# claims

claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:bfe088c2d6d9a850eff7
claim_id: claim:bfe088c2d6d9a850eff7
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Specifically, iron uptake receptor (TFRC), ferritin (FTL, FTH1), genes related to ferroptosis (SAT1, SOD2, GLUL) and lysosomal activation (LGMN, GPNMB, SLC14A3, CTSB, CTSS, CTSL, CTSZ) were upregulated again in SMC8-Mac, whereas they were not in SMC-Syn

summary:
In Homo sapiens, macrophage-like smooth muscle cell 8 (SMC8-Mac) shows upregulated TFRC, FTL, FTH1, SAT1, SOD2, GLUL, LGMN, GPNMB, SLC14A3, CTSB, CTSS, CTSL, and CTSZ compared to synthetic smooth muscle cells.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:4aea11acc0ab847999a1
claim_id: claim:4aea11acc0ab847999a1
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
On the other hand, SMC8-Mac showed upregulated TAGLN, ACTA2, MYL9 and ECM genes (COL1A2, COL6A2) compared to the Macrophage cluster, reflecting the characteristic of smooth muscle cells

summary:
In Homo sapiens, macrophage-like smooth muscle cell 8 (SMC8-Mac) shows upregulated TAGLN, ACTA2, MYL9, COL1A2, and COL6A2 compared to macrophages, reflecting smooth muscle cell characteristics.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:770c7b3c8ab985580528
claim_id: claim:770c7b3c8ab985580528
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Contractile cell clusters bore the hallmark signature of ACTA2, MYH11 and TAGLN genes39–41, while transitioning SMCs downregulated these contractile genes and upregulated SPP1, a known synthetic marker42.

summary:
In Homo sapiens, contractile smooth muscle cell clusters bear the hallmark signature of ACTA2, MYH11, and TAGLN, while transitioning smooth muscle cells downregulate these and upregulate SPP1, a known synthetic marker.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:9bc4d00a7d2374746354
claim_id: claim:9bc4d00a7d2374746354
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Contractile cell clusters bore the hallmark signature of ACTA2, MYH11 and TAGLN genes39–41, while transitioning SMCs downregulated these contractile genes and upregulated SPP1, a known synthetic marker42.

summary:
In Homo sapiens, transitioning smooth muscle cells downregulate ACTA2, MYH11, and TAGLN and upregulate SPP1, a known synthetic marker.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:911e47b79f2909cd3b6e
claim_id: claim:911e47b79f2909cd3b6e
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Synthetic SMC clusters were additionally identified by expressing elevated levels of ECM-related genes COL1A1, COL1A2, LUM and DCN, a finding that is similar to the “fibromyocyte” identity previously described17.

summary:
In Homo sapiens, synthetic smooth muscle cell clusters are identified by elevated expression of extracellular matrix-related genes COL1A1, COL1A2, LUM, and DCN.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:2c69a1a1562fef84b944
claim_id: claim:2c69a1a1562fef84b944
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Macrophage-like cells instead had elevated CD68, LGALS3, SPP122, whereas fibroblast-like SMCs had the ECM- remodeling signature with elevated ADAMTS1, FOS, EGR and A2M.

summary:
In Homo sapiens, macrophage-like smooth muscle cells have elevated CD68, LGALS3, and SPP1, whereas fibroblast-like smooth muscle cells have elevated ADAMTS1, FOS, EGR, and A2M.


claim_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81:claim:a60054cbe5788f9eaef6
claim_id: claim:a60054cbe5788f9eaef6
paper_key: biorxiv:558bd04f-7a31-1014-843e-87e03b8b4f81
span_literal:
Macrophage-like cells instead had elevated CD68, LGALS3, SPP122, whereas fibroblast-like SMCs had the ECM- remodeling signature with elevated ADAMTS1, FOS, EGR and A2M.

summary:
In Homo sapiens, fibroblast-like smooth muscle cells have elevated ADAMTS1, FOS, EGR, and A2M, reflecting an extracellular matrix remodeling signature.


claim_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21:claim:c5f70a2174d33e3977b3
claim_id: claim:c5f70a2174d33e3977b3
paper_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21
span_literal:
We identified only 10 genes that were significantly up-regulated in all cell types in response to all five type I IFN subtypes tested here: IFI44L, ISG15, IFIT3, XAF1, MX1, IFI6, IFIT1, TRIM22, MX2 and RSAD2 (Figure 4c, Figure S14).

summary:
In Homo sapiens peripheral blood mononuclear cells, IFI44L, ISG15, IFIT3, XAF1, MX1, IFI6, IFIT1, TRIM22, MX2, and RSAD2 are core interferon-stimulated genes up-regulated in all cell types in response to all type I interferons, universally marking the type I interferon response.


claim_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21:claim:01890b752eb109eeaa59
claim_id: claim:01890b752eb109eeaa59
paper_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21
span_literal:
Genes specifically up-regulated by monocytes included IFITM3, CXCL10 and SIGLEC1 while genes specifically up-regulated by lymphocytes included LAG3, ALOX5AP and CD48 (Figure 5b and c).

summary:
In Homo sapiens, IFITM3, CXCL10, and SIGLEC1 are specifically up-regulated by monocytes in response to type I interferons, distinguishing them from lymphocytes.


claim_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21:claim:fc3ce8ccae968a9fbe8b
claim_id: claim:fc3ce8ccae968a9fbe8b
paper_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21
span_literal:
Genes specifically up-regulated by monocytes included IFITM3, CXCL10 and SIGLEC1 while genes specifically up-regulated by lymphocytes included LAG3, ALOX5AP and CD48 (Figure 5b and c).

summary:
In Homo sapiens, LAG3, ALOX5AP, and CD48 are specifically up-regulated by lymphocytes in response to type I interferons, distinguishing them from monocytes.


claim_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21:claim:41f9e0a350fd12897d18
claim_id: claim:41f9e0a350fd12897d18
paper_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21
span_literal:
As expected, genes up-regulated by both monocytes and lymphocytes included those described as ISGs by many previous studies, such as ISG15, IFI44 and IFIT5 (Figure 5b and c).

summary:
In Homo sapiens, ISG15, IFI44, and IFIT5 are interferon-stimulated genes up-regulated by both monocytes and lymphocytes in response to type I interferons.


claim_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21:claim:4e3ffb52b36878ec337f
claim_id: claim:4e3ffb52b36878ec337f
paper_key: biorxiv:55d0fee5-7079-1014-8ef3-9aa3522a8f21
span_literal:
As expected, genes up-regulated by both monocytes and lymphocytes included those described as ISGs by many previous studies, such as ISG15, IFI44 and IFIT5 (Figure 5b and c).

summary:
In Homo sapiens, ISG15, IFI44, and IFIT5 are interferon-stimulated genes up-regulated by both lymphocytes and monocytes in response to type I interferons.


claim_key: biorxiv:57ac822b-6c7d-1014-a047-d6c2f45edeb7:claim:67fe761ef697adb93e39
claim_id: claim:67fe761ef697adb93e39
paper_key: biorxiv:57ac822b-6c7d-1014-a047-d6c2f45edeb7
span_literal:
CD21 was compared to CD19 and CD79 to CD20 for B cells, CD4 to CD25 for CD4?T cells, and CD94 to CD56 for NK cells.

summary:
In Homo sapiens, B cells are marked by CD19, CD20, CD21, and CD79; CD4+ T cells are marked by CD4 and CD25; and natural killer cells are marked by CD56 and CD94.


claim_key: biorxiv:57ac822b-6c7d-1014-a047-d6c2f45edeb7:claim:183665de63772e9eca60
claim_id: claim:183665de63772e9eca60
paper_key: biorxiv:57ac822b-6c7d-1014-a047-d6c2f45edeb7
span_literal:
Notably, CAPTAIN identified disease-dependent activation of the pro-inflammatory S100A9–CD36 axis, which remained inactive in healthy and asymptomatic individuals but became increasingly prominent in mild to severe cases.

summary:
In Homo sapiens, CAPTAIN identified disease-dependent activation of the S100A9-CD36 signaling axis between platelets and monocytes, which became increasingly prominent with COVID-19 severity.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:8aeb46ba00ad0ab14bb7
claim_id: claim:8aeb46ba00ad0ab14bb7
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal:
NSCs expressed NES (Lendahl, Zimmerman, and McKay 1990) and TPM1 (Nicholson-Flynn, Hitchcock-DeGregori, and Levitt 1996), with low expression of PAX6 (Götz, Stoykova, and Gruss 1998) and FOXG1 (Martynoga et al. 2005), unlike RGs and oRGs (Figure 1C).

summary:
In Homo sapiens cortical organoids, neuroepithelial stem cells express NES and TPM1, with low expression of PAX6 and FOXG1, unlike radial glia and outer radial glia.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:9d3a0d45f48b3e6197f7
claim_id: claim:9d3a0d45f48b3e6197f7
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal:
IP clusters share transcriptomic signatures with neurons (ROBO1 (Ip et al. 2011), CUX1 (Coviello et al. 2022)), as has been previously reported in organoid scRNA-seq studies (Quadrato et al. 2017; Velasco et al. 2019).

summary:
In Homo sapiens cortical organoids, intermediate progenitor clusters share transcriptomic signatures with neurons including ROBO1 and CUX1.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:779b85fb87f13b6cb647
claim_id: claim:779b85fb87f13b6cb647
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
summary: In Homo sapiens cortical organoids, neural progenitor cells express VIM and PAX6.
span_literal:
Some neural progenitor cells (NPCs) expressed S phase markers or G2/M phase markers in addition to VIM and PAX6.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:00ce46537cb1e531e041
claim_id: claim:00ce46537cb1e531e041
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal:
Dividing IPs, delineated by EOMES expression and G2/M phase markers, formed a separate cluster from non-dividing IPs.

summary:
In Homo sapiens cortical organoids, dividing intermediate progenitors are delineated by EOMES expression.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:1732f0df8ee9666536d7
claim_id: claim:1732f0df8ee9666536d7
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal:
Two upper layer neuron clusters were identified: group a expressed SATB2 and group b expressed CUX2.

summary:
In Homo sapiens cortical organoids, upper layer neuron group a expresses SATB2 and upper layer neuron group b expresses CUX2.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:baaebaac532b460337c9
claim_id: claim:baaebaac532b460337c9
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
summary: In Homo sapiens cortical organoids, pan cortical neurons express DCX and FOXG1.
span_literal:
A separate cluster of cortical neurons expressing DCX and FOXG1, but no layer specific markers, were labeled pan cortical neurons.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:829b586b21f5cb310db8
claim_id: claim:829b586b21f5cb310db8
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal:
hCOs generated a non-cortical cluster with a mix of medial pallium (TTR (Pellegrini et al. 2020)) and pioneer neuron markers (LMX1A (Yan et al. 2011)).

summary:
In Homo sapiens cortical organoids, the medial pallium cluster expresses TTR and the pioneer neuron marker LMX1A.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:924bca07b159471971bb
claim_id: claim:924bca07b159471971bb
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal:
We identified a pan neuron/Cajal-Retzius (PN/CR) cluster expressing gene markers for cortical neurons (SOX5 (Lai et al. 2008)), ventral brain regions or spinal cord (PAX3 (Terzić and Saraga-Babić 1999)) and cerebellum (MEIS1 (Owa et al. 2018)).

summary:
In Homo sapiens cortical organoids, the pan neuron/Cajal-Retzius cluster expresses SOX5, PAX3, and MEIS1.


claim_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e:claim:de9211bdf3cfcf7e186c
claim_id: claim:de9211bdf3cfcf7e186c
paper_key: biorxiv:581b3311-6d06-1014-8bb1-e34795ede71e
span_literal: Finally, we labeled an unspecified neuron cluster expressing SCN2A, but not FOXG1 or VIM.
summary:
In Homo sapiens cortical organoids, the unspecified neuron cluster expresses SCN2A but not FOXG1 or VIM.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:ab84c3259a10edd847c9
claim_id: claim:ab84c3259a10edd847c9
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Nine broad cell lineages were identified in the heart specimens: T and NK cells (characterized by the expression of CD3D and KLRB1), MNPs (CD14, CD68), DCs (CD1C, CLEC9A, IRF8), B cells and plasmablasts (CD79A, MZB1), endothelial cells (VWF, CA4), mural cells (RGS5, KCNJ8), fibroblasts (DCN, PDGFRA), cardiomyocytes (TNNI3, MB), and neuronal cells (PLP1, NRXN1)

summary:
In Homo sapiens heart tissue, T and natural killer cells are characterized by the expression of CD3D and KLRB1.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:702e842ae7ed86c58212
claim_id: claim:702e842ae7ed86c58212
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Nine broad cell lineages were identified in the heart specimens: T and NK cells (characterized by the expression of CD3D and KLRB1), MNPs (CD14, CD68), DCs (CD1C, CLEC9A, IRF8), B cells and plasmablasts (CD79A, MZB1), endothelial cells (VWF, CA4), mural cells (RGS5, KCNJ8), fibroblasts (DCN, PDGFRA), cardiomyocytes (TNNI3, MB), and neuronal cells (PLP1, NRXN1)

summary:
In Homo sapiens heart tissue, mononuclear phagocytes are characterized by the expression of CD14 and CD68.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:a37ef38199459a26d466
claim_id: claim:a37ef38199459a26d466
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Nine broad cell lineages were identified in the heart specimens: T and NK cells (characterized by the expression of CD3D and KLRB1), MNPs (CD14, CD68), DCs (CD1C, CLEC9A, IRF8), B cells and plasmablasts (CD79A, MZB1), endothelial cells (VWF, CA4), mural cells (RGS5, KCNJ8), fibroblasts (DCN, PDGFRA), cardiomyocytes (TNNI3, MB), and neuronal cells (PLP1, NRXN1)

summary:
In Homo sapiens heart tissue, dendritic cells are characterized by the expression of CD1C, CLEC9A, and IRF8.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:11a76e326a753dd0fc09
claim_id: claim:11a76e326a753dd0fc09
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
summary:
In Homo sapiens heart tissue, B cells and plasmablasts are characterized by the expression of CD79A and MZB1.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:97fff016d1b1cc6c71fb
claim_id: claim:97fff016d1b1cc6c71fb
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Unsupervised clustering of 232,929 cells that passed QC filters (Methods) identified all known blood immune cell lineages, defined by canonical markers: CD8 T cells and NK cells (CD3D, CD8A, KLRF1); CD4 T cells (CD3D, CD4); MNPs (LYZ, CD14); DCs, representing both plasmacytoid dendritic cells (pDCs) (LILRA4) and cDCs (CD1C, CLEC9A); and B and plasmablast cells (CD79A, JCHAIN)

summary:
In Homo sapiens blood, CD8 T cells and natural killer cells are defined by the canonical markers CD3D, CD8A, and KLRF1.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:dacdfd6d271850a60ae9
claim_id: claim:dacdfd6d271850a60ae9
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
summary:
In Homo sapiens blood, conventional dendritic cells are defined by the canonical markers CD1C and CLEC9A.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:9e8d58a0cfa2c10cb3fb
claim_id: claim:9e8d58a0cfa2c10cb3fb
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
summary:
In Homo sapiens blood, B and plasmablast cells are defined by the canonical markers CD79A and JCHAIN.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:e65a6904338ed449d103
claim_id: claim:e65a6904338ed449d103
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Two CD8 T cell subsets – cluster 2 (h-CD8TCD27,LAG3), which is defined by the expression of CD27 and LAG3, and cluster 6 (h-CD8Tcycling), which is defined by a cycling cell signature (e.g., STMN1, TOP2A) – expressed a spectrum of activation and exhaustion markers (e.g., CTLA4, PDCD1, and TOX) as well as the chemokine receptor CXCR3.

summary:
In Homo sapiens heart tissue, the h-CD8T CD27,LAG3 subset is defined by the expression of CD27 and LAG3 and expresses activation and exhaustion markers CTLA4, PDCD1, TOX, and the chemokine receptor CXCR3.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:737c1d45e1ae17850223
claim_id: claim:737c1d45e1ae17850223
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Two CD8 T cell subsets – cluster 2 (h-CD8TCD27,LAG3), which is defined by the expression of CD27 and LAG3, and cluster 6 (h-CD8Tcycling), which is defined by a cycling cell signature (e.g., STMN1, TOP2A) – expressed a spectrum of activation and exhaustion markers (e.g., CTLA4, PDCD1, and TOX) as well as the chemokine receptor CXCR3.

summary:
In Homo sapiens heart tissue, the h-CD8T cycling subset is defined by a cycling cell signature including STMN1 and TOP2A and expresses activation and exhaustion markers CTLA4, PDCD1, TOX, and the chemokine receptor CXCR3.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:d6dbee0a22a1488cb883
claim_id: claim:d6dbee0a22a1488cb883
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Cluster 4 (h-CD8TCCL5,NKG7) captured a CD8 T cell population expressing CCL5 and NKG7 and also included a small group of cycling cells with lower expression of exhaustion markers like LAG3 and TOX.

summary:
In Homo sapiens heart tissue, the h-CD8T CCL5,NKG7 subset is a CD8 T cell population expressing CCL5 and NKG7.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:6e0b4aaed0e614602910
claim_id: claim:6e0b4aaed0e614602910
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Finally, cluster 5 (h-CD8TKLRG1,CX3CR1) comprises CD8 T cells distinctly expressing KLRG1 and CX3CR1, which are markers known to define short-lived effector cells40.

summary:
In Homo sapiens heart tissue, the h-CD8T KLRG1,CX3CR1 subset comprises CD8 T cells distinctly expressing KLRG1 and CX3CR1, which are markers known to define short-lived effector cells.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:4f8f6a5b5ecf2cdfb1f0
claim_id: claim:4f8f6a5b5ecf2cdfb1f0
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Expression of LYVE1 and C1QA distinguished one MNP subset (cluster 2), which likely represents cardiac resident macrophages47,48.

summary:
In Homo sapiens heart tissue, expression of LYVE1 and C1QA distinguishes a mononuclear phagocyte subset that likely represents cardiac resident macrophages.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:92b4552df65e8fba756e
claim_id: claim:92b4552df65e8fba756e
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
MNP cluster 3 expressed FCGR3A, and the immune checkpoint molecules LILRB1 and LILRB2, which confer inhibitory signals to MNPs (Figure 4b, 4d)49,50.

summary:
In Homo sapiens heart tissue, mononuclear phagocyte cluster 3 (h-MNP FCGR3A,LILRB2) expresses FCGR3A, LILRB1, and LILRB2.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:568a8af607714a0f39de
claim_id: claim:568a8af607714a0f39de
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Additional MNP populations were characterized by the expression of S100A8, S100A12, and VCAN (cluster 4), and the expression of TREM2 and APOC1 (cluster 5) (Figure 4b).

summary:
In Homo sapiens heart tissue, mononuclear phagocyte cluster 4 is characterized by the expression of S100A8, S100A12, and VCAN, while mononuclear phagocyte cluster 5 is characterized by the expression of TREM2 and APOC1.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:2aff49cb7e51e9a6e3a9
claim_id: claim:2aff49cb7e51e9a6e3a9
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Additional MNP populations were characterized by the expression of S100A8, S100A12, and VCAN (cluster 4), and the expression of TREM2 and APOC1 (cluster 5) (Figure 4b).

summary:
In Homo sapiens heart tissue, mononuclear phagocyte cluster 5 is characterized by the expression of TREM2 and APOC1.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:79b25ac1967f2d9af9bd
claim_id: claim:79b25ac1967f2d9af9bd
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Among cDCs (cluster 6, defined by CLEC9A and CD1C expression), a subset expressed FLT3, which is a critical homeostatic signal for DC maintenance51 (Figure 4d).

summary:
In Homo sapiens heart tissue, conventional dendritic cells (cluster 6) are defined by CLEC9A and CD1C expression, and a subset expresses FLT3.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:193e246205ae9ab2a4a5
claim_id: claim:193e246205ae9ab2a4a5
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
summary: In Homo sapiens heart tissue, capillary endothelial cells are distinguished by CA4 expression.
span_literal:
Within the endothelial cell compartment, there were three capillary endothelial cell populations distinguished by CA4 expression63,64, two arterial endothelial cell populations characterized by HEY1 expression65, a population of inflammatory endothelial cells expressing multiple ISGs, such as GBP5 and IFITM1, a venous endothelial population expressing marker ACKR166, and lymphatic endothelial cells distinguished by PDPN and CCL21 expression63,67.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:74ee718b4f71177c67ed
claim_id: claim:74ee718b4f71177c67ed
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Within the endothelial cell compartment, there were three capillary endothelial cell populations distinguished by CA4 expression63,64, two arterial endothelial cell populations characterized by HEY1 expression65, a population of inflammatory endothelial cells expressing multiple ISGs, such as GBP5 and IFITM1, a venous endothelial population expressing marker ACKR166, and lymphatic endothelial cells distinguished by PDPN and CCL21 expression63,67.

summary:
In Homo sapiens heart tissue, inflammatory endothelial cells express multiple interferon-stimulated genes such as GBP5 and IFITM1.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:80232171d7ad5c7b6d77
claim_id: claim:80232171d7ad5c7b6d77
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
summary:
In Homo sapiens heart tissue, lymphatic endothelial cells are distinguished by PDPN and CCL21 expression.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:e4cf2a10a6ad69acbea3
claim_id: claim:e4cf2a10a6ad69acbea3
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
summary: In Homo sapiens heart tissue, fibroblasts are defined by expression of DCN and LUM.
span_literal:
Amongst all non-immune subsets, only fibroblasts (defined by expression of DCN and LUM) were more enriched in irMyocarditis tissue (cluster 4; OR 3.8; 95% CI 1.5 – 9.7; p = 0.042)


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:3ad7db2e278ed2a82c2a
claim_id: claim:3ad7db2e278ed2a82c2a
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
b-CD8Tcycling is defined by expression of CXCR3, cycling genes (MKI67, STMN1), and CD45RO surface protein, indicating that these are antigen-exposed and dividing cells (Figure 3i).

summary:
In Homo sapiens blood, the b-CD8T cycling subset is defined by expression of CXCR3, cycling genes MKI67 and STMN1, and CD45RO surface protein.


claim_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe:claim:8093b4a8d36901a6f41a
claim_id: claim:8093b4a8d36901a6f41a
paper_key: biorxiv:5a3c7d4e-70da-1014-80b6-cd48bfa975fe
span_literal:
Marker genes that defined h-CD4TIL7R,LTB include a mixture of naive (CCR7 and MAL), regulatory (IL2RA and FOXP3), and memory (LTB and FLT3LG) CD4 T cells39, but given the small number of cells in the h-CD4TIL7R,LTB subset (n = 1,401 cells), further subsetting analysis was not explored.

summary:
In Homo sapiens heart tissue, the h-CD4T IL7R,LTB subset is defined by marker genes including naive markers CCR7 and MAL, regulatory markers IL2RA and FOXP3, and memory markers LTB and FLT3LG.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:6166bb18f06cf91beb8c
claim_id: claim:6166bb18f06cf91beb8c
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
The two most abundant populations displayed mutually exclusive expression of known myoepithelial-like (e.g., ACTA2, CNN1, TP63) and ductal-like (KRT7, KRT18, ELF5) markers

summary:
In Homo sapiens adenoid cystic carcinoma, myoepithelial-like cells express ACTA2, CNN1, and TP63, while ductal-like cells express KRT7, KRT18, and ELF5.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:23a0bbcf901037647808
claim_id: claim:23a0bbcf901037647808
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
while a third population appeared to represent a highly proliferating (MKI67high, TOP2Ahigh, CDK1high, PCNAhigh) subset of the population expressing ductal-like markers

summary:
In Homo sapiens adenoid cystic carcinoma, proliferating ductal-like cells express high levels of MKI67, TOP2A, CDK1, and PCNA.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:e9cacc9c63ab3c2f4e4b
claim_id: claim:e9cacc9c63ab3c2f4e4b
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
Among the genes displaying the highest differential expression between the two main clusters, we identified cell-surface markers CD49f (ITGA6), and KIT/CD117 (KIT), which were preferentially detected in cells associated with myoepithelial-like and ductal-like markers, respectively

summary:
In Homo sapiens adenoid cystic carcinoma, ITGA6 (CD49f) is preferentially expressed in myoepithelial-like cells, while KIT (CD117) is preferentially expressed in ductal-like cells.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:e214e07947480a280293
claim_id: claim:e214e07947480a280293
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
Among the genes displaying the highest differential expression between the two main clusters, we identified cell-surface markers CD49f (ITGA6), and KIT/CD117 (KIT), which were preferentially detected in cells associated with myoepithelial-like and ductal-like markers, respectively

summary:
In Homo sapiens adenoid cystic carcinoma, KIT (CD117) is preferentially expressed in ductal-like cells compared to myoepithelial-like cells.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:82241d97330d0fe15c01
claim_id: claim:82241d97330d0fe15c01
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
Analysis of the same tumors by immunohistochemistry (IHC) confirmed that KIT expression was restricted to cells with ductal-like morphology, and mutually exclusive to expression of TP63, a marker of myoepithelial-like cells, in agreement with previous reports9

summary:
In Homo sapiens adenoid cystic carcinoma, KIT expression is restricted to ductal-like cells, while TP63 is a marker of myoepithelial-like cells.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:fc5b8976bac883a81c83
claim_id: claim:fc5b8976bac883a81c83
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
Analysis of the same tumors by immunohistochemistry (IHC) confirmed that KIT expression was restricted to cells with ductal-like morphology, and mutually exclusive to expression of TP63, a marker of myoepithelial-like cells, in agreement with previous reports9

summary:
In Homo sapiens adenoid cystic carcinoma, TP63 is a marker of myoepithelial-like cells, with expression mutually exclusive to KIT in ductal-like cells.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:b798e0b5a8e0e3b05856
claim_id: claim:b798e0b5a8e0e3b05856
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
Among the genes preferentially expressed by CD49fhigh/KITneg cells were several well-established markers of the myoepithelial lineage (e.g., ACTA2, MYH11, PDPN, TP63)16, 17.

