogenic cells compared to retinal progenitor cells, serving as a negative marker of neurogenic cells.


claim_key: biorxiv:e6391442-6c81-1014-9943-822578d46439:claim:6c7083d5b16a1331d132
claim_id: claim:6c7083d5b16a1331d132
paper_key: biorxiv:e6391442-6c81-1014-9943-822578d46439
span_literal:
We replicate Atoh7, Onecut2, Gadd45a, Mybl1 from Lu et al (Figure 4B) as differentially expressed between neurogenic and RPC.

summary:
In Homo sapiens, ATOH7, ONECUT2, GADD45A, and MYBL1 are replicated as differentially expressed markers between neurogenic cells and retinal progenitor cells.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:28f62d30835896fde496
claim_id: claim:28f62d30835896fde496
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
In this data set, we reannotated the original endothelium/pericytes/adventia cluster (cluster 10) as intramyocardial ECs, based on differentially expressed markers such as A2M, CD36, APLNR, ARHGAP18, IGFBP3, CLDN5, FABP4 and FABP5

summary:
In Homo sapiens fetal heart, intramyocardial endothelial cells are marked by A2M, CD36, APLNR, ARHGAP18, IGFBP3, CLDN5, FABP4 and FABP5.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:0d1953404e2b6cb0127d
claim_id: claim:0d1953404e2b6cb0127d
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
The cluster annotated as capillary endothelium (cluster 0) in the original publication was reannotated as endocardium, due to the presence of differentially expressed markers like NPR3, ALDH2, CDH11, ECE1, TMEM100, FOXC1 and EDN1

summary:
In Homo sapiens fetal heart, endocardium is marked by NPR3, ALDH2, CDH11, ECE1, TMEM100, FOXC1 and EDN1.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:3ffa452628212b9de12c
claim_id: claim:3ffa452628212b9de12c
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
Recent single-cell RNA sequencing (scRNA-seq) studies of the human fetal heart confirmed that some of the markers identified in mouse are conserved in human, including CD36 and FABP5 for iECs and NPR3 and CDH11 for eECs, among others (McCracken et al., 2022; Miao et al., 2020).

summary:
In Homo sapiens fetal heart, intramyocardial endothelial cells are marked by CD36 and FABP5, while endocardial endothelial cells are marked by NPR3 and CDH11.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:814cc2360b9575d5db0d
claim_id: claim:814cc2360b9575d5db0d
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
The cardiac mesoderm cluster was characterized by mesoderm and early cardiac genes, such as MESP1, SMARCD3, ABLIM1, TMEM88, ISL1, MYL5, as well as the cell cycle-related genes CDK6 and NEK2.

summary:
In Homo sapiens, the cardiac mesoderm cluster is characterized by MESP1, SMARCD3, ABLIM1, TMEM88, ISL1, MYL5, CDK6 and NEK2.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:4b34675b313915c4b142
claim_id: claim:4b34675b313915c4b142
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
The CMEC cluster was characterized by EC markers (CDH5, CD34, KDR, HEY2, TEK, TIE1, ACVRL1, SOX17, ENG, ICAM2, PECAM1).

summary:
In Homo sapiens, cardiac mesoderm-derived endothelial cells are characterized by CDH5, CD34, KDR, HEY2, TEK, TIE1, ACVRL1, SOX17, ENG, ICAM2 and PECAM1.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:fe75a1dc62dfdaf415e7
claim_id: claim:fe75a1dc62dfdaf415e7
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
Cardiomyocytes were identified by expression of cardiomyocyte-associated genes, including MYL4, TNNI1, MYL7, ACTA2, TNNT2, HAND2 and NKX2-5.

summary:
In Homo sapiens, cardiomyocytes are identified by expression of MYL4, TNNI1, MYL7, ACTA2, TNNT2, HAND2 and NKX2-5.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:606ddbbccdb6eee5483f
claim_id: claim:606ddbbccdb6eee5483f
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
The paraxial mesoderm cluster was characterized by expression of aPSM and dermomyotome genes, such as MEOX1, PDGFRB, SIX1, CRABP2, NR2F1, EYA1, FOXC1 and PAX3.