summary:
In Homo sapiens adenoid cystic carcinoma, CD49f-high/KIT-negative myoepithelial-like cells preferentially express ACTA2, MYH11, PDPN, and TP63, which are well-established markers of the myoepithelial lineage.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:e72316879a453a462a68
claim_id: claim:e72316879a453a462a68
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
Among the genes preferentially expressed by CD49flow/KIT+ cells were several well-established markers of the ductal and luminal lineage in ectodermal secretory glands (e.g., ELF5, KIT, SLPI, ANXA8)18–21.

summary:
In Homo sapiens adenoid cystic carcinoma, CD49f-low/KIT-positive ductal-like cells preferentially express ELF5, KIT, SLPI, and ANXA8, which are well-established markers of the ductal and luminal lineage.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:fe4d9bcd486a29014e7f
claim_id: claim:fe4d9bcd486a29014e7f
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
we identified two cell-surface markers (CD49f, KIT) that enable the differential purification of myoepithelial-like (CD49fhigh/KITneg) and ductal-like (CD49flow/KIT+) cells from ACC patient derived xenografts (PDX)

summary:
In Homo sapiens adenoid cystic carcinoma, CD49f (ITGA6) is highly expressed in myoepithelial-like cells while KIT is negative, enabling their differential purification from ductal-like cells.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:ae12f8ec8339ae4438b7
claim_id: claim:ae12f8ec8339ae4438b7
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
we identified two cell-surface markers (CD49f, KIT) that enable the differential purification of myoepithelial-like (CD49fhigh/KITneg) and ductal-like (CD49flow/KIT+) cells from ACC patient derived xenografts (PDX)

summary:
In Homo sapiens adenoid cystic carcinoma, KIT is positively expressed in ductal-like cells while CD49f is low, enabling their differential purification from myoepithelial-like cells.


claim_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650:claim:90eb15650e026f27d928
claim_id: claim:90eb15650e026f27d928
paper_key: biorxiv:5c1d40eb-7190-1014-a458-8ab6cf3c7650
span_literal:
IHC analysis of KIT and TP63 expression ACCX9 and ACCX11, showing ubiquitous expression of the ductal-specific marker KIT (c,e) and loss of the myoepithelial-specific marker TP63 (d,f).

summary:
In Homo sapiens solid adenoid cystic carcinoma, KIT is a ductal-specific marker with ubiquitous expression, while the myoepithelial-specific marker TP63 is lost.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:5d843dcac4f567b1e314
claim_id: claim:5d843dcac4f567b1e314
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
the 9 of 10 markers (CCR7, LEF1, SELL, LDLRAP1, NOSIP, PRKCQ−AS1, TXK, TMEM123, NELL2) in CRC_C4 were found in the cell markers of naïve CD8+ T cell

summary:
In Homo sapiens, CCR7, LEF1, SELL, LDLRAP1, NOSIP, PRKCQ-AS1, TXK, TMEM123, and NELL2 are markers of naïve CD8+ T cell in colorectal cancer.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:62da2d19c42c3b3a7f5b
claim_id: claim:62da2d19c42c3b3a7f5b
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
summary: In Homo sapiens, GZMK is a marker of an undefined common CD8+ T cell cluster across cancers.
span_literal:
We noted that there was a common cluster with a same marker named GZMK that couldn’t be well-defined, either.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:c097a15814212168eaf8
claim_id: claim:c097a15814212168eaf8
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
In the pre_exhausted vs. effector comparison, there were 73 DEGs existed in all three cancers, 71 of whom were in the same regulatory status (Figure 2B) including the known exhaustion marker PDCD1 (programmed cell deathLJ1) and CD27 (CD27 molecule).

summary:
In Homo sapiens, PDCD1 (programmed cell death 1) and CD27 are markers of pre-exhausted CD8+ T cells compared with effector CD8+ T cells across colorectal cancer, hepatocellular carcinoma, and non-small cell lung cancer.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:f41a1841186bd1821c1e
claim_id: claim:f41a1841186bd1821c1e
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
there were 7 upregulated DEGs, including GPR171 (G protein-coupled receptor 171), TNFAIP3 (TNF alpha induced protein 3), CD96 (CD96 molecule), SAMSN1 (SAM domain, SH3 domain and nuclear localization signals 1, also known as HACS1), ZFP36 (ZFP36 ring finger protein), DUSP1 (dual specificity phosphatase 1), PDCD1, enriched in the negative regulation of immune system process.

summary:
In Homo sapiens, GPR171, TNFAIP3, CD96, SAMSN1 (SAM domain, SH3 domain and nuclear localization signals 1), ZFP36, DUSP1, and PDCD1 are upregulated in pre-exhausted CD8+ T cells and enriched in negative regulation of immune system process.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:369b08bd0dbb0756598b
claim_id: claim:369b08bd0dbb0756598b
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
In the exhausted vs. effector comparison, there were 159 DEGs existed in all three cancers (Figure 2C) including multiple known exhaustion markers such as PDCD1, HAVCR2 (hepatitis A virus cellular receptor 2, also known as T cell immunoglobulin and mucin-domain containing-3, Tim-3), TIGIT (T cell immunoglobulin and ITIM domain), TOX (thymocyte selection associated high mobility group box).

summary:
In Homo sapiens, PDCD1, HAVCR2 (hepatitis A virus cellular receptor 2), TIGIT (T cell immunoglobulin and ITIM domain), and TOX (thymocyte selection associated high mobility group box) are markers of exhausted CD8+ T cells compared with effector CD8+ T cells.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:9332739896d0d6d81a20
claim_id: claim:9332739896d0d6d81a20
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
Correspondingly, there were 14 DEGs, including 9 upregulated genes PDCD1, TIGIT, HAVCR2, CCL3 (C-C Motif Chemokine Ligand 3), DUSP1, TNFAIP3, PAG1 (phosphoprotein membrane anchor with glycosphingolipid microdomains 1), CDK6 (cyclin dependent kinase 6), SAMSN1, participated in the negative regulation of immune system process.

summary:
In Homo sapiens, PDCD1, TIGIT, HAVCR2, CCL3 (C-C motif chemokine ligand 3), DUSP1, TNFAIP3, PAG1 (phosphoprotein membrane anchor with glycosphingolipid microdomains 1), CDK6 (cyclin dependent kinase 6), and SAMSN1 are upregulated in exhausted CD8+ T cells and participate in negative regulation of immune system process.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:a4ac771ec2f49cbcf4d6
claim_id: claim:a4ac771ec2f49cbcf4d6
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
We found SAMSN1 was dysregulated during exhaustion state, which participated in the negative regulation of immune system process in both pre_exhausted and exhausted cells, showed poor survival in the validation based on TCGA data except for CRC (Figure 3B).

summary:
In Homo sapiens, SAMSN1 is upregulated in exhausted CD8+ T cells and participates in negative regulation of immune system process.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:06f17dc33279f706f050
claim_id: claim:06f17dc33279f706f050
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
summary: In Homo sapiens, ATM, RORA, and TBX21 are significantly downregulated in exhausted CD8+ T cells.
span_literal:
ATM, RORA, TBX21, which were the TFs of DUSP1, TUBA1B (tubulin alpha 1b), CXCR3 (C-X-C motif chemokine receptor 3) and IFNG (Interferon Gamma) respectively, were significantly downregulated in exhausted cells.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:b26008554b674ee66afd
claim_id: claim:b26008554b674ee66afd
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
Among the upregulated factors, JUN regulated more than 100 DEGs and may play a critical role in the occurrence and development of exhausted CD8+ T cells.

summary:
In Homo sapiens, JUN is upregulated in exhausted CD8+ T cells and may play a critical role in the occurrence and development of CD8+ T cell exhaustion.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:3b3f060ebaa07f1dee4f
claim_id: claim:3b3f060ebaa07f1dee4f
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
summary: In Homo sapiens, CD69 is upregulated in both pre-exhausted CD8+ T cells and exhausted CD8+ T cells.
span_literal:
CD69 was a hub gene of the module with the highest score and was upregulated in both pre_exhausted and exhausted cells.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:81220292923b2d50a993
claim_id: claim:81220292923b2d50a993
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
CD69 was upregulated and S1PR1 was downregulated significantly in the exhausted cells according to our study (Figure 3A).

summary:
In Homo sapiens, CD69 is upregulated and S1PR1 (sphingosine-1-phosphate receptor 1) is downregulated in exhausted CD8+ T cells.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:7afde9e3c4bf5c456ee5
claim_id: claim:7afde9e3c4bf5c456ee5
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
summary: In Homo sapiens, JUN is upregulated in both pre-exhausted CD8+ T cells and exhausted CD8+ T cells.
span_literal:
Based on our findings, JUN was upregulated in both pre_exhausted and exhausted cells and regulated over 100 DEGs.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:247ce5d75de3f2c32db2
claim_id: claim:247ce5d75de3f2c32db2
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
In the comparison of the common DEGs between pre_exhausted or exhausted and effector cells, SAMSN1 showed greater upregulation in the exhausted cells and was associated with poor prognosis in HCC and NSCLC based on TCGA data.

summary:
In Homo sapiens, SAMSN1 shows greater upregulation in exhausted CD8+ T cells compared with effector CD8+ T cells and is associated with poor prognosis in hepatocellular carcinoma and non-small cell lung cancer.


claim_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820:claim:7b0d9d5bae12d0556764
claim_id: claim:7b0d9d5bae12d0556764
paper_key: biorxiv:5daa9342-6d02-1014-8cb5-fa421631d820
span_literal:
In the current study, we integrated three cancers and found some key genes associated with T cell exhaustion, including the known markers PDCD1, HAVCR2, TIGIT, TOX.

summary:
In Homo sapiens, PDCD1, HAVCR2, TIGIT, and TOX are known markers associated with CD8+ T cell exhaustion across colorectal cancer, hepatocellular carcinoma, and non-small cell lung cancer.


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:f0a78ded87c72d8c0d88
claim_id: claim:f0a78ded87c72d8c0d88
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
span_literal:
ELANE, PRTN3, AZU1, MPO, PRSS57, CTSG and RNASE2), coding for markers of neutrophil precursors [43, 44] were predominantly or exclusively expressed in a sub-group of 116 cells, which we designated “promyelocytes

summary:
In Homo sapiens, promyelocytes are marked by expression of ELANE, PRTN3, AZU1, MPO, PRSS57, CTSG, and RNASE2, which are markers of neutrophil precursors.


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:a98a04539ae6dafd3b70
claim_id: claim:a98a04539ae6dafd3b70
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
span_literal: RETN, S100A8, S100A9 and S100A12), encoding proteins secreted by activated neutrophils
summary:
In Homo sapiens, activated neutrophils are marked by expression of RETN, S100A8, S100A9, and S100A12, encoding proteins secreted under pro-inflammatory conditions.


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:bd45bbdecb3c80710c32
claim_id: claim:bd45bbdecb3c80710c32
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
summary: In Homo sapiens, monocytes are identified by expression of CD14 and CD68.
span_literal:
other groups of cells were identified based on their expression of known markers such as CD14 and CD68 (monocytes), CD207/langerin and CD1a (Langerhans cells), CD1b (monocyte-derived dendritic cells), and hemoglobins (erythrocytes)


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:94a424812d0124099efa
claim_id: claim:94a424812d0124099efa
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
summary: In Homo sapiens, the cluster 7 cell group differentially expressed CD52 and FCER1A.
span_literal:
its closest neighbors, group E, F, G and H, expressed markers typical of the monocytes, erythrocytes, promyelocytes and activated neutrophils clusters in Fig 4C, respectively (S8 Fig and S9 Dataset). The most isolated cluster of cells, group B, was related to CL7 in Fig 4C, and differentially expressed CD52 and FCER1A


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:3534973efc7209253497
claim_id: claim:3534973efc7209253497
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
span_literal:
five of these nine genes encoded well-known type I interferon (IFN)-inducible proteins involved in mediating innate immune responses to viruses, i.e. MX1, OAS1, OAS2, IFIT3, and USP18

summary:
In Homo sapiens, CMV-negative bystander cells express higher levels of MX1, OAS1, OAS2, IFIT3, and USP18, which are type I interferon-inducible antiviral genes, compared to CMV-positive cells.


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:45d14e3f6b935097eef3
claim_id: claim:45d14e3f6b935097eef3
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
summary: In Homo sapiens, CMV-negative bystander cells express CYTIP and CD80.
span_literal:
the majority of CMV− cells also expressed the TNF-α and LPS-inducible protein CYTIP [40], and the CD40 ligand-inducible costimulatory molecule CD80 [41]


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:45759119d32af0dd1f25
claim_id: claim:45759119d32af0dd1f25
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
span_literal:
CMV+ cells contained lower transcript amounts of genes promoting entry into S phase, such as CCNA2, CCND3, MKI67 and RB1, but higher transcript levels of genes encoding inhibitors of S phase progression, including BTG1, BTG3, CCNDBP1, CDKN1A (Cip1) and the HSC quiescence-promoting gene NDN [57], which was almost exclusively expressed in CMV+ cells

summary:
In Homo sapiens, CMV-positive cells show lower expression of CCNA2, CCND3, MKI67, and RB1, and higher expression of BTG1, BTG3, CCNDBP1, CDKN1A, and NDN compared to colony forming unit – granulocyte, erythrocyte, monocyte, megakaryocyte cells.


claim_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524:claim:f4d0aaba3c13e1cf94ed
claim_id: claim:f4d0aaba3c13e1cf94ed
paper_key: biorxiv:5dff1c13-6c00-1014-9211-b5130fed8524
span_literal:
multiple lines of evidence indicate that CMV+ cells derive from a cluster with the hallmarks of GEMM colony forming units, albeit devoid of transcripts coding for some of the markers traditionally used to describe this population, i.e. CD34, CD38, and CD123

summary:
In Homo sapiens, the colony forming unit – granulocyte, erythrocyte, monocyte, megakaryocyte population identified in this study lacks expression of CD34, CD38, and CD123, which are markers traditionally used to describe this population.


claim_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc:claim:40ce24b16e35188c6975
claim_id: claim:40ce24b16e35188c6975
paper_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc
span_literal:
One RNAScope/IF marker combination “Star” included SLC17A7 (marking Excit), TMEM119 (Micro), OLIG2 (Oligo), and AKT3.

summary:
In Homo sapiens dorsolateral prefrontal cortex, SLC17A7 is a positive marker of excitatory neurons, TMEM119 is a positive marker of microglia, and OLIG2 is a positive marker of oligodendrocytes.


claim_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc:claim:bed90d2950e0bf089448
claim_id: claim:bed90d2950e0bf089448
paper_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc
summary: In Homo sapiens dorsolateral prefrontal cortex, GFAP is a positive marker of astrocytes.
span_literal:
The second combination “Circle” included GFAP (Astro), CLDN5 (Endo), and GAD1 (Inhib), and AKT3 (Figure 2A, Fig S1B, Table S2).


claim_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc:claim:2751f3e0b517482e7338
claim_id: claim:2751f3e0b517482e7338
paper_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc
span_literal:
Segmentation was optimized for accurate identification of punctate AKT3 RNAScope/IF signals as well as each cellular object for excitatory neurons (SLC17A7), inhibitory neurons (GAD1), astrocytes (GFAP), microglia (TMEM119), oligodendrocytes (OLIG2), and endothelial/mural cells (Claudin 5: CLDN5), using user-defined size and intensity thresholds.

summary:
In Homo sapiens dorsolateral prefrontal cortex, SLC17A7 marks excitatory neurons, GAD1 marks inhibitory neurons, GFAP marks astrocytes, TMEM119 marks microglia, OLIG2 marks oligodendrocytes, and CLDN5 marks endothelial/mural cells.


claim_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc:claim:32c76d6f5e88d0c0f1e8
claim_id: claim:32c76d6f5e88d0c0f1e8
paper_key: biorxiv:5fae8fc7-72f2-1014-971d-e6aa985407bc
span_literal:
In contrast, the top marker genes selected by 1vALL showed some expression in non-target cell types (i.e., PLP1, an Oligo marker gene, had some expression in several non-Oligo cell types), (Figure 3D).

summary:
In Homo sapiens dorsolateral prefrontal cortex, PLP1 is a positive marker gene for oligodendrocytes, though it also shows some expression in non-oligodendrocyte cell types.


claim_key: biorxiv:5fd70652-7063-1014-8342-ff2da9e49a40:claim:9a18da5113f8f281015e
claim_id: claim:9a18da5113f8f281015e
paper_key: biorxiv:5fd70652-7063-1014-8342-ff2da9e49a40
summary: In Homo sapiens, the RETN gene is highly expressed in neutrophils and monocytes in sepsis patients.
span_literal:
The RETN gene, one of seven hub genes in the lactate metabolism pathway, was highly expressed in neutrophils and monocytes.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:e6d0a23a4318525de710
claim_id: claim:e6d0a23a4318525de710
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
FXYD2, SERPINF1, and RARRES2 are genes which have been identified as selectively expressed in pDCs in the literature and Human Protein Atlas

summary:
In Homo sapiens, FXYD2, SERPINF1, and RARRES2 are selectively expressed in plasmacytoid dendritic cells.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:823347e0476a5a111258
claim_id: claim:823347e0476a5a111258
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
summary: In Homo sapiens, MS4A1A and CD79A are marker genes associated with B cells.
span_literal:
Pf2 identified that component 12 was strongly associated with the amount of B cells in each drug perturbation experiment based on the genes identified by this component, including MS4A1A and CD79A


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:20c8f45fefc9c769fcb5
claim_id: claim:20c8f45fefc9c769fcb5
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
Component 14 selectively associated with Naïve CD4+ and CD8+ T cells, as well as Prolif, a subcategory of proliferating T cells (Fig. 4f). The sample associations of this component directly correlated with the cell abundances of these annotated lymphocyte populations (Fig. 4g). Consistent with explaining the abundance of these cell populations, the gene associations of component 14, including CCR7, LEF1, and PRKCQ-AS1 (Fig. 4e), have been previously characterized as crucial for early T cell development, cell identity, and T cell receptor complexes

summary:
In Homo sapiens, CCR7, LEF1, and PRKCQ-AS1 are marker genes associated with naïve CD4+ and CD8+ T cells.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:5edcd2dc729f67f77aab
claim_id: claim:5edcd2dc729f67f77aab
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
This component was associated with interferon (IFN)-induced genes, including IFI44, MX1, IFITM3, APOBEC3A, and ISG15 (Fig. 4e).

summary:
In Homo sapiens, IFI44, MX1, IFITM3, APOBEC3A, and ISG15 are interferon-induced genes associated with classical monocytes, non-classical monocytes, and conventional dendritic cell type 1.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:c82acb40dbcba470bfe7
claim_id: claim:c82acb40dbcba470bfe7
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
SPON2, FGFBP2, GZMB, PRF1 and GZMH were among the highly weighted genes associated with component 4 (Fig. 5a, S11). Many of the genes identified by this pattern also overlap with the genes previously used to define a cytotoxic signature for GZMH+ CD8+ T cells

summary:
In Homo sapiens, SPON2, FGFBP2, GZMB, PRF1, and GZMH are marker genes defining a cytotoxic signature for GZMH+ CD8+ T cells.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:94662497dc838a228f20
claim_id: claim:94662497dc838a228f20
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
In addition to RETN, the genes S100A8, S100A12, and S100A9 were highly weighted, which others have identified these as relevant to IL-6 signaling and activation of toll-like receptors 4 and 7 in SLE patients, prolonging inflammation (Fig. 5a, S11)

summary:
In Homo sapiens, RETN, S100A8, S100A12, and S100A9 are marker genes of a classical monocyte subpopulation relevant to interleukin-6 signaling in systemic lupus erythematosus patients.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:d39df46341504206855d
claim_id: claim:d39df46341504206855d
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal: component 28 identified many IFN genes including IFI27, IFI6, ISG15, IFITM3 and IFI44L (Fig 5c).
summary:
In Homo sapiens, IFI27, IFI6, ISG15, IFITM3, and IFI44L are interferon genes marking classical monocyte and CD4+ effector memory T cell subpopulations.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:eff2492e3ec531877d75
claim_id: claim:eff2492e3ec531877d75
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
Pf2 isolated rare subpopulations, such as pDCs, and their canonical markers including FXYD2 and RARRES2/chemerin

summary:
In Homo sapiens, FXYD2 and RARRES2 (chemerin) are canonical markers of plasmacytoid dendritic cells.


claim_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37:claim:c3cac64680bb4e4e2776
claim_id: claim:c3cac64680bb4e4e2776
paper_key: biorxiv:611722dd-8008-1014-b70e-fa0b81b0ac37
span_literal:
Component 20 described glucocorticoid-induced CD163 and MS4A6A expression across cMO and other cell types, as seen in earlier studies (Fig. 3b, q, S7)

summary:
In Homo sapiens, CD163 and MS4A6A are glucocorticoid-induced genes expressed in classical monocytes.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:d4129fd7f497f973d5fa
claim_id: claim:d4129fd7f497f973d5fa
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
Gene markers that distinguish the SCs from the pyramidal neurons are Reelin (RELN) and Calbindin (CALB1), respectively

summary:
In Homo sapiens, stellate cells are marked by Reelin (RELN) as distinguished from pyramidal neurons, while pyramidal neurons are marked by Calbindin (CALB1) as distinguished from stellate cells.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:144d8c44e3d716a07604
claim_id: claim:144d8c44e3d716a07604
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
Gene markers that distinguish the SCs from the pyramidal neurons are Reelin (RELN) and Calbindin (CALB1), respectively

summary:
In Homo sapiens, pyramidal neurons are marked by Calbindin (CALB1) as distinguished from stellate cells.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:295e893f942b7460ad12
claim_id: claim:295e893f942b7460ad12
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
The speed cells map to GABAergic inhibitory neurons which express parvalbumin (PVALB), but not somatostatin (SST)

summary:
In Homo sapiens, speed cells are GABAergic inhibitory neurons that express parvalbumin (PVALB) but not somatostatin (SST).


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:9d3913a3c6f71490d835
claim_id: claim:9d3913a3c6f71490d835
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
human induced pluripotent stem cells into stellate cell-like cells which expressed RELN, SATB2, LEF1 and BCL11B

summary:
In Homo sapiens, stellate cell-like cells reprogrammed from human induced pluripotent stem cells expressed RELN, SATB2, LEF1, and BCL11B.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:3deb2d750d101466ddd1
claim_id: claim:3deb2d750d101466ddd1
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
Together, the SC TFs induced co-expression of BCL11B, SATB2, and RELN, mirroring the unique molecular profile of EC SCs.

summary:
In Homo sapiens, entorhinal cortex stellate cells have a unique molecular profile characterized by co-expression of BCL11B, SATB2, and RELN.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:249e14776cd29554bb54
claim_id: claim:249e14776cd29554bb54
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
the coexpression of BCL11B and SATB2 highly favors a superficial or deep layer entorhinal neuron phenotype in the MEC

summary:
In Homo sapiens, co-expression of BCL11B and SATB2 is characteristic of entorhinal neurons in the medial entorhinal cortex.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:243224d6405102f75808
claim_id: claim:243224d6405102f75808
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
Interestingly, a significant increase (p <0.001) in RELN expression was observed only in the cells induced with expression of the SC TFs alone

summary:
In Homo sapiens, stellate cell-like cells induced with stellate cell transcription factors alone showed a significant increase in RELN expression.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:51724906ab6e7e358d7e
claim_id: claim:51724906ab6e7e358d7e
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal: LEF1 was upregulated in both treatments containing SC TFs but not in the Ngn2 alone treatment
summary:
In Homo sapiens, LEF1 was upregulated in stellate cell transcription factor-induced stellate cell-like cells but not in Ngn2-only neurons.


claim_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499:claim:cf5ca77645b31db91c48
claim_id: claim:cf5ca77645b31db91c48
paper_key: biorxiv:611ca78b-6e32-1014-bb2a-be11d7247499
span_literal:
The analyses indicate the SC TFs were able to induce the expression of BCL11B, SATB2, RELN, CALB1 and LEF1 in the human iPSCs derived neurons by D20.

summary:
In Homo sapiens, the stellate cell transcription factors induced expression of BCL11B, SATB2, RELN, CALB1, and LEF1 in human induced pluripotent stem cell-derived stellate cell-like neurons.


claim_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c:claim:e4fba33d8c7d6f8de266
claim_id: claim:e4fba33d8c7d6f8de266
paper_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c
span_literal:
by examining publicly available testicular scRNA-seq datasets from human infants and adults (GSE124263), we pinpointed a comparable CD34-MC subtype in both infantile and adult human testes

summary:
In Homo sapiens, a CD34-positive mesenchymal cell subtype was identified in both infantile and adult testes, marked by CD34 expression.


claim_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c:claim:62c51a63fd755495ca11
claim_id: claim:62c51a63fd755495ca11
paper_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c
span_literal:
Violin plots depict CD34 and SOX4 expression in human CD34-MC cells at both infant and adult developmental stages.

summary:
In Homo sapiens, CD34-positive mesenchymal cells in the testis express CD34 and SOX4 at both infant and adult developmental stages.


claim_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c:claim:bffc89445402c1fbc011
claim_id: claim:bffc89445402c1fbc011
paper_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c
span_literal:
Previous research has documented the presence of CD34+ mesenchymal cells within both fetal and adult human testes(Kuroda et al., 2004).

summary:
In Homo sapiens, CD34-positive mesenchymal cells have been documented in both fetal and adult testes, marked by CD34 expression.


claim_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c:claim:24a552e908cbeb3d073a
claim_id: claim:24a552e908cbeb3d073a
paper_key: biorxiv:63193ce6-7148-1014-9e66-9730890de51c
summary: In Homo sapiens, telocytes in the testicular interstitial spaces express CD34 and PDGFRα.
span_literal:
Recent morphological studies have further uncovered CD34+PDGFRα+ telocytes in the interstitial spaces of mouse, rat, and human testes.


claim_key: biorxiv:64ab9878-6ed8-1014-99e3-9a1ae6ef730b:claim:f7c248b97b7ea1d947e5
claim_id: claim:f7c248b97b7ea1d947e5
paper_key: biorxiv:64ab9878-6ed8-1014-99e3-9a1ae6ef730b
summary: In Homo sapiens, plasma cells are identified by IgA and CD138 as positive markers.
span_literal:
We demonstrated this capability using the GVHD dataset 40, where plasma cells are identified using a unique marker (IgA) instead of the more common CD138 marker.


claim_key: biorxiv:64ab9878-6ed8-1014-99e3-9a1ae6ef730b:claim:52fdbc42af87cdf6fbc6
claim_id: claim:52fdbc42af87cdf6fbc6
paper_key: biorxiv:64ab9878-6ed8-1014-99e3-9a1ae6ef730b
span_literal:
Despite sharing only the CD38 marker with other datasets (which is not exclusive to plasma cells), our model robustly recognizes plasma cells in the GVHD dataset when trained on all other datasets (Fig. 2g).

summary:
In Homo sapiens, CD38 is a positive marker of plasma cells, though it is not exclusive to plasma cells.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:12344529cda23454c08f
claim_id: claim:12344529cda23454c08f
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
A large fraction of loaded B cells exhibited a phenotype consistent with plasmablasts (PBs) or plasma cells (PCs; CD19loCD38+), which may represent antibody secreting cells (ASCs).

summary:
In Homo sapiens, plasmablasts and plasma cells are characterized by low CD19 and positive CD38 expression, representing antibody-secreting cells.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:ebf413da52de114d5e06
claim_id: claim:ebf413da52de114d5e06
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal: A small portion of loaded cells exhibited a phenotype of activated B cells (CD19hiCD38lo).
summary:
In Homo sapiens, activated B cells are characterized by high CD19 expression and low CD38 expression.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:fee828f52ab05094c7fd
claim_id: claim:fee828f52ab05094c7fd
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
Of the DN cells, we observed increased proportions of IgG secreting cells depending on the expression of PB/PC maturation markers: low in immature PBs (CD38+CD138lo; ∼20% IgG), intermediate in PBs (CD38++CD138lo; ∼60% IgG) and high in PCs (CD38++CD138hi; ∼80% IgG, Fig. 2c).

summary:
In Homo sapiens, immature plasmablasts are marked by CD38 positive and CD138 low expression, plasmablasts by CD38 high and CD138 low expression, and plasma cells by CD38 high and CD138 high expression.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:d65085ebd3d6211eb404
claim_id: claim:d65085ebd3d6211eb404
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
summary: In Homo sapiens, CD138 positivity is the best marker to identify a B cell as an IgG-secreting cell.
span_literal:
Overall, these data showed that CD138 positivity was the best marker to identify a B cell as an IgG secretor or not (Fig. 2c).


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:1e2ced6d6956d4c2f7ca
claim_id: claim:1e2ced6d6956d4c2f7ca
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
summary: In Homo sapiens, CD138-high plasma cells are the predominant source of secreted IgG.
span_literal:
Collectively, these data indicate that CD138hi PCs are the predominant source of secreted IgG in human plasma cell cultures.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:c82051801027da650375
claim_id: claim:c82051801027da650375
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
factors conventionally associated with PB/PC differentiation (XBP1, IRF4, PRDM1) were expressed uniformly in all subclusters, regardless of antibody isotype identity or IgG secretion level (Fig. 4d).

summary:
In Homo sapiens, XBP1, IRF4, and PRDM1 are conventionally associated with plasmablast and plasma cell differentiation and are expressed uniformly across all subclusters.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:4d337fbf18655bb914d1
claim_id: claim:4d337fbf18655bb914d1
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
summary: In Homo sapiens, plasma cell progenitors express the markers PAX5 and CD19.
span_literal:
One subcluster within the IgG group expressed the PC progenitor markers PAX5 and CD19 but exhibited a similar percentage of IgG-secretors (cluster 8, Fig. 5d-e), demonstrating that a subset of PC progenitors are capable of IgG secretion.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:6245acc2e3af7bf46b9a
claim_id: claim:6245acc2e3af7bf46b9a
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
Finally, although the PC markers CD38, PRDM1 (also known as BLIMP1), and TNFRSF17 (also known as BCMA) do not vary greatly among the subclusters, XBP1 (a master regulator of the unfolded protein response) is enriched in clusters 9 and 10,11 those that have the largest numbers of IgG-secreting cells (Fig. 5d-e).

summary:
In Homo sapiens, plasma cell markers include CD38, PRDM1 (also known as BLIMP1), and TNFRSF17 (also known as BCMA), while XBP1 is enriched in clusters with the largest numbers of IgG-secreting cells.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:2b9c60a624689c9c1317
claim_id: claim:2b9c60a624689c9c1317
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
Several UPR-relevant genes, e.g. SSR3, SSR4, and SEC61B, are known for being highly expressed in PCs11,14.

summary:
In Homo sapiens, the unfolded protein response-relevant genes SSR3, SSR4, and SEC61B are highly expressed in plasma cells.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:4f5023bdb8dc4759ace2
claim_id: claim:4f5023bdb8dc4759ace2
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
CD138 has long been identified as a marker of differentiated human PCs, including long-lived PCs20,21 that functionally regulates plasma cell survival in the bone marrow22,23.

summary:
In Homo sapiens, CD138 has long been identified as a marker of differentiated plasma cells, including long-lived plasma cells.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:0e582a4a2a70662edd86
claim_id: claim:0e582a4a2a70662edd86
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
Here, we provide definitive evidence that CD138 is a useful marker for ex vivo differentiated human PCs that are actively secreting IgG.

summary:
In Homo sapiens, CD138 is a useful marker for ex vivo differentiated plasma cells that are actively secreting IgG.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:9aa1809e09273cfa6277
claim_id: claim:9aa1809e09273cfa6277
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
Protein secretion by PCs is regulated by a transcriptional program dependent on PRDM1 (also known as Blimp1) and the unfolded protein response gene, XBP1.

summary:
In Homo sapiens, protein secretion by plasma cells is regulated by a transcriptional program dependent on PRDM1 (also known as BLIMP1) and the unfolded protein response gene XBP1.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:5906df4dfd5e4f369e25
claim_id: claim:5906df4dfd5e4f369e25
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
We also identified several unexpected genes that are increased in IgG secretors and may be critical for their function including CD79A, the complement regulator CD59 and macrophage inhibitory factor MIF, which could regulate cells in the PC bone marrow microenvironment.

summary:
In Homo sapiens, IgG-secreting plasma cells show increased expression of CD79A, the complement regulator CD59, and macrophage inhibitory factor MIF.


claim_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96:claim:5ee9a85427c4fa6c85b5
claim_id: claim:5ee9a85427c4fa6c85b5
paper_key: biorxiv:653bfd04-6cbf-1014-864b-c74846f5cd96
span_literal:
Contrary to our expectation, we found that transporters of fructose (SLC2A5), but not glucose (e.g. SLC2A1) were expressed more highly in IgG secretors.

summary:
In Homo sapiens, IgG-secreting plasma cells express higher levels of the fructose transporter SLC2A5 but not the glucose transporter SLC2A1 compared to non-secretors.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:4c02cc5392cfe94f5136
claim_id: claim:4c02cc5392cfe94f5136
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
co-expression of cell surface proteins CD24, CD44 and EpCAM/ESA marks cells with enhanced tumourigenic potential13

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, co-expression of CD24, CD44, and EpCAM marks stem-like cells with enhanced tumorigenic potential.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:62708caeb262f345b602
claim_id: claim:62708caeb262f345b602
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
cells positive for CD914, CD13315, Nestin24,25, DCLK121, ALDH28 or Musashi-1/226 have also been shown to have stem cell properties

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, cells positive for CD9, CD133, Nestin, DCLK1, ALDH, or Musashi-1/Musashi-2 have been shown to have stem cell properties.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:023c116e94033f7c11d7
claim_id: claim:023c116e94033f7c11d7
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
Based on the canonical marker expression, the epithelial cells (CD326/EpCAM+), fibroblasts (vimentin+, CD326/EpCAM- and CD45-) and immune cells (CD45+) were identified within every patient sample with the epithelial cells being the most abundant cell type

summary:
In Homo sapiens pancreatic ductal adenocarcinoma patient samples, epithelial cells are identified by CD326/EpCAM positivity.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:01c31e90f80334862226
claim_id: claim:01c31e90f80334862226
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
Based on the canonical marker expression, the epithelial cells (CD326/EpCAM+), fibroblasts (vimentin+, CD326/EpCAM- and CD45-) and immune cells (CD45+) were identified within every patient sample with the epithelial cells being the most abundant cell type

summary:
In Homo sapiens pancreatic ductal adenocarcinoma patient samples, fibroblasts are identified by vimentin positivity, EpCAM negativity, and CD45 negativity.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:c74685d944e56920f6ec
claim_id: claim:c74685d944e56920f6ec
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
Based on the canonical marker expression, the epithelial cells (CD326/EpCAM+), fibroblasts (vimentin+, CD326/EpCAM- and CD45-) and immune cells (CD45+) were identified within every patient sample with the epithelial cells being the most abundant cell type

summary:
In Homo sapiens pancreatic ductal adenocarcinoma patient samples, immune cells are identified by CD45 positivity.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:252805c4ad21607fcea7
claim_id: claim:252805c4ad21607fcea7
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
summary: In Homo sapiens, ROR gamma is a marker of T helper 17 cells.
span_literal:
The RORψ is a master transcriptional regulator of CD4 T cell differentiation and a marker of T helper 17 (Th17) cells47


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:98157a5b479856d224ad
claim_id: claim:98157a5b479856d224ad
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
This analysis highlighted Musashi-2, DCLK1 and CXCR4 as markers which are upregulated in all tested non-adherent samples

summary:
In Homo sapiens pancreatic ductal adenocarcinoma, Musashi-2, DCLK1, and CXCR4 are upregulated markers of stem-like cells enriched in non-adherent culture.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:ede5b554f99adfa4a67a
claim_id: claim:ede5b554f99adfa4a67a
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
In PANC-1 cell line, areas occupied by non-adherent cells are characterised by the high expression of Musashi-2, DCLK1, CXCR4 and CD24, and low or lower levels of ABCG2 and MET/HGFR

summary:
In Homo sapiens PANC-1 pancreatic ductal adenocarcinoma cell line, stem-like cells in non-adherent culture are characterized by high expression of Musashi-2, DCLK1, CXCR4, and CD24, and low levels of ABCG2 and MET/HGFR.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:9157edfaf80f7f330fbb
claim_id: claim:9157edfaf80f7f330fbb
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
In CFPAC1 cell line, non-adherent cells exhibit elevated levels of Musashi-1, Musashi-2, DCLK1, CXCR4 and ALDH, but express reduced levels of CD326/EpCAM, SSEA-4 and TRA-1-60

summary:
In Homo sapiens CFPAC1 pancreatic ductal adenocarcinoma cell line, stem-like cells in non-adherent culture exhibit elevated levels of Musashi-1, Musashi-2, DCLK1, CXCR4, and ALDH, but reduced levels of EpCAM, SSEA-4, and TRA-1-60.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:9088d032a5d40d4698b4
claim_id: claim:9088d032a5d40d4698b4
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
CXCR4 has been shown to mark a subpopulation of stem-like pancreatic cancer cells exhibiting enhanced invasive and metastatic properties15

summary:
In Homo sapiens pancreatic cancer, CXCR4 marks a subpopulation of stem-like cells exhibiting enhanced invasive and metastatic properties.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:9d6f84b9cb29fc8e3cfd
claim_id: claim:9d6f84b9cb29fc8e3cfd
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
DCLK1 is a bifunctional protein with kinase and microtubule-associated protein activity that identifies a rare population of long-lived, quiescent pancreatic progenitors facilitating regeneration and underlying tumour initiation104,105

summary:
In Homo sapiens, DCLK1 identifies a rare population of long-lived, quiescent pancreatic progenitor cells facilitating regeneration and underlying tumour initiation.


claim_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b:claim:aaab882d611ecfea450b
claim_id: claim:aaab882d611ecfea450b
paper_key: biorxiv:671955ed-77d7-1014-aa23-8c904fbe705b
span_literal:
Accordingly, DCLK1 is a putative marker of pancreatic cancer stem-like cells that is essential for their invasive and metastatic property108

summary:
In Homo sapiens, DCLK1 is a putative marker of pancreatic cancer stem-like cells essential for their invasive and metastatic properties.


claim_key: biorxiv:67812075-6cb0-1014-be80-b30d7aa39355:claim:3c72ac11d5b197d70e8b
claim_id: claim:3c72ac11d5b197d70e8b
paper_key: biorxiv:67812075-6cb0-1014-be80-b30d7aa39355
span_literal:
KI67 is a well-known marker of cell proliferation that decorates nucleoli in interphase cells and coats chromosomes during mitosis

summary:
In Homo sapiens, KI67 (MKI67) is a well-known positive marker of cell proliferation, decorating nucleoli in interphase cells and coating chromosomes during mitosis.


claim_key: biorxiv:67812075-6cb0-1014-be80-b30d7aa39355:claim:6ec4a744e4d5def0ae65
claim_id: claim:6ec4a744e4d5def0ae65
paper_key: biorxiv:67812075-6cb0-1014-be80-b30d7aa39355
span_literal:
Centromeres were visualized by indirect immunofluorescence for the integral kinetochore component CENP-C, which localizes to centromeres at all stages of the cell cycle

summary:
In Homo sapiens, CENP-C is a positive marker of centromeres, localizing to centromeres at all stages of the cell cycle in kinetochore-containing cells.


claim_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c:claim:e64b7ad42bad384e5276
claim_id: claim:e64b7ad42bad384e5276
paper_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c
span_literal: Gating of live CD56dim NK cells (i.e., CD45+ cisplatin- CD3- CD235- CD61- CD15-CD56dim CD16+)
summary:
In Homo sapiens, CD56dim natural killer cells are identified by positive expression of CD45, CD56dim, and CD16, and negative expression of CD3, CD235, CD61, and CD15.


claim_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c:claim:bd514f6f24ff4fef9f05
claim_id: claim:bd514f6f24ff4fef9f05
paper_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c
span_literal: The cell population in the G0 stage was gated based on pRb- Idu- CyclinB1low pH3- expression
summary:
In Homo sapiens, G0 stage cells are characterized by negative expression of phosphorylated retinoblastoma protein, 5-iodo-2-deoxyuridine, and phosphorylated histone 3, and low expression of cyclin B1.


claim_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c:claim:0cce98171a30b71c3828
claim_id: claim:0cce98171a30b71c3828
paper_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c
span_literal:
The cell populations in the G1, S, and G2 stages were gated based on pRb+ Idu- CyclinB1low pH3- expression, Idu+ pH3- expression, and Idu- CyclinB1high pH3- expression, respectively

summary:
In Homo sapiens, G1 stage cells are characterized by positive expression of phosphorylated retinoblastoma protein, negative 5-iodo-2-deoxyuridine, low cyclin B1, and negative phosphorylated histone 3.


claim_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c:claim:9d2b1badd81f6a87e9d1
claim_id: claim:9d2b1badd81f6a87e9d1
paper_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c
span_literal:
The cell populations in the G1, S, and G2 stages were gated based on pRb+ Idu- CyclinB1low pH3- expression, Idu+ pH3- expression, and Idu- CyclinB1high pH3- expression, respectively

summary:
In Homo sapiens, G2 stage cells are characterized by negative 5-iodo-2-deoxyuridine, high cyclin B1, and negative phosphorylated histone 3.


claim_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c:claim:980246f9b8ebe2eb24c1
claim_id: claim:980246f9b8ebe2eb24c1
paper_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c
span_literal:
CD107a is a marker of NK cell activity, indicating degranulation and cytotoxic function when present on the cell surface.

summary:
In Homo sapiens, CD107a is a positive marker of natural killer cell activity, indicating degranulation and cytotoxic function.


claim_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c:claim:6af37999201db9141ee3
claim_id: claim:6af37999201db9141ee3
paper_key: biorxiv:67d3e1aa-726e-1014-b774-e6c3f2e9206c
span_literal: we identified distinct populations of M-stage cells that are pH3+pS6+pMAPKAPK2+
summary:
In Homo sapiens, M-stage cells are identified by positive expression of phosphorylated histone 3, phosphorylated S6, and phosphorylated MAPKAPK2.


claim_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09:claim:84f5ec7621be5b5e3ea1
claim_id: claim:84f5ec7621be5b5e3ea1
paper_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09
span_literal:
Within the subset of CD8+ Tex cells, we distinguished two smaller subsets according to their gene expression markers, KLRG1+ CD8+ Tex cells and HSPA1B+ CD8+ Tex cells

summary:
In Homo sapiens colorectal cancer, exhausted CD8+ T cells were subdivided into KLRG1-positive exhausted CD8+ T cells and HSPA1B-positive exhausted CD8+ T cells based on their gene expression markers.


claim_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09:claim:9d52303eb8d37b8f958f
claim_id: claim:9d52303eb8d37b8f958f
paper_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09
span_literal:
KLRG1 is a marker of terminal differentiation of CD8+T cells (34), and the inhibitory receptor of ILC1s (group 1 innate lymphoid cells), ILC2s, and NK cells (38).

summary:
In Homo sapiens, KLRG1 is a marker of terminal differentiation of CD8+ T cells and an inhibitory receptor of group 1 innate lymphoid cells, group 2 innate lymphoid cells, and natural killer cells.


claim_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09:claim:3449a2194530c30ec64a
claim_id: claim:3449a2194530c30ec64a
paper_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09
summary: In Homo sapiens, group 1 innate lymphoid cells in tumors express high levels of KLRG1.
span_literal:
ILC1s in tumors express high levels of the KLRG1 gene and pro-angiogenic activity and may even promote tumor progression in TGF-beta-rich tumors (38).


claim_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09:claim:3591e84ebde2aa4546c5
claim_id: claim:3591e84ebde2aa4546c5
paper_key: biorxiv:6957b39f-6c1d-1014-b3ca-de0b9fc09a09
span_literal:
we re-clustered the Treg cells and identified four Treg cell subsets, namely, TXNIP+ Treg cells, TNFRSF4+ Treg cells, HSPA1A+ Treg cells, and IFIT1+ Treg cells

summary:
In Homo sapiens colorectal cancer, regulatory T cells were subdivided into TXNIP-positive regulatory T cells, TNFRSF4-positive regulatory T cells, HSPA1A-positive regulatory T cells, and IFIT1-positive regulatory T cells.


claim_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849:claim:8187f0e4989067bce4db
claim_id: claim:8187f0e4989067bce4db
paper_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849
span_literal: As expected, FOXC2 was also specifically expressed in the human SSCs, most of which were MKI67-
summary:
In Homo sapiens, forkhead box protein C2 (FOXC2) is a positive marker of spermatogonial stem cells, and most FOXC2-expressing spermatogonial stem cells are negative for MKI67.


claim_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849:claim:27c2bf8174b572251d15
claim_id: claim:27c2bf8174b572251d15
paper_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849
span_literal:
Immunofluorescence staining confirmed that FOXC2+ cells were a subset of ZBTB16+ spermatogonia in adult human testis, and most of them were MKI67-

summary:
In Homo sapiens adult testis, FOXC2-positive cells are a subset of ZBTB16-positive spermatogonia, and most FOXC2-positive spermatogonia are MKI67-negative.


claim_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849:claim:789319773ca07878894b
claim_id: claim:789319773ca07878894b
paper_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849
span_literal:
These results suggested that FOXC2 was similarly expressed in the SSCs of adult human and mouse testis and may possess a conserved function.

summary:
In Homo sapiens, FOXC2 (forkhead box protein C2) is expressed in spermatogonial stem cells of the adult testis.


claim_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849:claim:e93fb9ee2eefd4943691
claim_id: claim:e93fb9ee2eefd4943691
paper_key: biorxiv:6b7b2bfb-6c3e-1014-b4a7-d4f626fa4849
span_literal:
Pseudotime analysis showed that the FOXC2+ cells located at the start of the developmental trajectory with a proportion of about 90% that were MKI67-

summary:
In Homo sapiens, FOXC2-positive spermatogonial stem cells are located at the start of the developmental trajectory, and approximately 90% are MKI67-negative.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:fe89e9d834ea99fb8fc1
claim_id: claim:fe89e9d834ea99fb8fc1
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of primitive streak genes EOMES (pan-mesendoderm transcription factor), MESP1 (cardiogenic mesoderm transcription factor), and SOX17 (definitive endoderm transcription factor)

summary:
In Homo sapiens, EOMES is a marker of mesendoderm, MESP1 is a marker of cardiogenic mesoderm, and SOX17 is a marker of definitive endoderm during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:4eb223f750c7be915ae6
claim_id: claim:4eb223f750c7be915ae6
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of primitive streak genes EOMES (pan-mesendoderm transcription factor), MESP1 (cardiogenic mesoderm transcription factor), and SOX17 (definitive endoderm transcription factor)

summary:
In Homo sapiens, MESP1 is a marker of cardiogenic mesoderm during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:f95c8e6cddcc89122562
claim_id: claim:f95c8e6cddcc89122562
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of primitive streak genes EOMES (pan-mesendoderm transcription factor), MESP1 (cardiogenic mesoderm transcription factor), and SOX17 (definitive endoderm transcription factor)

summary:
In Homo sapiens, SOX17 is a marker of definitive endoderm during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:38a9800c2ac4cb7842dd
claim_id: claim:38a9800c2ac4cb7842dd
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of progenitor genes TAL1 (endothelial fate transcription factor), TNNI1 (early development sarcomere isoform of TNNI), and SOX17 (definitive endoderm transcription factor)

summary:
In Homo sapiens, TAL1 is a marker of endothelial fate during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:e679103254b3f5eac5be
claim_id: claim:e679103254b3f5eac5be
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of cardiac genes MYL7 (early development sarcomere isoform of MYL), NKX2-5 (cardiac transcription factor), and THY1 (fibroblast marker)

summary:
In Homo sapiens, MYL7 is a marker of cardiomyocyte, NKX2-5 is a cardiac transcription factor, and THY1 is a fibroblast marker during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:36c26467ca4dce71d540
claim_id: claim:36c26467ca4dce71d540
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of cardiac genes MYL7 (early development sarcomere isoform of MYL), NKX2-5 (cardiac transcription factor), and THY1 (fibroblast marker)

summary:
In Homo sapiens, NKX2-5 is a marker of cardiac cells during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:af12dfbe1c5aa488890a
claim_id: claim:af12dfbe1c5aa488890a
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
S1 was primarily characterized by GO enrichment for genes associated with extracellular matrix deposition, motility, and cell adhesion (Figure 2J and M) which was supported by identification of a significant number of fibroblast-like cells marked by THY 1 (CD90) in S1 (Figure 2I and L).

summary:
In Homo sapiens, fibroblast-like cells are marked by THY1 (CD90) during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:5d6d0123806ab5296f50
claim_id: claim:5d6d0123806ab5296f50
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
The first lineage (N1:N2) diverts from pluripotency into a SOX17/FOXA2/EPCAM+ definitive endoderm population that terminates at day 2 and is comprised almost exclusively of D2:S1 and D2:S3 (Figure 3A-B and Figure S4A).

summary:
In Homo sapiens, definitive endoderm is marked by SOX17, FOXA2, and EPCAM during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:f87562059e55e6111f51
claim_id: claim:f87562059e55e6111f51
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
node 5 at day 5, comprising FOXA2/EPCAM+ definitive endoderm cells (D5:S2 and D5:S4) (Figure 3A-B and Figure S4A).

summary:
In Homo sapiens, definitive endoderm cells are marked by FOXA2 and EPCAM at day 5 of in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:4351bd7d36e00b366140
claim_id: claim:4351bd7d36e00b366140
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
THY1+/NKX2-5- non-contractile cardiac derivatives (N8-10: D15:S1 and D30:S1) or NKX2-5+/MYH6+ committed CM (N7: D15:S2) that progress onto MYH7+/MYL2+ definitive CM (N9: D30:S2)

summary:
In Homo sapiens, non-contractile cardiac derivatives are marked by positive THY1 and negative NKX2-5 expression during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:b7e9fa4038985cd1e685
claim_id: claim:b7e9fa4038985cd1e685
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
THY1+/NKX2-5- non-contractile cardiac derivatives (N8-10: D15:S1 and D30:S1) or NKX2-5+/MYH6+ committed CM (N7: D15:S2) that progress onto MYH7+/MYL2+ definitive CM (N9: D30:S2)

summary:
In Homo sapiens, committed cardiomyocytes are marked by NKX2-5 and MYH6 during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:7caeeb6f3c11fc556b72
claim_id: claim:7caeeb6f3c11fc556b72
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
THY1+/NKX2-5- non-contractile cardiac derivatives (N8-10: D15:S1 and D30:S1) or NKX2-5+/MYH6+ committed CM (N7: D15:S2) that progress onto MYH7+/MYL2+ definitive CM (N9: D30:S2)

summary:
In Homo sapiens, definitive cardiomyocytes are marked by MYH7 and MYL2 during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:69fd35ffee441f012212
claim_id: claim:69fd35ffee441f012212
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
while D15 and D30 S2 cells expressed cardiac sarcomere genes and transcription factors associated with first heart field specification (IRX4 and HCN4), S1 cells exclusively expressed an extensive network of genes associated with OFT development including PITX2, TBX18, HOXA1-3, FGF10, GJA1, and KDR

summary:
In Homo sapiens, cardiomyocytes (S2) express first heart field specification markers IRX4 and HCN4, while outflow tract derivative cells (S1) exclusively express PITX2, TBX18, FGF10, GJA1, and KDR during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:7eda775c9acea69b9874
claim_id: claim:7eda775c9acea69b9874
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
while D15 and D30 S2 cells expressed cardiac sarcomere genes and transcription factors associated with first heart field specification (IRX4 and HCN4), S1 cells exclusively expressed an extensive network of genes associated with OFT development including PITX2, TBX18, HOXA1-3, FGF10, GJA1, and KDR

summary:
In Homo sapiens, outflow tract derivative cells (S1) exclusively express PITX2, TBX18, FGF10, GJA1, and KDR, distinguishing them from cardiomyocytes (S2) during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:b65fcfbdad8195539df1
claim_id: claim:b65fcfbdad8195539df1
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
single-cell visualization showing enrichment of OFT gene expression in S1 vs S2 by t-SNE analysis of THY1 (59% D30:S1 vs 2% D30:S2), BMP4 (70% D30:S1 vs 6% D30:S2), and PITX2 (73% D30:S1 vs 17% D30:S2)

summary:
In Homo sapiens, outflow tract derivative cells (D30:S1) are enriched for THY1, BMP4, and PITX2 expression compared to cardiomyocytes (D30:S2) during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:66bab0514c607d1a8388
claim_id: claim:66bab0514c607d1a8388
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
these data revealed new insights into the bifurcation of cardiac precursor cells at day 5 of differentiation into NKX2-5+/MYL2+ ventricular cardiomyocytes and a population of non-contractile cells with transcriptional networks similar to NKX2-5−/PITX2+ cardiac outflow tract (OFT) cells.