summary:
In Homo sapiens, the paraxial mesoderm cluster is characterized by MEOX1, PDGFRB, SIX1, CRABP2, NR2F1, EYA1, FOXC1 and PAX3.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:970983e6aca2e74c54f3
claim_id: claim:970983e6aca2e74c54f3
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal: PMECs were characterized by EC markers, like ETV2, CDH5, CD34, KDR, ENG, SOX17, PLVAP, APLN, NRP1.
summary:
In Homo sapiens, paraxial mesoderm-derived endothelial cells are characterized by ETV2, CDH5, CD34, KDR, ENG, SOX17, PLVAP, APLN and NRP1.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:e893bba25ff02c70c4ee
claim_id: claim:e893bba25ff02c70c4ee
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
The mixed LPM/sclerotome cluster was characterized by LPM and sclerotome specific genes, such as TMEM88, HAND1, TNNI1, PRRX1, ACTA2, DES, FOXH1, LEF1 and JAG1

summary:
In Homo sapiens, the mixed lateral plate mesoderm/sclerotome cluster is characterized by TMEM88, HAND1, TNNI1, PRRX1, ACTA2, DES, FOXH1, LEF1 and JAG1.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:ac82e73e32ff49d23b4a
claim_id: claim:ac82e73e32ff49d23b4a
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
ECs in cardiac MTs upregulated expression of markers enriched in human intramyocardial ECs (iECs), such as CD36, CLDN5, APLNR, NOTCH4, IGFBP3, ARHGAP18, which were previously identified in the single-cell RNA-seq dataset from the human fetal heart (6.5-7 weeks post coitum).

summary:
In Homo sapiens, intramyocardial endothelial cells in the heart are enriched for CD36, CLDN5, APLNR, NOTCH4, IGFBP3 and ARHGAP18.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:1bfd22aaed9aba93d854
claim_id: claim:1bfd22aaed9aba93d854
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
These hPSC-derived ECs expressed a number of cardiac specific genes like MEOX2, GATA4, GATA6 and ISL1, while tissue specific endocardial or intramyocardial markers were still absent, likely because of the lack of local microenvironmental cues.

summary:
In Homo sapiens, human pluripotent stem cell-derived endothelial cells from cardiac mesoderm express cardiac specific genes MEOX2, GATA4, GATA6 and ISL1.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:57fcc377b47c48883e57
claim_id: claim:57fcc377b47c48883e57
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
PMECs showed increased expression of genes important for the development of lymphatic vasculature, such as TBX1, FOXC1, LYVE1, VEGFC.

summary:
In Homo sapiens, paraxial mesoderm-derived endothelial cells show increased expression of TBX1, FOXC1, LYVE1 and VEGFC, genes important for lymphatic vasculature development.


claim_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8:claim:c6c4a16b94dff86a8d0a
claim_id: claim:c6c4a16b94dff86a8d0a
paper_key: biorxiv:e69e6aa5-6cf9-1014-aa41-9f7e5b3de6e8
span_literal:
At the same time, expression of the master regulator of lymphatic EC differentiation (PROX1) was not detected in PMECs either at day 6 or in cardiac MTs.

summary:
In Homo sapiens, paraxial mesoderm-derived endothelial cells do not express PROX1, the master regulator of lymphatic endothelial cell differentiation.


claim_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6:claim:865a66e88c2be69c541a
claim_id: claim:865a66e88c2be69c541a
paper_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6
span_literal:
the mRNA expression of T-cell specific genes such as CD3E and CD3D were only found 0.07% in the B-cells sorted on CD20

summary:
In Homo sapiens, T cell is marked by positive expression of CD3E and CD3D, which are largely absent in B cell.


claim_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6:claim:1855a2230d10d0cbeb7c
claim_id: claim:1855a2230d10d0cbeb7c
paper_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6
span_literal:
B-cell specific markers such as CD79A, CD79B and MS4A1 were only detected in 9.09% of T-cells sorted on CD8A or CD4

summary:
In Homo sapiens, B cell is marked by positive expression of CD79A, CD79B, and MS4A1, which are largely absent in T cell.


claim_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6:claim:5dee6068a7c2cee69cad
claim_id: claim:5dee6068a7c2cee69cad
paper_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6
summary: In Homo sapiens, B cell is marked by positive expression of CD79A, CD79B, and MS4A1.
span_literal:
Markers included CD79A, CD79B and MS4A1 for B-cells, CD3E and CD3D for T-cells, GNLY for NK-cells; and LYZ, S100A8 and S100A9 for monocytes.


claim_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6:claim:62458022ef5022a83f36
claim_id: claim:62458022ef5022a83f36
paper_key: biorxiv:e6e04172-6c15-1014-9229-c57ac33d21f6
summary: In Homo sapiens, B cell is marked by positive expression of MS4A1.
span_literal:
Cell clusters 2 and 3 were classified as B-cells (MS4A1+); cell clusters 5, 6, 7, 8, 9 and 11 were classified as T-cells (CD3D+/CD3E+); cell clusters 13 and 14 were identified as LYZ+ monocyte group; cell cluster 15 was identified as FCGR3A+ monocytes group; cell cluster 10 was identified as NKG7+ and GNLY+ NK-cell group; cell clusters 18 and 19 were identified as FCER1A+ dendritic cell group; cell cluster 4 was identified as IRF7+ and IRF8+ plasmacytoid dendritic cell group; cell cluster 16 was identified as PPBP+ Megakaryocytes; cell cluster 1 was identified as IGHG1+ and IGHG2+ plasma cell group; cell cluster 12 was identified as CD34+ cell group; cell cluster 17 is likely to be multiplets for it has shown IL7R, CD3D and CD14 markers.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:02cda2f1de7dd3392f2d
claim_id: claim:02cda2f1de7dd3392f2d
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal:
The Mix_2 cells specifically express numerous colon epithelial stem cells signature markers such as SMOC2, RGBM, OLFM4, AXIN2 and LGR5.