summary:
In Homo sapiens, ventricular cardiomyocytes are marked by NKX2-5 and MYL2, while cardiac outflow tract cells are marked by negative NKX2-5 and positive PITX2 during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:74b113c76ae7b37be779
claim_id: claim:74b113c76ae7b37be779
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
these data revealed new insights into the bifurcation of cardiac precursor cells at day 5 of differentiation into NKX2-5+/MYL2+ ventricular cardiomyocytes and a population of non-contractile cells with transcriptional networks similar to NKX2-5−/PITX2+ cardiac outflow tract (OFT) cells.

summary:
In Homo sapiens, cardiac outflow tract cells are marked by negative NKX2-5 and positive PITX2, distinguished from ventricular cardiomyocytes during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:6941bdd0d1f2b7b2933f
claim_id: claim:6941bdd0d1f2b7b2933f
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
previous studies have routinely described a non-contractile THY1+ (CD90+) fibroblast-like cell used commonly for tissue engineering applications

summary:
In Homo sapiens, non-contractile fibroblast-like cells are marked by THY1 (CD90) in cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:dcd8cd8efe06d62a3888
claim_id: claim:dcd8cd8efe06d62a3888
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal: HOPX is detected in only 16% of D30:S2 cardiomyocytes (Figure 4B-D).
summary:
In Homo sapiens, HOPX is detected in only 16% of day 30 subpopulation 2 cardiomyocytes during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:b8b5891239dc18525a78
claim_id: claim:b8b5891239dc18525a78
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
While HOPX is rarely detected, its expression level is equivalent to that of other cardiac TFs that are detected in a high percentage of D30:S2 cardiomyocytes (HAND1: 67%, HAND2: 64%, GATA4: 67%, NKX2-5: 86% vs HOPX: 16%) (Figure 4B-D).

summary:
In Homo sapiens, day 30 subpopulation 2 cardiomyocytes express HAND1, HAND2, GATA4, and NKX2-5 at high frequency, while HOPX is detected in only 16% of these cardiomyocytes.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:530893e44fe0a72c2401
claim_id: claim:530893e44fe0a72c2401
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of HOPX gene expression across populations shows that HOPX is most highly expressed in endothelial cells at day 5 and in committed cardiomyocytes at day 30 of directed differentiation (Figure 4A).

summary:
In Homo sapiens, HOPX is most highly expressed in endothelial cells at day 5 and in committed cardiomyocytes at day 30 of in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:4557f35e378356e86819
claim_id: claim:4557f35e378356e86819
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
analysis of HOPX gene expression across populations shows that HOPX is most highly expressed in endothelial cells at day 5 and in committed cardiomyocytes at day 30 of directed differentiation (Figure 4A).

summary:
In Homo sapiens, HOPX is most highly expressed in committed cardiomyocytes at day 30 of in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:98c3ce0b8f8a91dec9b0
claim_id: claim:98c3ce0b8f8a91dec9b0
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
an equal proportion of HOPX+ cells give rise to TNNI1+ cardiac precursor cells (N4: 389 cells) or TAL1+ expressing endothelial cells (N5: 381 cells)

summary:
In Homo sapiens, cardiac precursor cells are marked by TNNI1 and endothelial cells are marked by TAL1 during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:c6d96c19a4a9aba83178
claim_id: claim:c6d96c19a4a9aba83178
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
an equal proportion of HOPX+ cells give rise to TNNI1+ cardiac precursor cells (N4: 389 cells) or TAL1+ expressing endothelial cells (N5: 381 cells)

summary:
In Homo sapiens, endothelial cells are marked by TAL1 during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730:claim:1ab2ecc9c334fec9f398
claim_id: claim:1ab2ecc9c334fec9f398
paper_key: biorxiv:6c7d90a7-6cd2-1014-aa88-ae3f4e676730
span_literal:
HOPX cardiac precursor cells differentiate into MYL2/IRX4+ cardiomyocytes (N6-N7) while a separate branch governed by TFs such as PBX1 differentiate into non-contractile derivatives (N8-N9)

summary:
In Homo sapiens, cardiomyocytes are marked by MYL2 and IRX4 during in vitro cardiac directed differentiation.


claim_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043:claim:d3e9f977e2d7e9304e1a
claim_id: claim:d3e9f977e2d7e9304e1a
paper_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043
summary: In Homo sapiens, mural trophectoderm is known to express HAND1.
span_literal:
Mural trophectoderm (TE) lacks validated specific markers but is known to express HAND1 (Liu et al. 2022).


claim_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043:claim:2062615675b82735a22b
claim_id: claim:2062615675b82735a22b
paper_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043
span_literal:
FBP1 and SFRP2 shown as previously identified preIm-Epi and Embryonic disc markers respectively (Messmer et al. 2019).

summary:
In Homo sapiens, FBP1 is a previously identified marker of pre-implantation epiblast, and SFRP2 is a previously identified marker of embryonic disc.


claim_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043:claim:49a163f8b90bed9a8934
claim_id: claim:49a163f8b90bed9a8934
paper_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043
span_literal:
For example during the emergence of TE cells during blastocyst formation, SLC28A3 (Figures 6F) is first upregualted in the morula and maintains expression until day 7 TE, whilst being downregulated in the ICM, Epi and Hyp lineages.

summary:
In Homo sapiens, SLC28A3 is upregulated in the morula and maintains expression in trophectoderm, whilst being downregulated in the inner cell mass, epiblast, and hypoblast lineages.


claim_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043:claim:5771967ad5bb2f001afc
claim_id: claim:5771967ad5bb2f001afc
paper_key: biorxiv:6c878fac-7162-1014-9b25-c2cbd95b5043
span_literal:
Conversely, the TE marker HAPLN1 (Fig S7B) is upregulated later than SLC28A3 at around day 6 and is maintained in day 7 of TE.

summary:
In Homo sapiens, HAPLN1 is a trophectoderm marker that is upregulated around day 6 and maintained in day 7 trophectoderm.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:7580c671f06837d1adbe
claim_id: claim:7580c671f06837d1adbe
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung epithelium, basal cells are marked by TP63 and KRT5 expression.
span_literal:
In the epithelium, TP63+ cells subclustered into KRT5+ basal, KRT5+SERPINB13+suprabasal, KRT5+MKI67+ proliferating basal (basal.p), KRT5+ACTA2+PLD5+SMG myoepithelial cell (MEC), and SFTPB+ distal bronchiolar basal cells (br.basal).


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:5538556d62043d7e73f9
claim_id: claim:5538556d62043d7e73f9
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
In the epithelium, TP63+ cells subclustered into KRT5+ basal, KRT5+SERPINB13+suprabasal, KRT5+MKI67+ proliferating basal (basal.p), KRT5+ACTA2+PLD5+SMG myoepithelial cell (MEC), and SFTPB+ distal bronchiolar basal cells (br.basal).

summary:
In Homo sapiens lung epithelium, suprabasal cells are marked by TP63, KRT5, and SERPINB13 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:7d66b5e972b25fdaff93
claim_id: claim:7d66b5e972b25fdaff93
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
In the epithelium, TP63+ cells subclustered into KRT5+ basal, KRT5+SERPINB13+suprabasal, KRT5+MKI67+ proliferating basal (basal.p), KRT5+ACTA2+PLD5+SMG myoepithelial cell (MEC), and SFTPB+ distal bronchiolar basal cells (br.basal).

summary:
In Homo sapiens lung epithelium, proliferating basal cells are marked by TP63, KRT5, and MKI67 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:670fd54d4913362dd0a2
claim_id: claim:670fd54d4913362dd0a2
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung epithelium, submucosal gland myoepithelial cells are marked by TP63, KRT5, ACTA2, and PLD5 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:16daac1d8c459f329fc7
claim_id: claim:16daac1d8c459f329fc7
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung epithelium, distal bronchiolar basal cells are marked by TP63 and SFTPB expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:e5c63825f0d048e1e3a4
claim_id: claim:e5c63825f0d048e1e3a4
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, deuterosomal cells are marked by DEUP1 and FOXN4 expression.
span_literal:
We detected DEUP1+FOXN4+ deuterosomal cells, described as precursors to FOXJ1+CDHR3+RSPH1+multiciliated cells21.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:91e487824ae815902335
claim_id: claim:91e487824ae815902335
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
Iterative sub-clustering of all epithelial airway cells divided SCGB1A1+SCGB3A2-aw.secretory cells into TFF3+MUC5B+MSMB+goblet and ERN2+WNK2+ club cells.

summary:
In Homo sapiens lung, goblet cells are marked by positive expression of SCGB1A1, TFF3, MUC5B, and MSMB, and negative expression of SCGB3A2.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:0febd89cd4b9af09f50c
claim_id: claim:0febd89cd4b9af09f50c
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
Iterative sub-clustering of all epithelial airway cells divided SCGB1A1+SCGB3A2-aw.secretory cells into TFF3+MUC5B+MSMB+goblet and ERN2+WNK2+ club cells.

summary:
In Homo sapiens lung, club cells are marked by positive expression of SCGB1A1, ERN2, and WNK2, and negative expression of SCGB3A2.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:2c531e63409312ca1486
claim_id: claim:2c531e63409312ca1486
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
SCGB3A2+SFTPB+cells divided into SCGB1A1+ pre-terminal bronchiole (pre-TB-SC), SCGB1A1- terminal and respiratory bronchiole secretory cells (TRB-SC), SCGB1A1-SFTPC+bronchiolar alveolar type 0 (AT0), and SCGB1A1-SFTPC+ABCA3+intermediate AT0 - alveolar epithelial type 2 (AT0.AT2) cells9.

summary:
In Homo sapiens lung, pre-terminal bronchiole secretory cells are marked by SCGB3A2, SFTPB, and SCGB1A1 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:e9087055555ca64cfddc
claim_id: claim:e9087055555ca64cfddc
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
SCGB3A2+SFTPB+cells divided into SCGB1A1+ pre-terminal bronchiole (pre-TB-SC), SCGB1A1- terminal and respiratory bronchiole secretory cells (TRB-SC), SCGB1A1-SFTPC+bronchiolar alveolar type 0 (AT0), and SCGB1A1-SFTPC+ABCA3+intermediate AT0 - alveolar epithelial type 2 (AT0.AT2) cells9.

summary:
In Homo sapiens lung, terminal and respiratory bronchiole secretory cells are marked by positive SCGB3A2 and SFTPB expression and negative SCGB1A1 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:86a54070caef7d788192
claim_id: claim:86a54070caef7d788192
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
SCGB3A2+SFTPB+cells divided into SCGB1A1+ pre-terminal bronchiole (pre-TB-SC), SCGB1A1- terminal and respiratory bronchiole secretory cells (TRB-SC), SCGB1A1-SFTPC+bronchiolar alveolar type 0 (AT0), and SCGB1A1-SFTPC+ABCA3+intermediate AT0 - alveolar epithelial type 2 (AT0.AT2) cells9.

summary:
In Homo sapiens lung, bronchiolar alveolar type 0 cells are marked by positive SCGB3A2, SFTPB, and SFTPC expression and negative SCGB1A1 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:d76e1b4206cb6b53edb1
claim_id: claim:d76e1b4206cb6b53edb1
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung, intermediate alveolar type 0 - alveolar epithelial type 2 cells are marked by positive SCGB3A2, SFTPB, SFTPC, and ABCA3 expression and negative SCGB1A1 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:fa74fead4f02644ae6b7
claim_id: claim:fa74fead4f02644ae6b7
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung alveoli, alveolar epithelial type 2 cells are marked by ABCA3 expression.
span_literal:
In the alveoli, we classified ABCA3+ AT2 cells, including ABCA3+FABP5+DBI+AT2 signaling cells (AT2.sig)5 and ABCA3+SCEL+RAB27B+intermediate AT2.AT1 cells, AGER+SCEL+ AT1 cells, and MKI67+TOP2A+CIT+ proliferating ABCA3+ AT2 (AT2.p) and ABCA3+AGER+ alveolar epithelial transitional (AT.p) populations.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:407a282bd0d1013df1f6
claim_id: claim:407a282bd0d1013df1f6
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
In the alveoli, we classified ABCA3+ AT2 cells, including ABCA3+FABP5+DBI+AT2 signaling cells (AT2.sig)5 and ABCA3+SCEL+RAB27B+intermediate AT2.AT1 cells, AGER+SCEL+ AT1 cells, and MKI67+TOP2A+CIT+ proliferating ABCA3+ AT2 (AT2.p) and ABCA3+AGER+ alveolar epithelial transitional (AT.p) populations.

summary:
In Homo sapiens lung alveoli, alveolar epithelial type 2 signaling cells are marked by ABCA3, FABP5, and DBI expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:340d365bf14c09709e05
claim_id: claim:340d365bf14c09709e05
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
In the alveoli, we classified ABCA3+ AT2 cells, including ABCA3+FABP5+DBI+AT2 signaling cells (AT2.sig)5 and ABCA3+SCEL+RAB27B+intermediate AT2.AT1 cells, AGER+SCEL+ AT1 cells, and MKI67+TOP2A+CIT+ proliferating ABCA3+ AT2 (AT2.p) and ABCA3+AGER+ alveolar epithelial transitional (AT.p) populations.

summary:
In Homo sapiens lung alveoli, intermediate alveolar epithelial type 2 - alveolar epithelial type 1 cells are marked by ABCA3, SCEL, and RAB27B expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:e95d4a92107b2586b292
claim_id: claim:e95d4a92107b2586b292
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung alveoli, alveolar epithelial type 1 cells are marked by AGER and SCEL expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:bbf96f3a1ef6d9cd32f9
claim_id: claim:bbf96f3a1ef6d9cd32f9
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung alveoli, proliferating alveolar epithelial type 2 cells are marked by MKI67, TOP2A, CIT, and ABCA3 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:24bc515929ed81e5c242
claim_id: claim:24bc515929ed81e5c242
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung alveoli, alveolar epithelial transitional cells are marked by ABCA3 and AGER expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:5a51da1a0805a901e174
claim_id: claim:5a51da1a0805a901e174
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, alveolar fibroblasts are marked by ADRA1A, GRIA1, and PCDH15 expression.
span_literal:
Beyond the epithelium, we detected ADRA1A+GRIA1+PCDH15+alveolar fibroblasts (AlvFB) and SCARA5+MFAP5+ adventitial fibroblasts (AdvFB) along with an AdvFB subpopulation HAS1+WT1+subpleural fibroblasts (AdvFB.subpl).


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:fa964e86b7ac37fc4d27
claim_id: claim:fa964e86b7ac37fc4d27
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
Besides WT1 expression, AdvFB.subpl lacked additional mesothelial cell markers such as UPK3B, FREM2, and CALB2.

summary:
In Homo sapiens lung, subpleural fibroblasts lack expression of the mesothelial cell markers UPK3B, FREM2, and CALB2.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:96841dfea4638ec952b0
claim_id: claim:96841dfea4638ec952b0
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
In alignment with CellRef2, we identified ITGBL1+PDGFRA+FGF18+DACH2+secondary crest myofibroblasts (SCMF).

summary:
In Homo sapiens lung, secondary crest myofibroblasts are marked by ITGBL1, PDGFRA, FGF18, and DACH2 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:9efb035deee5d820ddb5
claim_id: claim:9efb035deee5d820ddb5
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, arterial endothelial cells are marked by DKK2 and GJA5 expression.
span_literal:
Endothelial cells included DKK2+GJA5+arterial endothelial cells (AEC), FCN3+IL7R+ capillary general endothelial cells (CAP1), HPGD+EDNRB+ capillary aerocyte endothelial cells (CAP2), and ACKR1+ venous endothelial cells (VEC) which separated into HDAC9+PLAT+PLA1A+pulmonary venous and COL15A1+PLVAP+ABCB1+systemic venous endothelial cells (PVEC, SVEC, respectively)


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:cc0eaecfde9250517e55
claim_id: claim:cc0eaecfde9250517e55
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung, pulmonary venous endothelial cells are marked by HDAC9, PLAT, and PLA1A expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:32f7eb83069dfc9fc814
claim_id: claim:32f7eb83069dfc9fc814
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary:
In Homo sapiens lung, systemic venous endothelial cells are marked by COL15A1, PLVAP, and ABCB1 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:4fa8ab45fc4109116a44
claim_id: claim:4fa8ab45fc4109116a44
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, macrophages are marked by BACH1, MRC1, and MSR1 expression.
span_literal:
BACH1+MRC1+MSR1+macrophages consisted of PPARG+MARCO+INHBA+alveolar macrophages (AM), MKI67+ proliferating AM (AM.p), FABP4+ intravascular macrophages (IVM)26, F13A1+interstitial macrophages (IM), and MKI67+ proliferating IM (IM.p).


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:6c884b4389368f3e4fdb
claim_id: claim:6c884b4389368f3e4fdb
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, monocytes are marked by FCN1 expression.
span_literal:
FCN1+ monocytes divided into LILRB2+FCGR3A+non-classical or patrolling monocytes (pMON) and VCAN+AMPH+classical or inflammatory monocytes (iMON).


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:0e7a6e14ce614967a4b0
claim_id: claim:0e7a6e14ce614967a4b0
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
FCN1+ monocytes divided into LILRB2+FCGR3A+non-classical or patrolling monocytes (pMON) and VCAN+AMPH+classical or inflammatory monocytes (iMON).

summary:
In Homo sapiens lung, non-classical or patrolling monocytes are marked by FCN1, LILRB2, and FCGR3A expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:4fa0b133bc93d4d2fa23
claim_id: claim:4fa0b133bc93d4d2fa23
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
FCN1+ monocytes divided into LILRB2+FCGR3A+non-classical or patrolling monocytes (pMON) and VCAN+AMPH+classical or inflammatory monocytes (iMON).

summary:
In Homo sapiens lung, classical or inflammatory monocytes are marked by FCN1, VCAN, and AMPH expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:e7a409ea476c6ab46180
claim_id: claim:e7a409ea476c6ab46180
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, neutrophils are marked by CSF3R, IL1R2, GLT1D1, and PADI4 expression.
span_literal:
Additional myeloid cells consisted of CSF3R+IL1R2+GLT1D1+PADI4+neutrophils, MKI67+ proliferating neutrophils (Neu.p), and TPSB2+KIT+MS4A2+ mast cells.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:9cd81bd28f7c9aafb2a3
claim_id: claim:9cd81bd28f7c9aafb2a3
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, T cells are marked by CAMK4 expression.
span_literal:
Immune lymphoid cells comprised of CAMK4+ T cells, CD3D- GNLY+KLRD1+NCAM1+ natural killer (NK) cells, BANK1+ B cells, JCHAIN+ plasma, and JCHAIN+MKI67+plasmablasts.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:d70ae2e11baeb25df987
claim_id: claim:d70ae2e11baeb25df987
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
Immune lymphoid cells comprised of CAMK4+ T cells, CD3D- GNLY+KLRD1+NCAM1+ natural killer (NK) cells, BANK1+ B cells, JCHAIN+ plasma, and JCHAIN+MKI67+plasmablasts.

summary:
In Homo sapiens lung, natural killer cells are marked by positive GNLY, KLRD1, and NCAM1 expression and negative CD3D expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:a800b5a8bb2dd4560330
claim_id: claim:a800b5a8bb2dd4560330
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, CD4+ T cells are marked by CAMK4 and CD4 expression.
span_literal:
CAMK4+ T cells divided into CD4+and CD8A+CD8B+ T cells (CD4.T and CD8.T) and CD3+GNLY+KLRD1+NCAM1+natural killer T cells (NKT) including MKI67+ NKT.p cells.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:a28a068dd51e958fe4f4
claim_id: claim:a28a068dd51e958fe4f4
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
At subclass.L2, SCGB1A1 and SCGB3A2 expression split into SCGB1A1+SCGB3A2- and SCGB3A2+SFTPB+populations classified as conducting airway secretory (aw.secretory) and bronchiolar airway secretory (BrAS) cells, respectively.

summary:
In Homo sapiens lung, conducting airway secretory cells are marked by positive SCGB1A1 expression and negative SCGB3A2 expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:6321b2035a62443edebc
claim_id: claim:6321b2035a62443edebc
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
span_literal:
At subclass.L2, SCGB1A1 and SCGB3A2 expression split into SCGB1A1+SCGB3A2- and SCGB3A2+SFTPB+populations classified as conducting airway secretory (aw.secretory) and bronchiolar airway secretory (BrAS) cells, respectively.

summary:
In Homo sapiens lung, bronchiolar airway secretory cells are marked by SCGB3A2 and SFTPB expression.


claim_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5:claim:6b0df8f1b61ce7a692d4
claim_id: claim:6b0df8f1b61ce7a692d4
paper_key: biorxiv:6ca25eee-7853-1014-8aed-fc8cff0a87e5
summary: In Homo sapiens lung, mesothelial cells are marked by WT1, UPK3B, and GAS1 expression.
span_literal:
the addition of WT1+UPK3B+GAS1+ mesothelial cells, likely due to differences in tissue composition and ability to use both spatial and gene expression to localize these cells to the pleural surface.


claim_key: biorxiv:6e282b1d-6f16-1014-8a8d-cdb431a7cef0:claim:35f350dbdcbe3cc8a3b0
claim_id: claim:35f350dbdcbe3cc8a3b0
paper_key: biorxiv:6e282b1d-6f16-1014-8a8d-cdb431a7cef0
span_literal:
The cellular insight was further illuminated by visualizing the expression of marker genes, such as MOBP for oligodendrocytes, GFAP for astrocytes, and CLDN5 for endothelial cells, distinguishing between control (Figure 4G) and AD conditions (Figure 4H).

summary:
In Homo sapiens, MOBP is a marker gene for oligodendrocytes, GFAP is a marker gene for astrocytes, and CLDN5 is a marker gene for endothelial cells in the context of Alzheimer's Disease brain tissue analysis.


claim_key: biorxiv:6e282b1d-6f16-1014-8a8d-cdb431a7cef0:claim:96e5dc68b4e499a105d6
claim_id: claim:96e5dc68b4e499a105d6
paper_key: biorxiv:6e282b1d-6f16-1014-8a8d-cdb431a7cef0
span_literal:
The cellular insight was further illuminated by visualizing the expression of marker genes, such as MOBP for oligodendrocytes, GFAP for astrocytes, and CLDN5 for endothelial cells, distinguishing between control (Figure 4G) and AD conditions (Figure 4H).

summary:
In Homo sapiens, GFAP is a marker gene for astrocytes in the context of Alzheimer's Disease brain tissue analysis.


claim_key: biorxiv:6e282b1d-6f16-1014-8a8d-cdb431a7cef0:claim:061b5de1aecd3f88cddf
claim_id: claim:061b5de1aecd3f88cddf
paper_key: biorxiv:6e282b1d-6f16-1014-8a8d-cdb431a7cef0
span_literal:
The cellular insight was further illuminated by visualizing the expression of marker genes, such as MOBP for oligodendrocytes, GFAP for astrocytes, and CLDN5 for endothelial cells, distinguishing between control (Figure 4G) and AD conditions (Figure 4H).

summary:
In Homo sapiens, CLDN5 is a marker gene for endothelial cells in the context of Alzheimer's Disease brain tissue analysis.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:0c95728844a3163b0035
claim_id: claim:0c95728844a3163b0035
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
span_literal:
We therefore re-clustered all CD8+ T cell clusters, thus retrieving a separate NK cell cluster characterized by high expression of TYROBP, TRDC, NCAM1 (CD56) and low expression of CD8A, CD4, and CD3E (Figure 1B, C and Table S3).

summary:
In Homo sapiens melanoma, natural killer cells are characterized by high expression of TYROBP, TRDC, and NCAM1 (CD56) and low expression of CD8A, CD4, and CD3E.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:00f4ecbb1bd2ede7262c
claim_id: claim:00f4ecbb1bd2ede7262c
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
span_literal:
Cells from this cluster displayed a cytotoxic phenotype, characterized by high expression of GNLY, GZMB and PRF1, ruling out overlap with other innate lymphoid cell populations28.

summary:
In Homo sapiens melanoma, natural killer cells display a cytotoxic phenotype characterized by high expression of GNLY, GZMB, and PRF1.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:3531c4b1e943a7f30192
claim_id: claim:3531c4b1e943a7f30192
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
summary: In Homo sapiens melanoma, memory CD8+ T cells are marked by IL7R, FOS, TCF7, and SELL.
span_literal:
In parallel, re-clustering identified four CD8+ T cells states: Memory (IL7R, FOS, TCF7, SELL)5, Activated (IFNG, CCL3, CCL4), Cytotoxic (GNLY, GZMB, PRF1), andDysfunctional (expressing higher levels of CXCL13, LAG3, CTLA4, and HAVCR2, and lower levels of cytotoxic genes and IFNG) 29.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:e94158d227e7bbc4574e
claim_id: claim:e94158d227e7bbc4574e
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
summary:
In Homo sapiens melanoma, dysfunctional CD8+ T cells express higher levels of CXCL13, LAG3, CTLA4, and HAVCR2 and lower levels of IFNG.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:6dafde9769167dce3133
claim_id: claim:6dafde9769167dce3133
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
summary: In Homo sapiens melanoma, the Macrophage_C1Q cluster expresses C1Q, APOE, and MRC1.
span_literal:
However, Macrophage_C1Q cluster both contained cells expressing genes associated with an anti-inflammatory (C1Q, APOE, MRC1) and a pro-inflammatory role (CLXL9, HLA genes), leading us to further re-cluster this group of cells.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:8f8751fec606a4c49829
claim_id: claim:8f8751fec606a4c49829
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
span_literal:
The Macrophages_LYVE1 cluster largely overlapped with a known perivascular, tissue-resident, M2-like phenotype, expressing both vascular growth factors involved in angiogenesis (CD209, LILRB5, PDGFC) and genes associated with M2 polarization (CD163, CSF1R, MRC1) (Table S5).

summary:
In Homo sapiens melanoma, the Macrophages_LYVE1 cluster expresses CD209, LILRB5, PDGFC, CD163, CSF1R, and MRC1.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:c438fda2e57b370501ad
claim_id: claim:c438fda2e57b370501ad
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
span_literal:
The Macrophage_CCL3 cluster was characterized by both pro-inflammatory cytokines (CCL3, CCL4, CXCL3, TNF) and transcription factors (FOS, JUN, ATF3, NFKB genes) associated with macrophage activation (Table S5)32,33.

summary:
In Homo sapiens melanoma, the Macrophage_CCL3 cluster is characterized by CCL3, CCL4, CXCL3, TNF, FOS, JUN, and ATF3.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:966cf4eab392980ea1d8
claim_id: claim:966cf4eab392980ea1d8
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
span_literal:
Moreover, further classification of this cluster into NKCYTO and NKREST, as previously described in a breast cancer cohort39 indicated that the association between NK cell abundance and lack of response is driven by the NKCYTO phenotype, characterized by FCGR3A (CD16), FGFB2 and cytotoxic molecules (GNLY, PRF1, GZMB).

summary:
In Homo sapiens, the cytotoxic natural killer cell (NKCYTO) phenotype is characterized by FCGR3A (CD16), FGFBP2, and cytotoxic molecules GNLY, PRF1, and GZMB.


claim_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668:claim:aef67ce3a19d4165a087
claim_id: claim:aef67ce3a19d4165a087
paper_key: biorxiv:6f28f2e1-6c20-1014-910c-d12c701e7668
span_literal:
This analysis revealed clusters corresponding to classical monocytes (Monocytes_CD14), non-classical monocytes (Monocytes_CD16), intermediary monocytes (Monocytes_TNFSF13), conventional type 1 dendritic cells (cDC1) and conventional type 2 dendritic cells (cDC2).

summary:
In Homo sapiens melanoma, classical monocytes are marked by CD14, non-classical monocytes by CD16, and intermediary monocytes by TNFSF13.


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:17b81251d41e4c0c8e3d
claim_id: claim:17b81251d41e4c0c8e3d
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
span_literal:
CD303+/VIM+ cells are likely a fibroblast subset involved in the fibrotic process after β-cell destruction or potentially an atypical plasmacytoid DC (pDC; CD303+HLA-DR-)

summary:
In Homo sapiens, CD303+/VIM+ cells are characterized by expression of CD303 and VIM, and are potentially an atypical plasmacytoid dendritic cell or fibroblast subset.


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:859d2aabd0219ad7e8c5
claim_id: claim:859d2aabd0219ad7e8c5
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
span_literal:
Further, we annotated conventional DCs (cDCs), characterized by high levels of TIM-3, HLA-DR, and CD11c and low levels of macrophage markers CD163 and CD206.

summary:
In Homo sapiens, conventional dendritic cells are characterized by high expression of TIM-3, HLA-DR, and CD11c and low expression of CD163 and CD206.


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:8732fab725661c89352d
claim_id: claim:8732fab725661c89352d
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
span_literal:
Clusters included activated and minimally activated CD45RO+CD45RA-CD27- ebector memory-like cells (T-EM-like act., T-EM-like low act.), CD45RO+CD45RA-CD27+ central memory-like cells (T-CM-like act., T-CM-like low act.), PD1+ T- CD4 memory cells (PD1+ act., PD1+ low act.), PD1low cells (PD1low act., PD1low low act.), as well as two regulatory phenotypes, CD73+ T-CD4 cells and regulatory T cells (T-regs).

summary:
In Homo sapiens, CD4+ effector memory-like T cells are characterized by CD45RO+CD45RA-CD27- expression.


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:771e243463d39de14d1b
claim_id: claim:771e243463d39de14d1b
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
span_literal:
Clusters included activated and minimally activated CD45RO+CD45RA-CD27- ebector memory-like cells (T-EM-like act., T-EM-like low act.), CD45RO+CD45RA-CD27+ central memory-like cells (T-CM-like act., T-CM-like low act.), PD1+ T- CD4 memory cells (PD1+ act., PD1+ low act.), PD1low cells (PD1low act., PD1low low act.), as well as two regulatory phenotypes, CD73+ T-CD4 cells and regulatory T cells (T-regs).

summary:
In Homo sapiens, CD4+ central memory-like T cells are characterized by CD45RO+CD45RA-CD27+ expression.


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:cda321430ca43e540058
claim_id: claim:cda321430ca43e540058
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
summary: In Homo sapiens, naive CD8+ T cells are characterized by CD45RA+CD27+CD57- expression.
span_literal:
CD45RA+CD27+CD57- naive T-CD8 cells, CD45RA+CD27lowCD57+ ebector memory cells re-expressing CD45RA T cells (T-EMRA), activated and marginally activated CD45RO+CD103+ tissue-resident memory cells (T-RM act., T-RM low act.), CD45RO+CD27mid ebector memory/central memory-like cells (T-EM/CM-like), GranB+ cytotoxic T-CD8 cells, an undefined set of T-CD8 cells (T-CD8 Other), and a T-CD8 memory cell subtype that expressed high-levels of markers of exhaustion (PD1, TIM-3), cytotoxicity (GranB), survival (CD27), and metabolism (e.g., citrate synthase (CS)), suggesting an exhausted-like phenotype with some cytotoxic ebector functions (T-exe7).


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:5039258ca57000771be8
claim_id: claim:5039258ca57000771be8
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
span_literal:
CD45RA+CD27+CD57- naive T-CD8 cells, CD45RA+CD27lowCD57+ ebector memory cells re-expressing CD45RA T cells (T-EMRA), activated and marginally activated CD45RO+CD103+ tissue-resident memory cells (T-RM act., T-RM low act.), CD45RO+CD27mid ebector memory/central memory-like cells (T-EM/CM-like), GranB+ cytotoxic T-CD8 cells, an undefined set of T-CD8 cells (T-CD8 Other), and a T-CD8 memory cell subtype that expressed high-levels of markers of exhaustion (PD1, TIM-3), cytotoxicity (GranB), survival (CD27), and metabolism (e.g., citrate synthase (CS)), suggesting an exhausted-like phenotype with some cytotoxic ebector functions (T-exe7).

summary:
In Homo sapiens, effector memory T cells re-expressing CD45RA (T-EMRA) are characterized by CD45RA+CD27lowCD57+ expression.


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:c9c73709001290e83aca
claim_id: claim:c9c73709001290e83aca
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
summary:
In Homo sapiens, exhausted-like effector CD8+ T cells (T-exe7) express high levels of PD1, TIM-3, GranB, CD27, and citrate synthase (CS).


claim_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd:claim:7e4aea42ce8e61bd27a3
claim_id: claim:7e4aea42ce8e61bd27a3
paper_key: biorxiv:6f8501d1-6fb7-1014-a0e2-ce465eab4dbd
span_literal:
CD11c+ macrophages expressed the highest level of TMEM173 (STING) of all myeloid cells, suggesting that they are type 1 IFN producing cells52

summary:
In Homo sapiens, CD11c+ macrophages express the highest level of TMEM173 (stimulator of interferon genes) of all myeloid cells.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:2511b75e9f02919016c3
claim_id: claim:2511b75e9f02919016c3
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
Within the eleven microglia subsets, a small subgroup characterized by the cell proliferation marker MKI67 expression (Mg_MKI67) were reduced in the PD cohort, revealing a subtle microglial vulnerability (log2FDR ≈ –1.8) in this microglia subtype (Fig. 2B).

summary:
In Homo sapiens, a microglia subtype (Mg_MKI67) is characterized by expression of the cell proliferation marker MKI67.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:4c16a14535f9b7bbb559
claim_id: claim:4c16a14535f9b7bbb559
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
summary: In Homo sapiens, the astrocyte subtype Astro_VIM_LHX2 is marked by VIM and LHX2.
span_literal:
In contrast, there are three subtypes of astrocytes that show increased proportion in PD patients: Astro_VIM_LHX2 (log2FDR ≈ 2.6), Astro_GBP2_SPOCD1 (log2FDR ≈ 1.2), and Astro_SERPINA3 (log2FDR ≈ 0.6) (Fig. 2D).


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:7a81ac448a9cede79a8f
claim_id: claim:7a81ac448a9cede79a8f
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
The marker genes they are annotated by are primarily associated with inflammatory processes (LHX2, SERPINA3 and GBP2), or with broad cellular functions including cell migration and attachment, and structural stability (VIM and SPOCD1).

summary:
In Homo sapiens, astrocyte subtypes are annotated by marker genes LHX2, SERPINA3, GBP2, VIM, and SPOCD1 associated with inflammatory processes and cellular functions.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:ca7d5570cee7b3b9a997
claim_id: claim:ca7d5570cee7b3b9a997
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
HLA-DRA, CX3CR1, and colony stimulating factor genes CSF2RA and CSF3R are strongly expressed in control microglia, and a decreased expression of these genes in PD microglia are suggestive of a loss or decrease in surveying, quiescent microglia.

summary:
In Homo sapiens, HLA-DRA, CX3CR1, CSF2RA, and CSF3R are strongly expressed in quiescent microglia and are downregulated in Parkinson's disease microglia.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:6ca362618c83b2dbb221
claim_id: claim:6ca362618c83b2dbb221
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
Recent studies indicate that P2RY12 is differentially expressed at higher levels in resting and non-inflammatory activated microglia [40, 41], with further evidence implying that microglial chemotaxis occurs in response to neuronal injury.

summary:
In Homo sapiens, P2RY12 is expressed at higher levels in resting and non-inflammatory activated microglia.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:1628420fafe6b477211e
claim_id: claim:1628420fafe6b477211e
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
While key markers of glial activation (HSP90AB1, GPNMB, IL-1B) continue to be present and upregulated in PD microglia, it is accompanied by a downregulation of genes associated with resting or surveillant microglia (P2RY12, CSF receptor genes, and TGFBR1).

summary:
In Homo sapiens, HSP90AB1, GPNMB, and IL-1B are markers of activated microglia, while P2RY12 and TGFBR1 are associated with resting or surveillant microglia.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:80ef43eb5d1d88a608eb
claim_id: claim:80ef43eb5d1d88a608eb
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
summary: In Homo sapiens, microglia are marked by the proliferation gene MKI67.
span_literal:
Microglia marked by proliferation gene MKI67 show a decreased expression in PD, hinting that physiological levels of proliferation are not maintained in PD.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:eb0c24aefc35da14cf5b
claim_id: claim:eb0c24aefc35da14cf5b
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
Notably, expression of genes associated with resting state microglia and non-inflammatory reactive state microglia are downregulated in PD microglia, including P2RY12, CSF1R, CSF2RA, CSF3R, and TGFBR1.

summary:
In Homo sapiens, P2RY12, CSF1R, CSF2RA, CSF3R, and TGFBR1 are associated with resting state microglia and non-inflammatory reactive state microglia and are downregulated in Parkinson's disease microglia.


claim_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1:claim:9230a330ca3736966a0b
claim_id: claim:9230a330ca3736966a0b
paper_key: biorxiv:700d25d7-7306-1014-9c30-ec481bfe1ae1
span_literal:
Concurrently, genes associated with activated microglial states such as HSP90AB1 and GPNMB are upregulated.

summary:
In Homo sapiens, HSP90AB1 and GPNMB are associated with activated microglial states and are upregulated in Parkinson's disease.


claim_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481:claim:702e4e9ad760ea2b2d35
claim_id: claim:702e4e9ad760ea2b2d35
paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
span_literal:
they should exhibit a spindle-shape morphology and express PDGFRβ (may also express FAP) while simultaneously being devoid of PAX8 expression (marker of HGSC cancer cells) (Figure 2)

summary:
In Homo sapiens, cancer-associated fibroblasts express PDGFRβ and may also express FAP, while being devoid of PAX8 expression, which is a marker of high-grade serous carcinoma cancer cells.


claim_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481:claim:590740935f1a8c730347
claim_id: claim:590740935f1a8c730347
paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
span_literal:
they should exhibit a spindle-shape morphology and express PDGFRβ (may also express FAP) while simultaneously being devoid of PAX8 expression (marker of HGSC cancer cells) (Figure 2)

summary:
In Homo sapiens, high-grade serous carcinoma cancer cells express PAX8 as a marker, distinguishing them from cancer-associated fibroblasts.


claim_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481:claim:064290f6da2796aa3f3a
claim_id: claim:064290f6da2796aa3f3a
paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
summary: In Homo sapiens, mesothelial cells express calretinin.
span_literal:
mesothelial cell cultures may present similar growth rates, exhibit a cobblestone morphology and express calretinin (Figure 3)


claim_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481:claim:1c51bd40c8c01dbdd1d4
claim_id: claim:1c51bd40c8c01dbdd1d4
paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
span_literal:
All CAF cultures expressed PDGFRβ while FAP was only detected in cultures derived from Patients 4-6.

summary:
In Homo sapiens, cancer-associated fibroblast cultures express PDGFRβ, while FAP is expressed in a subset of cancer-associated fibroblast cultures.


claim_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481:claim:c7aa7fcd53ef29153697
claim_id: claim:c7aa7fcd53ef29153697
paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
span_literal:
Immunoblotting for PDGFRβ and FAP (CAF markers) and PAX8 (HGSC marker) in 8 established CAF cultures and 2 HGSC cell lines (i.e. OVCAR8 and OVCAR3; used as positive controls for PAX8 expression).

summary:
In Homo sapiens, PDGFRβ and FAP are markers of cancer-associated fibroblasts, while PAX8 is a marker of high-grade serous carcinoma cells.


claim_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481:claim:a4e0b98cef87c9faa5e0
claim_id: claim:a4e0b98cef87c9faa5e0
paper_key: biorxiv:705dbe14-6f1d-1014-86fa-92dddf16a481
summary: In Homo sapiens, PAX8 is a marker of high-grade serous carcinoma cancer cells.
span_literal:
The model was grown in 20 µL matrix domes in a 6-well plate for 10 days, fixed and stained for Ki67 (growth marker), PAX8 (HGSC cancer cell marker) and F-actin (cytoskeleton).


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:35454e87df8648f31b94
claim_id: claim:35454e87df8648f31b94
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal: These effector populations included follicular helper T cells (Tfh; Cd200, Izumo1r, Slamf6)
summary:
In Homo sapiens, follicular helper T cells are marked by positive expression of CD200, IZUMO1R, and SLAMF6.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:a27fa21e95d49c627f44
claim_id: claim:a27fa21e95d49c627f44
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal: Th17 (Il17a, Tmem176a, Tmem176b)
summary:
In Homo sapiens, T helper 17 cells are marked by positive expression of IL17A, TMEM176A, and TMEM176B.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:f89c69012a8fc245190b
claim_id: claim:f89c69012a8fc245190b
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Tumor-associated neutrophils, characterized by an activated phenotype of CD62Llow (SELL)/CD54high (ICAM1) (comparable to our scRNA-seq clusters C0 and C3), have high rates of phagocytosis and ROS production, and can directly induce cytokine production in activated T cells (Eruslanov et al., 2014), which our data suggests could occur through either CD80 or IL-23 expressed by the neutrophils.

summary:
In Homo sapiens, tumor-associated neutrophils are characterized by low expression of SELL (CD62L) and high expression of ICAM1 (CD54).


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:aac58fc8a1eeefdba273
claim_id: claim:aac58fc8a1eeefdba273
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Within the DCs, we identified MoDCs (Ccl5, Ccr7, Fscn1), conventional DCs clusters cDC1 (Clec9a, Itgae, Xcr1) (Minoda et al., 2017) and cDC2 (Mgl2, Irf4), and plasmacytoid DCs (Bst2, Pacsin1, Siglech)

summary:
In Homo sapiens, monocyte-derived dendritic cells are marked by positive expression of CCL5, CCR7, and FSCN1.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:1aa146f806123a976241
claim_id: claim:1aa146f806123a976241
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Within the DCs, we identified MoDCs (Ccl5, Ccr7, Fscn1), conventional DCs clusters cDC1 (Clec9a, Itgae, Xcr1) (Minoda et al., 2017) and cDC2 (Mgl2, Irf4), and plasmacytoid DCs (Bst2, Pacsin1, Siglech)

summary:
In Homo sapiens, conventional dendritic cell type 1 is marked by positive expression of CLEC9A, ITGAE, and XCR1.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:f8ab5d09421c3046d186
claim_id: claim:f8ab5d09421c3046d186
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Within the DCs, we identified MoDCs (Ccl5, Ccr7, Fscn1), conventional DCs clusters cDC1 (Clec9a, Itgae, Xcr1) (Minoda et al., 2017) and cDC2 (Mgl2, Irf4), and plasmacytoid DCs (Bst2, Pacsin1, Siglech)

summary:
In Homo sapiens, conventional dendritic cell type 2 is marked by positive expression of MGL2 and IRF4.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:261d646438b0dec4074e
claim_id: claim:261d646438b0dec4074e
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
summary:
In Homo sapiens, plasmacytoid dendritic cells are marked by positive expression of BST2, PACSIN1, and SIGLECH.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:980241960b799ac6fbb1
claim_id: claim:980241960b799ac6fbb1
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Overall, we identified two clusters of naïve monocytes (Cd14+; Fcgr3-, CD16), three activated monocyte clusters (Act Mono; Cd14+, Fcgr3+), one cycling monocyte cluster (Mki67, Stmn1, Top2a), three macrophage clusters (Cd68), and four DC clusters (Syngr2)

summary:
In Homo sapiens, naïve monocytes are marked by positive expression of CD14 and negative expression of FCGR3 (CD16).


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:601cf73e79ff04c384cc
claim_id: claim:601cf73e79ff04c384cc
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Overall, we identified two clusters of naïve monocytes (Cd14+; Fcgr3-, CD16), three activated monocyte clusters (Act Mono; Cd14+, Fcgr3+), one cycling monocyte cluster (Mki67, Stmn1, Top2a), three macrophage clusters (Cd68), and four DC clusters (Syngr2)

summary:
In Homo sapiens, activated monocytes are marked by positive expression of CD14 and positive expression of FCGR3.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:cf02101ee772921c7979
claim_id: claim:cf02101ee772921c7979
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Within the macrophages, we identified two clusters of tumor-associated macrophages (TAMs; Fcgr2b, Ccl4, Trem2)

summary:
In Homo sapiens, tumor-associated macrophages are marked by positive expression of FCGR2B, CCL4, and TREM2.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:94036b590a7568011576
claim_id: claim:94036b590a7568011576
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
summary: In Homo sapiens, gamma delta T cells are marked by positive expression of TCRG-C1 and TRDC.
span_literal:
which corresponded to γδ T cells (Tcrg-C1, Trdc), double negative (DN) naïve (Ccr7, Lef1, Sell, Tcf7), and a DN Treg-like population (Areg, Gata3, Il1rl1)


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:23e9be2e061d36c2cc4d
claim_id: claim:23e9be2e061d36c2cc4d
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
which corresponded to γδ T cells (Tcrg-C1, Trdc), double negative (DN) naïve (Ccr7, Lef1, Sell, Tcf7), and a DN Treg-like population (Areg, Gata3, Il1rl1)

summary:
In Homo sapiens, double negative naïve T cells are marked by positive expression of CCR7, LEF1, SELL, and TCF7.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:660681493a9a62661ca8
claim_id: claim:660681493a9a62661ca8
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
which corresponded to γδ T cells (Tcrg-C1, Trdc), double negative (DN) naïve (Ccr7, Lef1, Sell, Tcf7), and a DN Treg-like population (Areg, Gata3, Il1rl1)

summary:
In Homo sapiens, double negative regulatory T cell-like population is marked by positive expression of AREG, GATA3, and IL1RL1.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:da2208aacac129ae20e7
claim_id: claim:da2208aacac129ae20e7
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Our results showed Il17a and its transcription factor Rorc were largely restricted to Th17 and γδ T cells while Ifng and its transcription factor Stat4 were highly expressed in non-naïve T cells

summary:
In Homo sapiens, T helper 17 cells are marked by positive expression of IL17A and its transcription factor RORC.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:925d9b869074377abe55
claim_id: claim:925d9b869074377abe55
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Our results showed Il17a and its transcription factor Rorc were largely restricted to Th17 and γδ T cells while Ifng and its transcription factor Stat4 were highly expressed in non-naïve T cells

summary:
In Homo sapiens, gamma delta T cells are marked by positive expression of IL17A and its transcription factor RORC.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:1a68a360fdb573e4b21c
claim_id: claim:1a68a360fdb573e4b21c
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Markers associated with circulating neutrophils (Sellhl, CD62L; Cxcr4lo) were higher in clusters C1 and C2 while markers linked to increased effector function (Icam1), immunosuppression (Cd274, PD-L1), and tumor-promotion (Siglecf) were higher in clusters C0 and C3; these expression patterns generally corresponded with treatment group

summary:
In Homo sapiens, circulating neutrophils are marked by positive expression of SELL (CD62L) and low expression of CXCR4, while tumor-associated neutrophils are marked by positive expression of ICAM1, CD274 (PD-L1), and SIGLECF.


claim_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35:claim:369b290697e69ef92e3d
claim_id: claim:369b290697e69ef92e3d
paper_key: biorxiv:71ccac17-6c3e-1014-a6e6-b99fd2cc2f35
span_literal:
Markers associated with circulating neutrophils (Sellhl, CD62L; Cxcr4lo) were higher in clusters C1 and C2 while markers linked to increased effector function (Icam1), immunosuppression (Cd274, PD-L1), and tumor-promotion (Siglecf) were higher in clusters C0 and C3; these expression patterns generally corresponded with treatment group

summary:
In Homo sapiens, tumor-associated neutrophils are marked by positive expression of ICAM1, CD274 (PD-L1), and SIGLECF, compared to circulating neutrophils.


claim_key: biorxiv:72d8cdf5-6fa5-1014-b805-ea9c7c557043:claim:9dba33268fdafde0dd56
claim_id: claim:9dba33268fdafde0dd56
paper_key: biorxiv:72d8cdf5-6fa5-1014-b805-ea9c7c557043
span_literal:
Recently, CXCL13 was found to play a critical role in T cells for effective responses to anti-PD-L1 therapies (Zhang et al., 2021).

summary:
In Homo sapiens, CXCL13 plays a critical role in T cells for effective responses to anti-PD-L1 therapies.


claim_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964:claim:2a575634d844bb814bcf
claim_id: claim:2a575634d844bb814bcf
paper_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964
summary: In Homo sapiens, CD8-positive T cell is marked by CD3 and CD8.
span_literal:
For example, when both CD3 and CD8 markers are missing, the accuracy of classifying a CD8+ T cell image is 0 without marker imputation but increases to 65.16% when using imputed images of CD3 and CD8 with the immune full panel model.


claim_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964:claim:7da8bce9b9295067d539
claim_id: claim:7da8bce9b9295067d539
paper_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964
span_literal:
Note that CD45 in the tissue structure and nerve cell panels serves as a negatively expressed marker to distinguish immune cells.

summary:
In Homo sapiens, CD45 serves as a negatively expressed marker in nerve cell and tissue structure panels to distinguish from immune cell.


claim_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964:claim:1abab57fd15cd0bb59af
claim_id: claim:1abab57fd15cd0bb59af
paper_key: biorxiv:7325dd4b-6f8e-1014-8543-942cb0c9e964
span_literal:
we replaced some channels with closely related markers; for example, we used CD21 instead of CD20 and occasionally CD38 instead of CD138 in lymphoma datasets (10) for plasma cells.

summary:
In Homo sapiens, plasma cell is marked by CD20, CD21, CD138, and CD38, where CD21 can substitute for CD20 and CD38 can substitute for CD138.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:745c55148e0442c66a53
claim_id: claim:745c55148e0442c66a53
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
summary: In Homo sapiens, LGR5 is a positive marker gene for hair follicle stem cells.
span_literal:
MP2 also included LGR5 (Fig. 1D), a gene marker for hair follicle stem cells with rapid adaptive capacity during wound healing