summary:
In Homo sapiens, Mix_2 epithelial cells specifically express colon epithelial stem cell signature markers including SMOC2, RGMB, OLFM4, AXIN2, and LGR5.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:1a83373706abf19e0f85
claim_id: claim:1a83373706abf19e0f85
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal: A dominance of CEACAM5high epithelial cells were identified in LS-paraCA.
summary:
In Homo sapiens, a dominant population of CEACAM5-high epithelial cells was identified in Lynch Syndrome para-carcinoma tissue.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:9a6e1558bae2d956556d
claim_id: claim:9a6e1558bae2d956556d
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal: CEACAM5 is well-known cancer stem cell biomarker and immune checkpoint target
summary:
In Homo sapiens, carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) is a well-known cancer stem cell biomarker.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:d9f373e06a5dce8a38f2
claim_id: claim:d9f373e06a5dce8a38f2
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal:
Six major T cell subtypes were identified: Naïve CD4-T, NKT, Treg, IL7R+CD8_T, GZMA+CD8_T, and GZMK+CD8_T.

summary:
In Homo sapiens, six major T cell subtypes were identified, including IL7R-positive CD8 T cells, GZMA-positive CD8 T cells, and GZMK-positive CD8 T cells.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:ed85014b3c68e10e6641
claim_id: claim:ed85014b3c68e10e6641
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal:
LS carcinoma has a high stemness score and numerous biomarkers including CEACAM5, BACE2, GPRC5A and OLFM4 may be utilized as novel molecular markers for tracing the malignant transition in LS.

summary:
In Homo sapiens, Lynch Syndrome carcinoma has high stemness and carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), BACE2, GPRC5A, and OLFM4 may be utilized as novel molecular markers for tracing malignant transition in cancer stem cell-like cells.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:eb8d8513956c0eb71e9d
claim_id: claim:eb8d8513956c0eb71e9d
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal:
we observed an increase in primitive cancer stem-cell-like cells with high expression of a general cancer biomarker CarcinoEmbryonic Antigen-related Cell Adhesion Molecule 5 (CEACAM5) in the epithelium of the LS.

summary:
In Homo sapiens, primitive cancer stem-cell-like cells in Lynch Syndrome epithelium show high expression of carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5).


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:2151c6d5f0ff0960330e
claim_id: claim:2151c6d5f0ff0960330e
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal:
the expression of BACE2, GPRC5A and OLFM4 and their encoded proteins was much higher in malignant CRC and LS-CA tissues, while their expression in LS-paraCA tissues was limited.

summary:
In Homo sapiens, the expression of BACE2, GPRC5A, and OLFM4 is much higher in malignant colorectal cancer and Lynch Syndrome carcinoma epithelial cells compared to Lynch Syndrome para-carcinoma epithelial cells.


claim_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30:claim:34a4637a82a2f9726f06
claim_id: claim:34a4637a82a2f9726f06
paper_key: biorxiv:e70d54a8-74bd-1014-b600-d60c5a656b30
span_literal: IL7RhighCD8+T cells transitioning into GZMKhighCD8+T, GZMAhighCD8+T, and NKT cells
summary:
In Homo sapiens, IL7R-high CD8-positive T cells transition into GZMK-high CD8-positive T cells, GZMA-high CD8-positive T cells, and natural killer T cells.


claim_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da:claim:0bf138970b931308a794
claim_id: claim:0bf138970b931308a794
paper_key: biorxiv:e7144333-745a-1014-ab12-e9455a30c9da
span_literal:
As with the mouse, the human scANVI model also utilised the expression of some traditional markers, such as the surface marker PDGFRA for PrE, the TGF-β ligands NODAL and GDF3 for the EPI and several critical genes in placental development KRT18, CGF and PGF for TE (Suppl. Table 4, S4).

summary:
In Homo sapiens, the human scANVI model identified platelet-derived growth factor receptor alpha (PDGFRA) as a marker for primitive endoderm, NODAL and GDF3 as markers for epiblast, and KRT18, CGF, and PGF as markers for trophectoderm.