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:edd6281ea31472333ed7
claim_id: claim:edd6281ea31472333ed7
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
Examination of the most influential genes and gene set enrichment analysis suggested potential roles in cell radial projection for MP2 (LAMB1 and LRP8); in epidermal differentiation for MP3 (CLDN4, CALML5, LGALS7B and KRT75); and in epidermal response to wounding for MP7 (TIMP1, CHI3L1, and IFITM3)

summary:
In Homo sapiens basal cell carcinoma, metaprogram 7 cancer cells associated with epidermal response to wounding are marked by TIMP1, CHI3L1, and IFITM3.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:cc633aa3a6eac66f3f35
claim_id: claim:cc633aa3a6eac66f3f35
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
Examination of the most influential genes and gene set enrichment analysis suggested potential roles in cell radial projection for MP2 (LAMB1 and LRP8); in epidermal differentiation for MP3 (CLDN4, CALML5, LGALS7B and KRT75); and in epidermal response to wounding for MP7 (TIMP1, CHI3L1, and IFITM3)

summary:
In Homo sapiens basal cell carcinoma, metaprogram 3 cancer cells associated with epidermal differentiation are marked by CLDN4, CALML5, LGALS7B, and KRT75.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:66820e76ea7b91040c45
claim_id: claim:66820e76ea7b91040c45
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
Examination of the most influential genes and gene set enrichment analysis suggested potential roles in cell radial projection for MP2 (LAMB1 and LRP8); in epidermal differentiation for MP3 (CLDN4, CALML5, LGALS7B and KRT75); and in epidermal response to wounding for MP7 (TIMP1, CHI3L1, and IFITM3)

summary:
In Homo sapiens basal cell carcinoma, metaprogram 2 cancer cells associated with cell radial projection are marked by LAMB1 and LRP8.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:467299bb85d755277c01
claim_id: claim:467299bb85d755277c01
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
However, when considering MP-specific genes, such as Tissue Inhibitor of Metalloproteinases 1 (TIMP1) for MP7 and Claudin 4 (CLDN4) for MP3 (Fig. 1D and Fig. S3C), we found a largely mutually exclusive activation pattern, magnified within the infiltrative, KRT6A-expressing tumor cells

summary:
In Homo sapiens basal cell carcinoma, Tissue Inhibitor of Metalloproteinases 1 (TIMP1) is a specific marker of metaprogram 7 cancer cells, while Claudin 4 (CLDN4) is a specific marker of metaprogram 3 cancer cells, and infiltrative tumor cells express KRT6A.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:c1838e986ffbaf8535dd
claim_id: claim:c1838e986ffbaf8535dd
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
However, when considering MP-specific genes, such as Tissue Inhibitor of Metalloproteinases 1 (TIMP1) for MP7 and Claudin 4 (CLDN4) for MP3 (Fig. 1D and Fig. S3C), we found a largely mutually exclusive activation pattern, magnified within the infiltrative, KRT6A-expressing tumor cells

summary:
In Homo sapiens basal cell carcinoma, Claudin 4 (CLDN4) is a specific marker of metaprogram 3 cancer cells, while Tissue Inhibitor of Metalloproteinases 1 (TIMP1) is a specific marker of metaprogram 7 cancer cells.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:4870da223567cb786ca8
claim_id: claim:4870da223567cb786ca8
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
CAFs upregulated the expression of metalloproteases (MMP3 and MMP1), glycolysis-related genes (GAPDH, ENO1, BASP1, PKM, and TPI1), contractile protein genes (TPM2), and cellular stress genes (NFKBIA and IER3)

summary:
In Homo sapiens basal cell carcinoma, wound-responding cancer-associated fibroblasts upregulate MMP3, MMP1, GAPDH, ENO1, BASP1, PKM, TPI1, TPM2, NFKBIA, and IER3.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:3771344fef7d315d2a47
claim_id: claim:3771344fef7d315d2a47
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
In particular, MP7 and MP3 include genes implicated in epithelial cell migration (e.g. TNC, TIMP1, MMP1, ITGAV, ITGB6) and epidermal barrier restoration (e.g. CLDN4, DSG1, KRT1, KRT77, SPRR1B) respectively, and display a spatial coordination – at the basal and suprabasal layers - that reflects the specific architecture of the wound migrating edge

summary:
In Homo sapiens basal cell carcinoma, metaprogram 7 cancer cells express TNC, TIMP1, MMP1, ITGAV, and ITGB6, genes implicated in epithelial cell migration.


claim_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f:claim:06f78c1752be4d900029
claim_id: claim:06f78c1752be4d900029
paper_key: biorxiv:736bec2d-70bc-1014-bc7a-9d003fe8a69f
span_literal:
In particular, MP7 and MP3 include genes implicated in epithelial cell migration (e.g. TNC, TIMP1, MMP1, ITGAV, ITGB6) and epidermal barrier restoration (e.g. CLDN4, DSG1, KRT1, KRT77, SPRR1B) respectively, and display a spatial coordination – at the basal and suprabasal layers - that reflects the specific architecture of the wound migrating edge

summary:
In Homo sapiens basal cell carcinoma, metaprogram 3 cancer cells express CLDN4, DSG1, KRT1, KRT77, and SPRR1B, genes implicated in epidermal barrier restoration.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:65f9bfbfe7bec80440d6
claim_id: claim:65f9bfbfe7bec80440d6
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
span_literal: Using an unbiased proteomics approach, CD47 was identified a novel marker of human MSCs.
summary:
In Homo sapiens, CD47 was identified as a novel marker of mesenchymal stem cells using an unbiased proteomics approach.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:593efe6cfc09c04b0a56
claim_id: claim:593efe6cfc09c04b0a56
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
span_literal:
An aspect of this proteomic workflow that was interesting was that the MSC sub-type expressed significantly more CD47 than the non-MSCs.

summary:
In Homo sapiens, the mesenchymal stem cell sub-type expressed significantly more CD47 than the non-mesenchymal stem cells.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:f3b302acec767d9a121b
claim_id: claim:f3b302acec767d9a121b
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
span_literal:
Additionally, the expression of CD271 varied among MSC clones, with none of the clones demonstrating multi-potential differentiation capacity expressing CD271.

summary:
In Homo sapiens, none of the mesenchymal stem cell clones demonstrating multi-potential differentiation capacity expressed CD271, suggesting CD271 is a negative marker of multipotent mesenchymal stem cells.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:41fd8503594d5f47e7fc
claim_id: claim:41fd8503594d5f47e7fc
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
span_literal:
Collectively, the common trend observed in the clones presented and those from the entire cohort was that despite a heterogeneous cell surface marker expression profile in situ; the marker profile aligned in vitro with nearly all clones (normal and OA) expressing CD90, CD44, CD73, and CD105 (Figure S3, Tables S4 and S5).

summary:
In Homo sapiens, nearly all synovial mesenchymal stem cell clones expressed CD90, CD44, CD73, and CD105 after in vitro culture.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:e46b38cb071f26867ca8
claim_id: claim:e46b38cb071f26867ca8
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
span_literal:
When the differentiation capacity of the clones was compared to the cells in situ (pre-culture) cell surface marker expression, the most frequent marker phenotype of cells that met the minimal criteria for MSCs (in situ) was CD90+CD44+CD73+.

summary:
In Homo sapiens, the most frequent in situ marker phenotype of synovial cells meeting the minimal criteria for mesenchymal stem cells was CD90-positive, CD44-positive, and CD73-positive.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:65184297297901a75413
claim_id: claim:65184297297901a75413
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
summary: In Homo sapiens, mesenchymal stem cell markers include CD90, CD271, CD105, CD73, and CD44.
span_literal:
mesenchymal stem cell (MSC) markers, including CD90 (PE), CD271 (BV421), CD105 (BV650), CD73 (APC), and CD44


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:2f90a005e462e7a2e2b1
claim_id: claim:2f90a005e462e7a2e2b1
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
summary: In Homo sapiens, CD68 is used to target the macrophage population.
span_literal:
Additionally, cells were stained with the viability marker FVS510 (BV510) at a 1:100 dilution for 30 minutes on ice and with CD68 (FITC) to target the macrophage population.


claim_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57:claim:d377d029196e340e8515
claim_id: claim:d377d029196e340e8515
paper_key: biorxiv:74193868-6d98-1014-a02e-d07ed370ea57
span_literal:
In the current study, we have identified a subpopulation of synovial cells that express high levels of CD47.

summary:
In Homo sapiens, a subpopulation of synovial cells was identified that expresses high levels of CD47.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:9271fe3c74a29b086dea
claim_id: claim:9271fe3c74a29b086dea
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
CD45RA is the result of alternative splicing of CD45 and serves as a canonical marker to distinguish between naïve T/central memory T (TCM) cells (naive T is CD45RA+ while TCM is CD45RA-) and effector memory T (TEM)/effector memory re-expressing CD45RA T (TEMRA) cells

summary:
In Homo sapiens, naive T cells are positive for PTPRC isoform CD45RA, distinguishing them from central memory T cells.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:5f5c13598e73a98366be
claim_id: claim:5f5c13598e73a98366be
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
CD45RA is the result of alternative splicing of CD45 and serves as a canonical marker to distinguish between naïve T/central memory T (TCM) cells (naive T is CD45RA+ while TCM is CD45RA-) and effector memory T (TEM)/effector memory re-expressing CD45RA T (TEMRA) cells

summary:
In Homo sapiens, central memory T cells are negative for PTPRC isoform CD45RA, distinguishing them from naive T cells.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:809e99dd7f43e917641f
claim_id: claim:809e99dd7f43e917641f
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
CD45RA is the result of alternative splicing of CD45 and serves as a canonical marker to distinguish between naïve T/central memory T (TCM) cells (naive T is CD45RA+ while TCM is CD45RA-) and effector memory T (TEM)/effector memory re-expressing CD45RA T (TEMRA) cells

summary:
In Homo sapiens, effector memory re-expressing CD45RA T cells are positive for PTPRC isoform CD45RA, distinguishing them from effector memory T cells.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:9ceb7a254f19209ea2fe
claim_id: claim:9ceb7a254f19209ea2fe
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
summary: In Homo sapiens, CD28 is a costimulatory receptor expressed on naive T cells.
span_literal:
Specifically, CD28 is a costimulatory receptor expressed on naive T cells, essential for T cell activation


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:6b352e6ae77c9a1b64b6
claim_id: claim:6b352e6ae77c9a1b64b6
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
Interleukin 7 Receptor (IL7R, alias CD127) is a receptor that binds to interleukin-7 (IL-7) and plays a crucial role in the development and homeostasis of naive T cells

summary:
In Homo sapiens, interleukin 7 receptor (IL7R) plays a crucial role in the development and homeostasis of naive T cells.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:c5478534fedd9c408323
claim_id: claim:c5478534fedd9c408323
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
The expression profile showed that the CCR7+SELL+IL7R+TCF7+ cluster 1 was likely to be naive T cells or TCMs, and the CCR7−SELL−IL7RlowKLRG1+NKG7+ cluster 3 had an obvious TEM/TEMRA similarity (Figure. 2C-D)[13].

summary:
In Homo sapiens, naive T cells or central memory T cells express CCR7, SELL, IL7R, and TCF7, while effector memory T cells or effector memory re-expressing CD45RA T cells express KLRG1 and NKG7 and are negative for CCR7 and SELL.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:16cbe53a9335ec7e2e25
claim_id: claim:16cbe53a9335ec7e2e25
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
The expression profile showed that the CCR7+SELL+IL7R+TCF7+ cluster 1 was likely to be naive T cells or TCMs, and the CCR7−SELL−IL7RlowKLRG1+NKG7+ cluster 3 had an obvious TEM/TEMRA similarity (Figure. 2C-D)[13].

summary:
In Homo sapiens, effector memory T cells are negative for CCR7 and SELL, have low IL7R, and express KLRG1 and NKG7.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:76e9a7b85e6d9586acf7
claim_id: claim:76e9a7b85e6d9586acf7
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
summary:
In Homo sapiens, effector memory re-expressing CD45RA T cells are negative for CCR7 and SELL, have low IL7R, and express KLRG1 and NKG7.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:3da68f4bab88068a9855
claim_id: claim:3da68f4bab88068a9855
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
Gene expression profiles of these 3 clusters showed they were likely to be resting (C5, C10; PRF1−GZMB−NKG7−) and activated (C11; PRF1+GZMB+NKG7+) CD4+ TEMs given their CCR7−SELL−IL7R+TNF+IFNG+ pattern (Figure. 3B-C).

summary:
In Homo sapiens, resting CD4+ effector memory T cells are negative for PRF1, GZMB, and NKG7, and express CCR7 negatively, SELL negatively, IL7R, TNF, and IFNG.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:3ca6da5e8a1f7bda2428
claim_id: claim:3ca6da5e8a1f7bda2428
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
Gene expression profiles of these 3 clusters showed they were likely to be resting (C5, C10; PRF1−GZMB−NKG7−) and activated (C11; PRF1+GZMB+NKG7+) CD4+ TEMs given their CCR7−SELL−IL7R+TNF+IFNG+ pattern (Figure. 3B-C).

summary:
In Homo sapiens, activated CD4-positive effector memory T cells express PRF1, GZMB, and NKG7, and are negative for CCR7 and SELL, while expressing IL7R, TNF, and IFNG.


claim_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0:claim:6b39a8769393495e895f
claim_id: claim:6b39a8769393495e895f
paper_key: biorxiv:750a2ba6-6eaa-1014-b156-e23e824a62e0
span_literal:
we suggested that the transcription of genes like NPDC1 and AQP3 could be potentially indicative of the CD45RA protein level in human T cells

summary:
In Homo sapiens, the transcription of neural proliferation differentiation and control 1 (NPDC1) and aquaporin 3 (AQP3) could be potentially indicative of the CD45RA protein level in T cells.


claim_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702:claim:a9b481b78ed8ad25c770
claim_id: claim:a9b481b78ed8ad25c770
paper_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702
summary: In Homo sapiens, CRYAB is a unique marker for truncated radial glia.
span_literal:
CRYAB, encoding a molecular chaperone (Yamamoto et al, 2014) is a unique marker for human tRG (Nowakowski et al, 2016); therefore, we designated them as tRG-like cells in ferrets.


claim_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702:claim:f39f37ddb0efdc00a638
claim_id: claim:f39f37ddb0efdc00a638
paper_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702
summary: In Homo sapiens, HOPX is a typical marker for outer radial glia.
span_literal:
HOPX, a typical marker for oRG in human tissues (Fig. 2E, S3D; Pollen et al, 2015), has been indeed detected in both oRG and vRG at late stages in vivo in ferrets (Fig. S3D; Johnson et al, 2018; Kawaue et al, 2019).


claim_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702:claim:6305ce0519bffb5f0fc9
claim_id: claim:6305ce0519bffb5f0fc9
paper_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702
span_literal:
tRG cells also showed a remarkable similarity between the two species (Fig. 6C, 6D), as represented by a high level of expression for the combination of CRYAB, EGR1, and CYR61 (Fig. 6E).

summary:
In Homo sapiens, truncated radial glia show a high level of expression for the combination of CRYAB, EGR1, and CYR61.


claim_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702:claim:d0a1635d3d85b90badb6
claim_id: claim:d0a1635d3d85b90badb6
paper_key: biorxiv:771e3d5c-7119-1014-bcb2-db210f671702
span_literal:
Consistent with the human dataset (Bhaduri et al, 2021), the expression of HOPX, CLU, and CRYM was higher in oRG-like cells than in other ferret NPCs (Fig. 7J, S8E).

summary:
In Homo sapiens, the expression of HOPX, CLU, and CRYM is higher in outer radial glia than in other neural progenitor cells.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:48d76f3d9fb6272e178e
claim_id: claim:48d76f3d9fb6272e178e
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We confirmed absence of mouse-specific pluripotency markers FBXO15, GBX2, ESRRB, UTF1 and KLF2 in the marmoset preimplantation epiblast, similar to recent reports in human

summary:
In Homo sapiens, the preimplantation epiblast lacks expression of FBXO15, GBX2, ESRRB, UTF1, and KLF2, which are mouse-specific pluripotency markers.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:81b56cc676722f17ff9e
claim_id: claim:81b56cc676722f17ff9e
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
NANOG, ARGFX, TFAP2C, MILR1 and KHDC3L were already expressed in morulae and early ICM and retained in the EPI, but downregulated in PrE

summary:
In Homo sapiens, NANOG, ARGFX, TFAP2C, MILR1, and KHDC3L are positive markers of the epiblast, retained from morulae and early inner cell mass, and downregulated in primitive endoderm.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:0991f371f79d95146a47
claim_id: claim:0991f371f79d95146a47
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
TDGF1, LEFTY2, FGF4, IFITM5 and IGFBP2 were expressed at low abundance at earlier stages, but sharply upregulated upon EPI specification

summary:
In Homo sapiens, TDGF1, LEFTY2, FGF4, IFITM5, and IGFBP2 are sharply upregulated upon epiblast specification.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:c5fb15cb52047eca6a06
claim_id: claim:c5fb15cb52047eca6a06
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We identified GATA6, LRP2, TBX3 and ANXA3 as early PrE markers robustly expressed prior to PrE specification, while APOA1, COL4A1, GDF6, RSPO3 and FST were exclusive to the mature PrE lineage

summary:
In Homo sapiens, GATA6, LRP2, TBX3, and ANXA3 are early primitive endoderm markers, while APOA1, COL4A1, GDF6, RSPO3, and FST are exclusive to the mature primitive endoderm lineage.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:9b5baa443a6744023120
claim_id: claim:9b5baa443a6744023120
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
The conserved EPI network included the core pluripotency factors POU5F1, SOX2 and NANOG as well as TFCP2L1, ZNF296, ZFP36L1 and SOX15.

summary:
In Homo sapiens, the conserved epiblast network includes the core pluripotency factors POU5F1, SOX2, and NANOG, as well as TFCP2L1, ZNF296, ZFP36L1, and SOX15.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:ec760754a894a7304496
claim_id: claim:ec760754a894a7304496
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We also noted the presence of transcriptional repressor RBPJ and ERK-signalling associated factors ETV4 and ETV5.

summary:
In Homo sapiens, the epiblast network also includes the transcriptional repressor RBPJ and ERK-signalling associated factors ETV4 and ETV5.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:fa56fb9375c006306a44
claim_id: claim:fa56fb9375c006306a44
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We identified a substantial fraction of transcriptional repressors (IKZF5, IFI16, BHLME40 and CBFA2T2), genes associated with DNA mismatch repair (PMS1, MBD4) and several components of NFκβ (BCL3, RELA) and WNT (CDX1, HBP1, HMGN3) signalling pathways.

summary:
In Homo sapiens, primate-specific epiblast transcription factors include IKZF5, IFI16, BHLME40, CBFA2T2, PMS1, MBD4, BCL3, RELA, CDX1, HBP1, and HMGN3.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:7bfdf8e8877cf321a6af
claim_id: claim:7bfdf8e8877cf321a6af
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
Interestingly, the network also contained TFAP2C and GCM1, which in mouse are associated with trophoblast lineage specification (Kaiser et al., 2015; Sharma et al., 2016) and regulation of syncytium formation (Kashif et al., 2011; Lu et al., 2016), respectively.

summary:
In Homo sapiens, the primate-specific epiblast network contains TFAP2C and GCM1, which in mouse are associated with trophoblast lineage specification.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:88a8cb03d76b8bfb01b9
claim_id: claim:88a8cb03d76b8bfb01b9
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
The conserved core transcription factor network for human, marmoset and mouse PrE contained many established lineage markers, including GATA6, SOX17, HNF4A and GATA4

summary:
In Homo sapiens, the conserved core transcription factor network for primitive endoderm contains established lineage markers GATA6, SOX17, HNF4A, and GATA4.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:30447f3d07a3b6b934cb
claim_id: claim:30447f3d07a3b6b934cb
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We identified pluripotency-associated factors TBX3 and KLF5, downstream targets of BMP signalling (ID2, ID3) and new potential regulators (WDR77, PDLIM1, PCBD1 and GTF2A2) within the common PrE circuitry.

summary:
In Homo sapiens, the common primitive endoderm circuitry includes TBX3, KLF5, ID2, ID3, WDR77, PDLIM1, PCBD1, and GTF2A2.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:1be5805cee5ce689715d
claim_id: claim:1be5805cee5ce689715d
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
However, SOX7 expression remained low in marmoset throughout all developmental stages and absent in human.

summary:
In Homo sapiens, SOX7 is absent in the primitive endoderm, unlike in mouse where it is part of the sequential activation cascade.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:a9b591e1d13e27d3cb20
claim_id: claim:a9b591e1d13e27d3cb20
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
Surprisingly, the mouse ICM and postimplantation EPI-associated gene OTX2 (Buecker et al., 2014; Acampora et al., 2016) was robustly expressed in the primate PrE

summary:
In Homo sapiens, OTX2 is robustly expressed in the primitive endoderm, in contrast to its association with the inner cell mass and postimplantation epiblast in mouse.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:ce64d8f43f9f55b38813
claim_id: claim:ce64d8f43f9f55b38813
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We (Boroviak et al., 2015; Stirparo et al., 2018) and others (Blakeley et al., 2015; Nakamura et al., 2016) demonstrated that a substantial fraction of mouse pluripotency-associated factors are absent from primate ICM, including KLF2, NR0B1, ESRRB, FBXO15 and JAM2.

summary:
In Homo sapiens, a substantial fraction of mouse pluripotency-associated factors are absent from the primate inner cell mass, including KLF2, NR0B1, ESRRB, FBXO15, and JAM2.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:4dbcc216d21558fbcabb
claim_id: claim:4dbcc216d21558fbcabb
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
Cross-species analyses defined primate-specific transcription and chromatin remodelling factor circuitry in the EPI. We identified TFAP2C and GCM1, regarded as TE-associated factors in mouse, in the naïve primate pluripotency network with KLF17, ARGFX, HESX1, ELF3, HMGB3 and several zinc-finger proteins, including ZNF675, ZNF257, and ZNF146.

summary:
In Homo sapiens, the naïve primate epiblast pluripotency network includes TFAP2C, GCM1, KLF17, ARGFX, HESX1, ELF3, HMGB3, ZNF675, ZNF257, and ZNF146.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:16d4bec8d00344cbec32
claim_id: claim:16d4bec8d00344cbec32
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We identified an array of new core PrE-associated factors present in human, marmoset and mouse. These included KLF5, KLF6, TBX3, EGR1 and BMP signalling components ID2/3.

summary:
In Homo sapiens, new core primitive endoderm-associated factors include KLF5, KLF6, TBX3, EGR1, and BMP signalling components ID2 and ID3.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:38b57c6f5d6cde880145
claim_id: claim:38b57c6f5d6cde880145
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal: Primate PrE consistently expressed RSPO3, a potent WNT signalling enhancer (de Lau et al., 2014).
summary:
In Homo sapiens, the primitive endoderm consistently expresses RSPO3, a potent WNT signalling enhancer.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:6a2307475e74fe5f6caa
claim_id: claim:6a2307475e74fe5f6caa
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal: Human EPI featured WNT3, (marmoset WNT5B) in contrast to complete absence of WNT ligand in mouse.
summary:
In Homo sapiens, the epiblast features WNT3 expression, in contrast to complete absence of WNT ligand in mouse.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:41bb1e6bb40879885275
claim_id: claim:41bb1e6bb40879885275
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
The primate-specific PrE transcription factor network contained ANKRD1, PITX2, MSX2, CEBPD, HDGF and mouse trophoblast markers GATA2 and GATA3, which were robustly expressed in PrE, although orders of magnitude lower than in the TE lineage.

summary:
In Homo sapiens, the primate-specific primitive endoderm transcription factor network contains ANKRD1, PITX2, MSX2, CEBPD, HDGF, GATA2, and GATA3.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:45c93fb0f19560b034db
claim_id: claim:45c93fb0f19560b034db
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
However, our re-analysis of human datasets (Stirparo et al., 2018) with stage-matched marmoset and mouse samples showed that DPPA4 is consistently upregulated in the EPI.

summary:
In Homo sapiens, DPPA4 is consistently upregulated in the epiblast rather than the primitive endoderm.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:fb48b738ff834e90d2e7
claim_id: claim:fb48b738ff834e90d2e7
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
The absence of HHEX in human and marmoset PrE suggests potentially divergent mechanisms for the establishment of asymmetry in primates.

summary:
In Homo sapiens, HHEX is absent in the primitive endoderm, suggesting potentially divergent mechanisms for the establishment of asymmetry.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:67a1f1d5238b9b22ca1d
claim_id: claim:67a1f1d5238b9b22ca1d
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We found GATA2 was absent in EPI, at intermediate levels in PrE and highly expressed in all trophectoderm cells

summary:
In Homo sapiens, GATA2 is absent in the epiblast, at intermediate levels in the primitive endoderm, and highly expressed in all trophectoderm cells.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:71a3ab94965bfbad42e0
claim_id: claim:71a3ab94965bfbad42e0
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
We found GATA2 was absent in EPI, at intermediate levels in PrE and highly expressed in all trophectoderm cells

summary:
In Homo sapiens, GATA2 is at intermediate levels in the primitive endoderm and highly expressed in all trophectoderm cells.


claim_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181:claim:b22f324325e73ad9890f
claim_id: claim:b22f324325e73ad9890f
paper_key: biorxiv:77d5f6bb-6c27-1014-a74d-a25d8b68d181
span_literal:
GATA6 was robustly expressed in morulae and early ICM and subsequently confined to PrE in the late ICM, while GATA4 and SOX17 were specifically upregulated in PrE.

summary:
In Homo sapiens, GATA6 is robustly expressed in morulae and early inner cell mass and subsequently confined to primitive endoderm, while GATA4 and SOX17 are specifically upregulated in primitive endoderm.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:c0fe30bd0cc8b3081934
claim_id: claim:c0fe30bd0cc8b3081934
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens lung, chondrocytes are marked by ACAN, CHAD, COL9A3, HAPLN1, and CYTL1.
span_literal:
we transcriptionally defined chondrocytes for the first time in human lungs (ACAN, CHAD, COL9A3, HAPLN1 and CYTL1)


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:05b9c3c9e523dc3bbe13
claim_id: claim:05b9c3c9e523dc3bbe13
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens, immune recruiting fibroblasts express CCL19, CCL21, GREM1, CXCL13, and FDCSP.
span_literal:
This rare type expressed the chemokines CCL19 and CCL21, also highly expressed in fibroblast reticular cells responsible for T-cell positioning in the lymph nodes, and GREM1 (Kapoor et al. 2021), CXCL13 and FDCSP, a follicular dendritic cell (FDC) marker responsible for B-cell positioning


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:61d61006961f6512040a
claim_id: claim:61d61006961f6512040a
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
For the first time we provide the human transcriptome for PB-fibro with COL15A1 and ENTPD1 markers and localisation around the airway epithelium

summary:
In Homo sapiens, peribronchial fibroblasts are marked by COL15A1 and ENTPD1 and localize around the airway epithelium.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:eab9bcd06916b37a3415
claim_id: claim:eab9bcd06916b37a3415
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
The cell type was located around the chondrocytes within cartilage in our Visium ST (Figure 2g) and could be identified by the expression of the marker gene COL12A1 in the human protein atlas

summary:
In Homo sapiens, perichondrial fibroblasts can be identified by expression of the marker gene COL12A1.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:15da72b676bc64157ac0
claim_id: claim:15da72b676bc64157ac0
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
myelinating Schwann cells (NFASC, NCMAP, MBP, PRX), non-myelinating Schwann cells (nmScwann) (NGFR, SCN7A, CHD2, L1CAM, NCAM1)

summary:
In Homo sapiens, myelinating Schwann cells are marked by NFASC, NCMAP, MBP, and PRX, while non-myelinating Schwann cells are marked by NGFR, SCN7A, CHD2, L1CAM, and NCAM1.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:08dc89e2d8b80660e3ce
claim_id: claim:08dc89e2d8b80660e3ce
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens, EVX1 is identified as a potential regulator of myelinating Schwann cells.
span_literal:
This analysis further reveals EVX1 - a homeobox gene in spinal cord development - as a potential regulator of myelinating Schwann cells.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:f44cb731b29b74f3141a
claim_id: claim:f44cb731b29b74f3141a
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens, non-myelinating Schwann cells express SOX10, ERBB3, and LGI4.
span_literal:
Second, the nmSchwann expressed some genes involved in Schwann cell development and maintenance (SOX10) and myelination (ERBB3 and LGI4)


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:26dcf3f6019feb1d2a0e
claim_id: claim:26dcf3f6019feb1d2a0e
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens, immune recruiting venous perivascular cells express ABCC and ICAM1 but not CSPG4.
span_literal:
we identified another perivascular cell type in the airways, expressing ABCC and ICAM1, but not CSPG4 - similarly to the postcapillary venous perivascular cells with a role in the homing of immune cells in peripheral lymph nodes


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:074a34d4bb108bb31aed
claim_id: claim:074a34d4bb108bb31aed
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens, intravascular macrophages express LYVE1 and MAF.
span_literal:
Previously identified macrophage subsets included intravascular macrophages (expressing LYVE1 and MAF)


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:52803ff0d3b6120e4ed8
claim_id: claim:52803ff0d3b6120e4ed8
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
We identified a new cluster expressing both monocyte CD14 and macrophage markers, termed Macro-intermediate

summary:
In Homo sapiens, Macro-intermediate cells express monocyte marker CD14 along with macrophage markers.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:b63dcc2d3686af9a482e
claim_id: claim:b63dcc2d3686af9a482e
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal: a novel cell cluster expressing metallothioneins (Macro-alv-MT) including MT1G, MT1X and MT1F
summary:
In Homo sapiens, alveolar macrophage metallothionein subset (Macro-alv-MT) expresses MT1G, MT1X, and MT1F.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:67159fdb7e6905c5a7f2
claim_id: claim:67159fdb7e6905c5a7f2
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
summary: In Homo sapiens, Macro-CCL macrophages express CXCL8, CCL4, and CCL20.
span_literal:
The final rare novel population of macrophages expressed chemokines including CXCL8, CCL4 and CCL20 and was named Macro-CCL.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:eba065a633e8cb036bc7
claim_id: claim:eba065a633e8cb036bc7
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
NK subsets included clusters with markers ITGAD/CD11d, LAG3, KLRC3/NKG3E, KLRC2/NKG2C (NK-CD11d), CD16+ (NK-CD16hi) and CD56 bright NK cells (NK-CD56 bright)

summary:
In Homo sapiens, NK-CD11d natural killer cells are marked by ITGAD, LAG3, KLRC3, and KLRC2; NK-CD16hi natural killer cells are marked by CD16; and NK-CD56 bright natural killer cells are marked by CD56.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:f8dc7e7762fc64f130c5
claim_id: claim:f8dc7e7762fc64f130c5
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
we saw two distinct CD8+ clusters analogous to populations found in the lung in cross tissue analysis (Conde et al., n.d.) expressing CX3CR1 and GZMB (CD8-EM/EMRA) and CRTAM and GZMK (CD8-TRM/EM)

summary:
In Homo sapiens lung, CD8-EM/EMRA T cells express CX3CR1 and GZMB, while CD8-TRM/EM T cells express CRTAM and GZMK.


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:964ae59d576ef789a92c
claim_id: claim:964ae59d576ef789a92c
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
The distinguishing markers for IgA versus IgG plasma cells included CCR10 and B-cell maturation antigen BCMA (TNFRSF17)

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


claim_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8:claim:b6626311408ce183122a
claim_id: claim:b6626311408ce183122a
paper_key: biorxiv:78211bc7-6c0f-1014-bc42-c103d41718b8
span_literal:
smFISH staining for ALDH1A3, MIA and RARRES1 validated the localisation at the SMG and distinguished these cells from the serous, mucous and other epithelial cells

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


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:30f5ef7804a2f2304830
claim_id: claim:30f5ef7804a2f2304830
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
span_literal:
As expected, POU4F1 and GPR151 were enriched in human Hb subpopulations compared to thalamic and non-neuronal populations

summary:
In Homo sapiens, POU4F1 and GPR151 are enriched in habenula neuron subpopulations compared to thalamic and non-neuronal populations.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:3553a70bdef7bfae495c
claim_id: claim:3553a70bdef7bfae495c
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
summary: In Homo sapiens, CHRNB4 is a marker gene for medial habenula subpopulations.
span_literal:
We also identified CHRNB4 and HTR2C as marker genes for MHb and LHb subpopulations, respectively (ETable 6).


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:1f8af252548ecf2cb987
claim_id: claim:1f8af252548ecf2cb987
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
span_literal:
CHRNB4 encodes a nicotinic acetylcholine receptor (nAChR) subunit, and is an MHb marker gene in both rodents and humans along with CHRNA3, another nAChR subunit listed as a top mean ratio marker for MHb

summary:
In Homo sapiens, CHRNB4 and CHRNA3, both encoding nicotinic acetylcholine receptor subunits, are marker genes for medial habenula neurons.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:7ca0637df75a88a3c555
claim_id: claim:7ca0637df75a88a3c555
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
summary: In Homo sapiens, medial habenula 2 cholinergic neurons express high levels of CHAT.
span_literal:
the identification of cholinergic neurons (MHb.2) expressing high levels of CHAT and the identification of a LHb.2 subpopulation expressing high levels of CRH and OPRM1.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:45845777d1fa688b36ab
claim_id: claim:45845777d1fa688b36ab
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
summary: In Homo sapiens, medial habenula 1 neurons express relatively high levels of CCK, TAC1, and TAC3.
span_literal:
Human MHb.1 neurons express relatively high levels of CCK, TAC1, and TAC3, which encode various neuropeptides; human MHb.2 neurons are cholinergic as evidenced by relative high levels of CHAT expression (Fig 1E).


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:86a1fe58ea2e54368a55
claim_id: claim:86a1fe58ea2e54368a55
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
span_literal:
Human MHb.1 neurons express relatively high levels of CCK, TAC1, and TAC3, which encode various neuropeptides; human MHb.2 neurons are cholinergic as evidenced by relative high levels of CHAT expression (Fig 1E).

summary:
In Homo sapiens, medial habenula 2 neurons are cholinergic as evidenced by high levels of CHAT expression.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:e7c3d2f381a178585f7c
claim_id: claim:e7c3d2f381a178585f7c
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
span_literal:
cells that highly expressed CHAT (putative MHb.2 neurons) clustered separately from other MHb cell types (Fig 3C).

summary:
In Homo sapiens, medial habenula 2 neurons highly express CHAT and cluster separately from other medial habenula cell types.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:c1c09d114f88d4cda3d2
claim_id: claim:c1c09d114f88d4cda3d2
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
span_literal:
we identified a spatially-organized cholinergic cell type (MHb.2), which was distinguished from other CHRNB4-expressing MHb subpopulations by enrichment of CHAT and CHRNA6.

summary:
In Homo sapiens, medial habenula 2 is distinguished from other CHRNB4-expressing medial habenula subpopulations by enrichment of CHAT and CHRNA6.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:1e16eea0eca641edff2e
claim_id: claim:1e16eea0eca641edff2e
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
summary: In Homo sapiens, HES5 is enriched in astrocytes in the epithalamus.
span_literal:
Interestingly, HES5 is enriched in astrocytes (Fig 1; enrichment t-stat = 7.794), suggesting this glial population in epithalamus may be affected in SCZD.


claim_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f:claim:1ecf5493923c06b55661
claim_id: claim:1ecf5493923c06b55661
paper_key: biorxiv:783f7e3b-7683-1014-81ff-bc1eeadb858f
summary: In Homo sapiens, PHOSPHO1 is enriched in the lateral habenula 3 subpopulation.
span_literal:
PHOSPHO1, an upregulated DEG in both Hb-enriched samples and caudate, showed enrichment in the human LHb.3 subpopulation (enrichment t-stat = 4.415).


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:33f91666e083fd7ac0b0
claim_id: claim:33f91666e083fd7ac0b0
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
Whole mounting immunostaining of organoids for NPHS1 (podocyte marker), LTL (proximal tubule marker), and CDH1 (distal tubule marker) indicate segmented nephron-like structures in WT organoids (E) and absence of such structures in CEP83-/- organoids (F).

summary:
In Homo sapiens, NPHS1 is a marker of podocyte, LTL is a marker of proximal tubule cell, and CDH1 is a marker of distal tubule cell in kidney organoids.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:49b392dc0e8d80c50da4
claim_id: claim:49b392dc0e8d80c50da4
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
Several genes associated with kidney development and kidney epithelial differentiation were differentially expressed with high expression in WT organoids, but showed comparatively low or absent expression in CEP83-/- organoids: these genes included kidney-specific lineage genes (PAX2, PAX8), and lineage/differentiation markers of glomerular cells (NPHS1, PODXL, WT1, PTPRO), proximal (HNF1B, LRP2, CUBN) and distal (EMX2, MAL2, EPCAM, GATA3) kidney epithelial cells.

summary:
In Homo sapiens, NPHS1, PODXL, WT1, and PTPRO are lineage/differentiation markers of glomerular cells in kidney organoids.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:3cf10cf82854b9b8a5cb
claim_id: claim:3cf10cf82854b9b8a5cb
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
Several genes associated with kidney development and kidney epithelial differentiation were differentially expressed with high expression in WT organoids, but showed comparatively low or absent expression in CEP83-/- organoids: these genes included kidney-specific lineage genes (PAX2, PAX8), and lineage/differentiation markers of glomerular cells (NPHS1, PODXL, WT1, PTPRO), proximal (HNF1B, LRP2, CUBN) and distal (EMX2, MAL2, EPCAM, GATA3) kidney epithelial cells.

summary:
In Homo sapiens, HNF1B, LRP2, and CUBN are lineage/differentiation markers of proximal kidney epithelial cells in kidney organoids.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:9a0efe5bd7ed9f26d02b
claim_id: claim:9a0efe5bd7ed9f26d02b
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
Several genes associated with kidney development and kidney epithelial differentiation were differentially expressed with high expression in WT organoids, but showed comparatively low or absent expression in CEP83-/- organoids: these genes included kidney-specific lineage genes (PAX2, PAX8), and lineage/differentiation markers of glomerular cells (NPHS1, PODXL, WT1, PTPRO), proximal (HNF1B, LRP2, CUBN) and distal (EMX2, MAL2, EPCAM, GATA3) kidney epithelial cells.

summary:
In Homo sapiens, EMX2, MAL2, EPCAM, and GATA3 are lineage/differentiation markers of distal kidney epithelial cells in kidney organoids.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:b96b20de6121eea13d9d
claim_id: claim:b96b20de6121eea13d9d
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
summary: In Homo sapiens, GATA3, HOXB7, HOXD11, and EYA1 are marker genes of nephron progenitor cells.
span_literal:
A marked upregulation of nephron progenitor marker genes (GATA3, HOXB7, HOXD11, EYA1)35–42 was observed in both WT and CEP83-/- cells at day 7 (Figure 4-figure supplement 3A-D), suggesting that the differentiation path of pluripotent CEP83-/- cells to IM nephron progenitors was largely intact.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:5c318a4abeed83452f6a
claim_id: claim:5c318a4abeed83452f6a
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
summary: In Homo sapiens, kidney progenitor/nascent nephron cells express PAX8, EYA1, and HOXB7.
span_literal:
We identified marker genes for each cluster (Figure 4C), indicating that clusters 1, 3 and 4 represented kidney progenitors/nascent nephrons (expressing e. g. PAX8, EYA1, HOXB7) in different phases of the cell cycle.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:a81359ba232f68357e8b
claim_id: claim:a81359ba232f68357e8b
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
From this analysis, we observed a consistent upregulation of genes that are normally expressed in early lateral plate mesoderm (LPM), including OSR1, FOXF1, FOXF2, FENDRR, HAND1, HAND2, CXCL12, GATA5, and GATA645–69 (Figure 6A-I).

summary:
In Homo sapiens, OSR1, FOXF1, FOXF2, FENDRR, HAND1, HAND2, CXCL12, GATA5, and GATA6 are normally expressed in early lateral plate mesoderm.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:7592b9105a9f471df884
claim_id: claim:7592b9105a9f471df884
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
A subset of LPM genes enriched for expression in CEP83-mutant cells at D25 of differentiation were indicative of cardiac or cardiopharyngeal (ISL1, TBX1) as well as of vascular progenitor (SOX7, SOX11, NAP1L3, LMO2, GATA2) differentiation70–77 (Figure 6J-P).

summary:
In Homo sapiens, ISL1 and TBX1 are markers indicative of cardiac or cardiopharyngeal progenitor differentiation.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:5eae509ad1fbe4168fb2
claim_id: claim:5eae509ad1fbe4168fb2
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
A subset of LPM genes enriched for expression in CEP83-mutant cells at D25 of differentiation were indicative of cardiac or cardiopharyngeal (ISL1, TBX1) as well as of vascular progenitor (SOX7, SOX11, NAP1L3, LMO2, GATA2) differentiation70–77 (Figure 6J-P).

summary:
In Homo sapiens, SOX7, SOX11, NAP1L3, LMO2, and GATA2 are markers indicative of vascular progenitor differentiation.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:ae6f22e86e9509dbb68f
claim_id: claim:ae6f22e86e9509dbb68f
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
Of note, CEP83-deficient cells at D25 expressed increased levels of LPM genes expressed in mesothelial (including OSR1, CXCL12, HAND1/2), cardiopharyngeal (including ISL1, TBX1), and endothelial/hematopoietic (including TAL1, LMO2, GATA2) progenitors33, 60.

summary:
In Homo sapiens, OSR1, CXCL12, HAND1, and HAND2 are lateral plate mesoderm genes expressed in mesothelial progenitors.


claim_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc:claim:32602fc2827438ad9067
claim_id: claim:32602fc2827438ad9067
paper_key: biorxiv:7883a920-6c54-1014-9611-e2c343a4c7dc
span_literal:
Of note, CEP83-deficient cells at D25 expressed increased levels of LPM genes expressed in mesothelial (including OSR1, CXCL12, HAND1/2), cardiopharyngeal (including ISL1, TBX1), and endothelial/hematopoietic (including TAL1, LMO2, GATA2) progenitors33, 60.

summary:
In Homo sapiens, TAL1, LMO2, and GATA2 are lateral plate mesoderm genes expressed in endothelial/hematopoietic progenitors.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:54e029dc69e914fef09e
claim_id: claim:54e029dc69e914fef09e
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
DA neurons of the human adult substantia nigra pars compacta (SNc), corresponding to the ventral A9 region, are marked by the expression of SOX6 and AGTR1, express higher levels of PD-causative genes and have been shown to be more vulnerable to Parkinson’s disease (PD) (Kamath et al., 2022).

summary:
In Homo sapiens, dopaminergic neurons of the ventral A9 region of the substantia nigra pars compacta are marked by the expression of SOX6 and AGTR1.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:0fb02523e56451f4b0cd
claim_id: claim:0fb02523e56451f4b0cd
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
On the other hand, both the dorsal A9 region of the SNc and the neighboring ventral tegmental area (A10), contain DA neurons that highly express CALB1 and are more resilient to neuronal death in PD (Kamath et al., 2022).

summary:
In Homo sapiens, dopaminergic neurons of the dorsal A9 region of the substantia nigra pars compacta and the ventral tegmental area (A10) highly express CALB1 and are more resilient to neuronal death in Parkinson's disease.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:d89e1999ed198ad2fae8
claim_id: claim:d89e1999ed198ad2fae8
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
We found a high percentage of SOX6 and ALDH1A1 positive cells that represent the more ventral SNc (A9) population, and low percentages of Calb1 positive cells that correspond to the dorsal SNc (A9) and the ventral tegmental region (A10)

summary:
In Homo sapiens, SOX6-positive and ALDH1A1-positive iPSC-derived dopaminergic neurons represent the ventral substantia nigra pars compacta (A9) population.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:3cdc67e6c949fd8980ab
claim_id: claim:3cdc67e6c949fd8980ab
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
We found a high percentage of SOX6 and ALDH1A1 positive cells that represent the more ventral SNc (A9) population, and low percentages of Calb1 positive cells that correspond to the dorsal SNc (A9) and the ventral tegmental region (A10)

summary:
In Homo sapiens, CALB1-positive iPSC-derived dopaminergic neurons correspond to the dorsal substantia nigra pars compacta (A9) and the ventral tegmental area (A10).


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:edf7cd8c0802d48f45f5
claim_id: claim:edf7cd8c0802d48f45f5
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
we identified two subgroups based on the expression pattern of CCN1, a cell cycle gene – roughly 20% of the cells expressing CCN1 were classified as the progenitor subgroup, and ∼80% of the cells lacking CCN1 expression were deemed terminally differentiated post cell cycle exit

summary:
In Homo sapiens iPSC-derived patterned Ascl1-driven dopaminergic neurons, CCN1 expression marks the progenitor subgroup, while cells lacking CCN1 are terminally differentiated.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:26315a662111528400c9
claim_id: claim:26315a662111528400c9
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
other cell cycle genes such as TOP2A and CDK1 were restricted to the progenitor subgroup and neural specific markers such as TH and SNAP25 expressed more highly in the clusters corresponding to the induced DA subgroup

summary:
In Homo sapiens iPSC-derived patterned Ascl1-driven dopaminergic neurons, TOP2A and CDK1 are restricted to the progenitor subgroup, while TH and SNAP25 are more highly expressed in the induced dopaminergic neuron subgroup.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:9f197a4e2969ce645a3b
claim_id: claim:9f197a4e2969ce645a3b
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
other cell cycle genes such as TOP2A and CDK1 were restricted to the progenitor subgroup and neural specific markers such as TH and SNAP25 expressed more highly in the clusters corresponding to the induced DA subgroup

summary:
In Homo sapiens iPSC-derived patterned Ascl1-driven dopaminergic neurons, TH and SNAP25 are more highly expressed in the induced dopaminergic neuron subgroup compared to the progenitor subgroup.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:9c0316daddd16e3af406
claim_id: claim:9c0316daddd16e3af406
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
Unsupervised clustering and visualization of Day 15 PA-DANs revealed a small progenitor population expressing CDK1 and a terminally differentiated population lacking CDK1 expression, which was enriched in TH mRNA

summary:
In Homo sapiens iPSC-derived patterned Ascl1-driven dopaminergic neurons at Day 15, the progenitor population expresses CDK1, while the terminally differentiated population lacks CDK1 and is enriched in TH.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:9b7801cd78260ea9db7c
claim_id: claim:9b7801cd78260ea9db7c
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
Unsupervised clustering and visualization of Day 15 PA-DANs revealed a small progenitor population expressing CDK1 and a terminally differentiated population lacking CDK1 expression, which was enriched in TH mRNA

summary:
In Homo sapiens iPSC-derived patterned Ascl1-driven dopaminergic neurons at Day 15, the terminally differentiated population lacks CDK1 expression and is enriched in TH.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:6079aa173340c5ec3e90
claim_id: claim:6079aa173340c5ec3e90
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal: SNCA and STMN2 – where clusters in Class 1 showed low expression, and clusters in Classes 2 and 3
summary:
In Homo sapiens iPSC-derived patterned Ascl1-driven dopaminergic neurons, SNCA and STMN2 are neuron-specific markers with high expression in Classes 2 and 3 and low expression in Class 1.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:a672b6ec5e70391a45f5
claim_id: claim:a672b6ec5e70391a45f5
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
we found a moderate to high expression of DA markers such as TH, DDC and KCNJ6 as well as GABA receptors and receptor associated proteins, GABARAP and ABAT, across clusters, typical of A9-DA subtypes

summary:
In Homo sapiens, A9 dopaminergic neuron subtypes are marked by moderate to high expression of TH, DDC, KCNJ6, GABARAP, and ABAT.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:99f7ef0b4bf5b7c7b515
claim_id: claim:99f7ef0b4bf5b7c7b515
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
We also confirmed the absence of striatal GABAergic neurons based on the sparse expression of PPP1R1B

summary:
In Homo sapiens, striatal GABAergic neurons are marked by PPP1R1B expression, which was sparse in the iPSC-derived patterned Ascl1-driven dopaminergic neuron population confirming their absence.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:318f5feff937f799c76a
claim_id: claim:318f5feff937f799c76a
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
We found high DDT expression in our PA-DANs similar to that found in the SOX6_DDT and CALB1_RBP4 A9-DA subtypes

summary:
In Homo sapiens, the SOX6_DDT and CALB1_RBP4 A9 dopaminergic neuron subtypes show high DDT expression.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:7d73bd900f73bbac1176
claim_id: claim:7d73bd900f73bbac1176
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
our A9-like 3D assembled midbrain organoids generated using these PA-DANs show markers of PD sensitive DA neurons, such as SOX6, AGTR1 and ALDH1A1

summary:
In Homo sapiens, Parkinson's disease-sensitive dopaminergic neurons of the A9 region are marked by SOX6, AGTR1, and ALDH1A1.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:fbfc1e263b001be83195
claim_id: claim:fbfc1e263b001be83195
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
NGN2 expression under a doxycycline-inducible promoter primarily yields vGlut1- or vGlut2-positive cortical or motor neurons

summary:
In Homo sapiens, NGN2 expression primarily yields vGlut1-positive or vGlut2-positive cortical or motor neurons from iPSCs.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:d5ba2c1f1a2418b6fc22
claim_id: claim:d5ba2c1f1a2418b6fc22
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
Representative images of 5-weeks old A9-like 3D assembled organoids showing nuclear localization of ventral A9 marker SOX6 (green), midbrain marker, FOXA2 (magenta), cytoplasmic localization of dorsal A9 and A10 marker CALB1 (red), and nuclear marker DAPI (blue).

summary:
In Homo sapiens iPSC-derived A9-like 3D assembled organoids, SOX6 is a ventral A9 dopaminergic neuron marker, FOXA2 is a midbrain marker, and CALB1 is a dorsal A9 and A10 dopaminergic neuron marker.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:035b9b4c8e555625265e
claim_id: claim:035b9b4c8e555625265e
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal:
Representative images of 5-weeks old A9-like 3D assembled organoids showing nuclear localization of ventral A9 marker SOX6 (green), midbrain marker, FOXA2 (magenta), cytoplasmic localization of dorsal A9 and A10 marker CALB1 (red), and nuclear marker DAPI (blue).

summary:
In Homo sapiens iPSC-derived A9-like 3D assembled organoids, CALB1 is a marker of dorsal A9 and A10 dopaminergic neurons, while SOX6 marks ventral A9 dopaminergic neurons.


claim_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662:claim:14dbfa6252778d0ca859
claim_id: claim:14dbfa6252778d0ca859
paper_key: biorxiv:78e3a11a-7eb2-1014-99eb-f342cda99662
span_literal: the ventral SOX6-positive DA subtypes are more vulnerable
summary:
In Homo sapiens, the ventral SOX6-positive dopaminergic neuron subtypes of the substantia nigra pars compacta are more vulnerable in Parkinson's disease.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:64e2ed269d8da18651ec
claim_id: claim:64e2ed269d8da18651ec
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
we first identified the clusters of clear neural/glial (neuronal) or myeloid/immune origin by measuring the expression of known markers for immune cells (CD4, CD83 & HLA-DRA) and neuronal cells (S100B, OLIG1 & SCG2)

summary:
In Homo sapiens glioblastoma, CD4, CD83, and HLA-DRA are used as markers for immune cells, while S100B, OLIG1, and SCG2 are used as markers for neuronal cells.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:e5da571fb246a12193ac
claim_id: claim:e5da571fb246a12193ac
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal: In both groups, qGSCs had a markedly high expression of DCX, SOX4, SOX11 and DLL3 genes.
summary:
In Homo sapiens glioblastoma, quiescent glioblastoma stem-like cells have markedly high expression of DCX, SOX4, SOX11, and DLL3.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:9df22cf4d0afd084ffb5
claim_id: claim:9df22cf4d0afd084ffb5
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
On the other hand, cGSCs in both groups were marked by overexpression of HMGB2, HSP90B1 and KPNA2 apart from TOP2A (figure 3 C).

summary:
In Homo sapiens glioblastoma, cycling glioblastoma stem-like cells are marked by overexpression of HMGB2, HSP90B1, KPNA2, and TOP2A.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:1b287e1ca60ca0a5a276
claim_id: claim:1b287e1ca60ca0a5a276
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
summary: In Homo sapiens glioblastoma, SLC1A2 is expressed by astrocytes as a cell type specific marker.
span_literal:
Whilst SLC1A2, APOD, PLP1, CD74, and RTN1 are cell type specific proteins and expressed by astrocytes, oligodendrocytes, OPCs and endothelial cells respectively[25], TOP2A and HMGB2 expression is specific to transcriptional activation and cell cycle[26, 27].


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:fbb27982330497729d41
claim_id: claim:fbb27982330497729d41
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
Whilst SLC1A2, APOD, PLP1, CD74, and RTN1 are cell type specific proteins and expressed by astrocytes, oligodendrocytes, OPCs and endothelial cells respectively[25], TOP2A and HMGB2 expression is specific to transcriptional activation and cell cycle[26, 27].

summary:
In Homo sapiens glioblastoma, APOD and PLP1 are expressed by oligodendrocytes as cell type specific markers.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:785a4467630c0dcc37d8
claim_id: claim:785a4467630c0dcc37d8
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
Whilst SLC1A2, APOD, PLP1, CD74, and RTN1 are cell type specific proteins and expressed by astrocytes, oligodendrocytes, OPCs and endothelial cells respectively[25], TOP2A and HMGB2 expression is specific to transcriptional activation and cell cycle[26, 27].

summary:
In Homo sapiens glioblastoma, CD74 is expressed by oligodendrocyte precursor cells as a cell type specific marker.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:a695d6e74acbb79930df
claim_id: claim:a695d6e74acbb79930df
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
summary:
In Homo sapiens glioblastoma, RTN1 is expressed by endothelial cells as a cell type specific marker.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:5ddef982ea25d7942511
claim_id: claim:5ddef982ea25d7942511
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
while the set of clusters overexpressing a large number of ribosomal genes (RP), especially RPL23, RPL34, RPS3, RPS13, RPS29 also correlate with qGSC cells, the cGSC dominant set was marked by the overexpression of a number of high mobility group (HMG) genes including HMGB1 and HMGB2 and heterogeneous nuclear ribonucleoprotein (hnRNP) genes, notably HNRNPA3 and HNRNPD.

summary:
In Homo sapiens glioblastoma, quiescent glioblastoma stem-like cells overexpress ribosomal protein genes RPL23, RPL34, RPS3, RPS13, and RPS29.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:60b9b18a6bb8b94ae520
claim_id: claim:60b9b18a6bb8b94ae520
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
while the set of clusters overexpressing a large number of ribosomal genes (RP), especially RPL23, RPL34, RPS3, RPS13, RPS29 also correlate with qGSC cells, the cGSC dominant set was marked by the overexpression of a number of high mobility group (HMG) genes including HMGB1 and HMGB2 and heterogeneous nuclear ribonucleoprotein (hnRNP) genes, notably HNRNPA3 and HNRNPD.

summary:
In Homo sapiens glioblastoma, cycling glioblastoma stem-like cells overexpress high mobility group genes HMGB1 and HMGB2 and heterogeneous nuclear ribonucleoprotein genes HNRNPA3 and HNRNPD.


claim_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d:claim:9d223c7eb75253f62766
claim_id: claim:9d223c7eb75253f62766
paper_key: biorxiv:7a206a01-6c0e-1014-b046-f87c164ca53d
span_literal:
Key overexpressed genes include DCX, SOX4 and DLL3, known markers for quiescence, stemness and tumorigenicity.

summary:
In Homo sapiens glioblastoma, DCX, SOX4, and DLL3 are overexpressed as known markers for quiescence, stemness, and tumorigenicity in glioblastoma stem-like cells.


claim_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82:claim:91f0595ab98f32a91d88
claim_id: claim:91f0595ab98f32a91d88
paper_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82
span_literal:
As an initial validation, we examined two genes with well-established cell type specificity: KRT14, a structural keratin predominantly expressed by keratinocytes, and HLA-DRB1, a canonical antigen-presentation gene enriched in antigen-presenting cells.

summary:
In Homo sapiens, KRT14 is a structural keratin predominantly expressed by keratinocytes, and HLA-DRB1 is a canonical antigen-presentation gene enriched in antigen-presenting cells.


claim_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82:claim:c0433048d1e79e425fac
claim_id: claim:c0433048d1e79e425fac
paper_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82
span_literal:
As an initial validation, we examined two genes with well-established cell type specificity: KRT14, a structural keratin predominantly expressed by keratinocytes, and HLA-DRB1, a canonical antigen-presentation gene enriched in antigen-presenting cells.

summary:
In Homo sapiens, HLA-DRB1 is a canonical antigen-presentation gene enriched in antigen-presenting cells.


claim_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82:claim:4322135a782b24c4bd6a
claim_id: claim:4322135a782b24c4bd6a
paper_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82
span_literal:
S3R recovered spatially coherent coefficient fields that attributed KRT14 to keratinocytes and HLA-DRB1 to macrophage and dendritic-cell compartments, with boundaries that mirrored histological features (Fig. 3b).

summary:
In Homo sapiens, S3R attributed KRT14 expression to keratinocytes and HLA-DRB1 expression to macrophage and dendritic cell compartments in skin tissue.


claim_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82:claim:fbe001fd911a03e5e83e
claim_id: claim:fbe001fd911a03e5e83e
paper_key: biorxiv:7c369d90-739f-1014-825b-83f20b310b82
span_literal:
A downstream contribution analysis that ranks predictors by marginal effect confirmed keratinocytes as the dominant source attributed for KRT14 and macrophages/dendritic cells for HLA-DRB1 (Fig. 3c).

summary:
In Homo sapiens, keratinocytes are the dominant source of KRT14 expression, and macrophages and dendritic cells are the dominant sources of HLA-DRB1 expression.


claim_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1:claim:54c99589d5f7d7b1fb75
claim_id: claim:54c99589d5f7d7b1fb75
paper_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1
summary: In Homo sapiens brain, microglia are identified by the marker gene CSF1R.
span_literal:
we identified and annotated the major cell types of the brain based on known marker genes, including microglia (CSF1R), endothelial including pericytes (VWF, FLT1), astrocytes (CABLES1, AQP4), oligodendrocyte precursors (VCAN), oligodendrocytes (ANLN), and neurons (GAD1, NRGN)


claim_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1:claim:3f63695349f46526d8b5
claim_id: claim:3f63695349f46526d8b5
paper_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1
span_literal:
we identified and annotated the major cell types of the brain based on known marker genes, including microglia (CSF1R), endothelial including pericytes (VWF, FLT1), astrocytes (CABLES1, AQP4), oligodendrocyte precursors (VCAN), oligodendrocytes (ANLN), and neurons (GAD1, NRGN)

summary:
In Homo sapiens brain, endothelial cells including pericytes are identified by the marker genes VWF and FLT1.


claim_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1:claim:4fe63d554b5d239addef
claim_id: claim:4fe63d554b5d239addef
paper_key: biorxiv:7c5d5c2e-7293-1014-98d5-eebfad1ae1b1
summary: In Homo sapiens, APOE, TREM2, and INPP5D are upregulated in Alzheimer's disease microglia.
span_literal:
A few genes upregulated in human AD that our differential expression analysis revealed were APOE, TREM2, and INPP5D


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:3ed110b8c53820d50c38
claim_id: claim:3ed110b8c53820d50c38
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
Kupffer cell (KC)-like liver resident macrophages (VSIG4, MARCO and CD5L), recently recruited monocyte-like (Mono-Mac) myeloid cells (S100A8/9 and LYZ) or major histocompatibility class II (MHC II) high myeloid cells (HLA-DRA/DPB1/DQB1)

summary:
In Homo sapiens liver, Kupffer cell-like liver resident macrophages are marked by VSIG4, MARCO, and CD5L.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:eae7feb8539dd24a2a0f
claim_id: claim:eae7feb8539dd24a2a0f
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
Kupffer cell (KC)-like liver resident macrophages (VSIG4, MARCO and CD5L), recently recruited monocyte-like (Mono-Mac) myeloid cells (S100A8/9 and LYZ) or major histocompatibility class II (MHC II) high myeloid cells (HLA-DRA/DPB1/DQB1)

summary:
In Homo sapiens liver, recently recruited monocyte-like myeloid cells are marked by S100A8, S100A9, and LYZ.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:6a810823b4bf64521860
claim_id: claim:6a810823b4bf64521860
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
Kupffer cell (KC)-like liver resident macrophages (VSIG4, MARCO and CD5L), recently recruited monocyte-like (Mono-Mac) myeloid cells (S100A8/9 and LYZ) or major histocompatibility class II (MHC II) high myeloid cells (HLA-DRA/DPB1/DQB1)

summary:
In Homo sapiens liver, major histocompatibility complex class II high myeloid cells are marked by HLA-DRA, HLA-DPB1, and HLA-DQB1.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:c395c57f565f844e7c20
claim_id: claim:c395c57f565f844e7c20
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
A minor population of MHC II and CLEC9A high cells was seen in both pediatric and adult livers. These may be conventional type 1 dendritic cells (cDC1)

summary:
In Homo sapiens liver, a minor population of CLEC9A high cells may represent conventional type 1 dendritic cells.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:ae022c4056ceda5a4bd6
claim_id: claim:ae022c4056ceda5a4bd6
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
pediatric Kupffer-like cells (MARCO+C1QA+VSIG4+) exhibited higher expression of immune activation genes, including CCL4, CCL3 and IL1B

summary:
In Homo sapiens, pediatric Kupffer-like cells marked by MARCO, C1QA, and VSIG4 exhibited higher expression of CCL4, CCL3, and IL1B compared to adult.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:cdbd972ab3bedc798050
claim_id: claim:cdbd972ab3bedc798050
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
summary: In Homo sapiens liver, plasmacytoid dendritic cells are positive for IL3RA and PLAC8.
span_literal:
We also identified plasmacytoid dendritic cells (pDCs; IL3RA+ and PLAC8+) 2 which were more abundant in IFALD


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:8fab170bf94e6642e799
claim_id: claim:8fab170bf94e6642e799
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
Comparing these two HSC populations we saw fibrosis genes (PDGFRA, CXCL12, COL1A1 and IGFBP3) more highly expressed in HSC population two which is mainly adult and IFALD cells

summary:
In Homo sapiens liver, hepatic stellate cell population two (enriched in adult and Intestinal Failure-Associated Liver Disease cells) shows higher expression of PDGFRA, CXCL12, COL1A1, and IGFBP3 compared to hepatic stellate cell population one.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:6da7b4bf2c9a6a507f32
claim_id: claim:6da7b4bf2c9a6a507f32
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal: In KC-like cells we saw higher expression of profibrotic genes (i.e LY96)
summary:
In Homo sapiens Intestinal Failure-Associated Liver Disease liver, Kupffer cell-like cells show higher expression of the profibrotic gene LY96.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:ef5ccabc6686f3961914
claim_id: claim:ef5ccabc6686f3961914
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal: MHC II high myeloid cells HMOX1 and APOE
summary:
In Homo sapiens liver, major histocompatibility complex class II high myeloid cells show higher expression of HMOX1 and APOE in pediatric compared to adult cells.


claim_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6:claim:aec17381c5057633247c
claim_id: claim:aec17381c5057633247c
paper_key: biorxiv:7d48f408-80c3-1014-8100-959ab60f80b6
span_literal:
In the Mono-Mac cells, genes associated with cellular stress pathways were more expressed in pediatric cells with AREG 60 and several heat shock protein-related genes were more highly expressed

summary:
In Homo sapiens liver, monocyte-like myeloid cells show higher expression of AREG in pediatric compared to adult cells.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:631061fcf58096e9b3b5
claim_id: claim:631061fcf58096e9b3b5
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
Four features were uniquely upregulated in CD14 Monocytes, which constitute the largest proportion of cells: ERVLB4-4q31.21a (intergenic), HARLEQUIN_7q33a (intergenic), HML2-1q22, and MER34B-4q21.2.

summary:
In Homo sapiens peripheral blood mononuclear cells, CD14 monocytes are marked by upregulation of ERVLB4-4q31.21a, HARLEQUIN_7q33a, HML2-1q22, and MER34B-4q21.2.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:53981c385752dfc33d92
claim_id: claim:53981c385752dfc33d92
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
One feature, MER4B-19q13.42a, was uniquely upregulated in CD16 Monocytes, while MER34B-1q23.3b and MER4-22q12.3 were significantly upregulated for both monocyte subsets, suggesting that these may be useful in distinguishing monocytes from other cell types, but less useful in resolving subsets.

summary:
In Homo sapiens peripheral blood mononuclear cells, MER4B-19q13.42a is uniquely upregulated in CD16 monocytes, while MER34B-1q23.3b and MER4-22q12.3 are upregulated in both monocyte subsets.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:25dbfde908f04e4703ab
claim_id: claim:25dbfde908f04e4703ab
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Significant upregulation of MER4B-19q13.42b was detected in both CD16 monocytes and pDCs.
summary:
In Homo sapiens peripheral blood mononuclear cells, MER4B-19q13.42b is significantly upregulated in CD16 monocytes.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:0b4876538218a4c4c255
claim_id: claim:0b4876538218a4c4c255
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Significant upregulation of MER4B-19q13.42b was detected in both CD16 monocytes and pDCs.
summary:
In Homo sapiens peripheral blood mononuclear cells, MER4B-19q13.42b is significantly upregulated in plasmacytoid dendritic cells.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:2f4f3a35c83f3422ebf8
claim_id: claim:2f4f3a35c83f3422ebf8
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Two of these, ERV316A3-21q21.2g and PRIMA4-12p11.21b, were unique to pDCs.
summary:
In Homo sapiens peripheral blood mononuclear cells, ERV316A3-21q21.2g and PRIMA4-12p11.21b are uniquely expressed in plasmacytoid dendritic cells.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:d0247b5ccc66ec9d2b0d
claim_id: claim:d0247b5ccc66ec9d2b0d
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
Considering the strength of this marker compared with canonical marker genes, expression of HARLEQUIN-1q32.1 in pDCs has the greatest effect size and significance of all features tested (adjusted p value < 1e-122 ; average log2 fold change = 4.213),and is among the top markers for all cell subtypes.

summary:
In Homo sapiens peripheral blood mononuclear cells, HARLEQUIN-1q32.1 is a top marker of plasmacytoid dendritic cells with the greatest effect size and significance of all features tested.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:b6559d2b678e925b4083
claim_id: claim:b6559d2b678e925b4083
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: cDC2 were marked by HARLEQUIN-6q21.31.
summary:
In Homo sapiens peripheral blood mononuclear cells, conventional type 2 dendritic cells are marked by HARLEQUIN-6q21.31.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:461c742a57148e91f0a3
claim_id: claim:461c742a57148e91f0a3
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: pDC were marked by ERV316A3-21q21g and PRIMA4-12p11.21b.
summary:
In Homo sapiens peripheral blood mononuclear cells, plasmacytoid dendritic cells are marked by ERV316A3-21q21g and PRIMA4-12p11.21b.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:66888930d5d6ae785f66
claim_id: claim:66888930d5d6ae785f66
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Naive B cells were marked by HML5-8p21.2 and MER4-17q21.2d.
summary:
In Homo sapiens peripheral blood mononuclear cells, naive B cells are marked by HML5-8p21.2 and MER4-17q21.2d.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:51859f097ebcb3580e0b
claim_id: claim:51859f097ebcb3580e0b
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Memory B cells were marked by MER101-16p11.2c and MER61-1q23.1c.
summary:
In Homo sapiens peripheral blood mononuclear cells, memory B cells are marked by MER101-16p11.2c and MER61-1q23.1c.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:d7020feabe864b958919
claim_id: claim:d7020feabe864b958919
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: MAIT cells were marked by HERVS71-8p23.1b, and NK cells were marked by HML5-1q23.1.
summary:
In Homo sapiens peripheral blood mononuclear cells, mucosal-associated invariant T cells are marked by HERVS71-8p23.1b, and natural killer cells are marked by HML5-1q23.1.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:5d2aaf2f796db6a638fb
claim_id: claim:5d2aaf2f796db6a638fb
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Both NK cells and the NK_CD56bright subtype shared expression of HERVH-12p13.31d.
summary:
In Homo sapiens peripheral blood mononuclear cells, natural killer cells and the NK_CD56bright subtype share expression of HERVH-12p13.31d.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:3648eeca75cb8772c820
claim_id: claim:3648eeca75cb8772c820
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Both NK cells and the NK_CD56bright subtype shared expression of HERVH-12p13.31d.
summary:
In Homo sapiens peripheral blood mononuclear cells, the NK_CD56bright subtype shares expression of HERVH-12p13.31d with natural killer cells.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:c634769e286caea4e956
claim_id: claim:c634769e286caea4e956
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
Finally, CD4+ TCM, naive CD8+ T cells and CD8+ TEM shared expression of HARLEQUIN-17q12, which may be a T cell lineage marker LTR transcript.

summary:
In Homo sapiens peripheral blood mononuclear cells, CD4+ central memory T cells, naive CD8+ T cells, and CD8+ effector memory T cells share expression of HARLEQUIN-17q12, which may be a T cell lineage marker.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:e4ae4fb635037ea7a2c2
claim_id: claim:e4ae4fb635037ea7a2c2
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
Finally, CD4+ TCM, naive CD8+ T cells and CD8+ TEM shared expression of HARLEQUIN-17q12, which may be a T cell lineage marker LTR transcript.

summary:
In Homo sapiens peripheral blood mononuclear cells, naive CD8+ T cells share expression of HARLEQUIN-17q12, which may be a T cell lineage marker.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:a07b7380cbcf67ce7026
claim_id: claim:a07b7380cbcf67ce7026
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
Finally, CD4+ TCM, naive CD8+ T cells and CD8+ TEM shared expression of HARLEQUIN-17q12, which may be a T cell lineage marker LTR transcript.

summary:
In Homo sapiens peripheral blood mononuclear cells, CD8+ effector memory T cells share expression of HARLEQUIN-17q12, which may be a T cell lineage marker.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:04802526a64ddd3a4b58
claim_id: claim:04802526a64ddd3a4b58
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
CD8+ TEM also shared expression of PRIMA4-14q22.1 with and NK cells and CD4+ subtypes, as well as MER101-16p12.2c with NK proliferating cells and dnT cells.

summary:
In Homo sapiens peripheral blood mononuclear cells, CD8+ effector memory T cells express PRIMA4-14q22.1 and MER101-16p12.2c.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:18c669dbbb9291f1d519
claim_id: claim:18c669dbbb9291f1d519
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: CD4+ TCM, CD4+ Naive and B intermediate cells expressed ERV316A3-2q22.2b.
summary:
In Homo sapiens peripheral blood mononuclear cells, CD4+ central memory T cells, CD4+ naive T cells, and B intermediate cells express ERV316A3-2q22.2b.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:92d0e8789aa13d1a59c1
claim_id: claim:92d0e8789aa13d1a59c1
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Additionally, intermediate B cells and memory B cells shared expression of HARLEQUIN-1q23.1.
summary:
In Homo sapiens peripheral blood mononuclear cells, intermediate B cells and memory B cells share expression of HARLEQUIN-1q23.1.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:365cd401e09b2aa1cc6f
claim_id: claim:365cd401e09b2aa1cc6f
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal: Additionally, intermediate B cells and memory B cells shared expression of HARLEQUIN-1q23.1.
summary:
In Homo sapiens peripheral blood mononuclear cells, memory B cells share expression of HARLEQUIN-1q23.1 with intermediate B cells.


claim_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb:claim:9cb7f888d54a00a01bf5
claim_id: claim:9cb7f888d54a00a01bf5
paper_key: biorxiv:7e2bfe95-6d70-1014-a610-a94ffdb50ceb
span_literal:
Memory and intermediate B cell subtypes also shared differential relative expression of ERVLE-4q24e with naive B cells and HERVEA-5q22.2 with plasmablasts showing common retrotranscriptomic patterns across B lineage cells.

summary:
In Homo sapiens peripheral blood mononuclear cells, memory B cells, intermediate B cells, and naive B cells share differential expression of ERVLE-4q24e, while memory B cells, intermediate B cells, and plasmablasts share expression of HERVEA-5q22.2.


claim_key: biorxiv:8060bfa3-6d4f-1014-b2ea-be74caad434f:claim:428f4662848499c0e6fa
claim_id: claim:428f4662848499c0e6fa
paper_key: biorxiv:8060bfa3-6d4f-1014-b2ea-be74caad434f
span_literal:
Expression of T cell exhaustion markers in single CD4+ T cells of patients with low vs. high TERT expression in malignant tumor cells (</>0.05 TPM). Jerby-Arnon cohort, pre therapy samples.

summary:
In Homo sapiens melanoma, CD4+ T cells from tumors with high TERT expression show increased expression of T cell exhaustion markers.


claim_key: biorxiv:8060bfa3-6d4f-1014-b2ea-be74caad434f:claim:faee32b9da04014da95a
claim_id: claim:faee32b9da04014da95a
paper_key: biorxiv:8060bfa3-6d4f-1014-b2ea-be74caad434f
span_literal:
if malignant cells expressed higher levels of TERT, the corresponding CD4+ T cells from these tumors expressed exhaustion markers at higher levels (CTLA4, PDCD1/PD1, HAVCR2/TIM3 and TIGIT, not LAG3, Fig. 1B).

summary:
In Homo sapiens melanoma, CD4+ T cells from tumors with high TERT expression show elevated expression of the exhaustion markers CTLA4, PDCD1, HAVCR2, and TIGIT, but not LAG3.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:4eb953d7f650edc19d9a
claim_id: claim:4eb953d7f650edc19d9a
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
a basal lineage (marked by KRT5, KRT14, and ACTA2), a hormone receptor–associated luminal lineage (LumHR, marked by KRT8, KRT18, and KRT19), and a secretory luminal lineage (LumSec, expressing KRT15 and SCGB2A2)

summary:
In Homo sapiens breast cancer, the basal lineage of epithelial cells is marked by KRT5, KRT14, and ACTA2.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:525a467e2dadff993d3a
claim_id: claim:525a467e2dadff993d3a
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
a basal lineage (marked by KRT5, KRT14, and ACTA2), a hormone receptor–associated luminal lineage (LumHR, marked by KRT8, KRT18, and KRT19), and a secretory luminal lineage (LumSec, expressing KRT15 and SCGB2A2)

summary:
In Homo sapiens breast cancer, the hormone receptor-associated luminal lineage (LumHR) of epithelial cells is marked by KRT8, KRT18, and KRT19.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:6fde916e2c9ae7d28199
claim_id: claim:6fde916e2c9ae7d28199
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
a basal lineage (marked by KRT5, KRT14, and ACTA2), a hormone receptor–associated luminal lineage (LumHR, marked by KRT8, KRT18, and KRT19), and a secretory luminal lineage (LumSec, expressing KRT15 and SCGB2A2)

summary:
In Homo sapiens breast cancer, the secretory luminal lineage (LumSec) of epithelial cells expresses KRT15 and SCGB2A2.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:d61961d6285b17ad3967
claim_id: claim:d61961d6285b17ad3967
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary: In Homo sapiens breast cancer, naïve B cells are marked by TCL1A expression.
span_literal:
Four major B cell subtypes were identified: naïve B cells (TCL1A+), memory B cells (MS4A1+IGHG1+), T-like B cells (CD3D+), and plasma-like B cells (MZB1+XBP1+)


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:7ba4b2792c673b2713f9
claim_id: claim:7ba4b2792c673b2713f9
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
myofibroblastic CAFs (myCAF, ACTA2+TAGLN+), inflammatory CAFs (iCAF, CXCL12+CCL2+), extracellular matrix–remodeling CAFs (ECM-CAF, COL1A1+COL3A1+), antigen-presenting CAFs (apCAF, CD74+HLA-DRA+), and mesenchymal stem–like CAFs (MSC-like CAF, THY1+MGP+)

summary:
In Homo sapiens breast cancer, myofibroblastic cancer-associated fibroblasts are marked by ACTA2 and TAGLN expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:bef1639dafa66f3d29c9
claim_id: claim:bef1639dafa66f3d29c9
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
myofibroblastic CAFs (myCAF, ACTA2+TAGLN+), inflammatory CAFs (iCAF, CXCL12+CCL2+), extracellular matrix–remodeling CAFs (ECM-CAF, COL1A1+COL3A1+), antigen-presenting CAFs (apCAF, CD74+HLA-DRA+), and mesenchymal stem–like CAFs (MSC-like CAF, THY1+MGP+)

summary:
In Homo sapiens breast cancer, inflammatory cancer-associated fibroblasts are marked by CXCL12 and CCL2 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:cac2cf6f630b7b5666e1
claim_id: claim:cac2cf6f630b7b5666e1
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
myofibroblastic CAFs (myCAF, ACTA2+TAGLN+), inflammatory CAFs (iCAF, CXCL12+CCL2+), extracellular matrix–remodeling CAFs (ECM-CAF, COL1A1+COL3A1+), antigen-presenting CAFs (apCAF, CD74+HLA-DRA+), and mesenchymal stem–like CAFs (MSC-like CAF, THY1+MGP+)

summary:
In Homo sapiens breast cancer, extracellular matrix-remodeling cancer-associated fibroblasts are marked by COL1A1 and COL3A1 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:a882e89a4ca6d3b0b9fb
claim_id: claim:a882e89a4ca6d3b0b9fb
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary:
In Homo sapiens breast cancer, antigen-presenting cancer-associated fibroblasts are marked by CD74 and HLA-DRA expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:27bf9271822ce90880fd
claim_id: claim:27bf9271822ce90880fd
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary:
In Homo sapiens breast cancer, mesenchymal stem-like cancer-associated fibroblasts are marked by THY1 and MGP expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:87dacee06aa0557817f0
claim_id: claim:87dacee06aa0557817f0
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary: In Homo sapiens breast cancer, venous endothelial cells are marked by ACKR1 expression.
span_literal:
venous (Endo Vas-venous, ACKR1+), capillary (Endo Vas-capillary, RGCC+CD36+), arterial (Endo Vas-arterial, IGFBP3+), lymphatic (Endo Lymphatic, LYVE1+), pericyte-like (Endo Pericyte, ACTA2+COL17A1+), and CAF-like endothelial cells (Endo CAF, COL1A1+)


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:bba41e0d17e56f9ffe74
claim_id: claim:bba41e0d17e56f9ffe74
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary:
In Homo sapiens breast cancer, pericyte-like endothelial cells are marked by ACTA2 and COL17A1 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:18b8e48bff532a24bca5
claim_id: claim:18b8e48bff532a24bca5
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary:
In Homo sapiens breast cancer, cancer-associated fibroblast-like endothelial cells are marked by COL1A1 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:9cae80aa2239d4d438f6
claim_id: claim:9cae80aa2239d4d438f6
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
PVL cells were classified into four groups, including two pericyte subsets (one characterized by CSPG4+CD44+ expression, and another additionally expressing high CCL2), vascular smooth muscle cells (VSMCs; TAGLN+CNN1+MYL9+), and mesenchymal-like PVL cells (MGP+COL1A1+)

summary:
In Homo sapiens breast cancer, a pericyte subset of perivascular-like cells is characterized by CSPG4 and CD44 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:44ee68d5133e0f0a7a20
claim_id: claim:44ee68d5133e0f0a7a20
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
PVL cells were classified into four groups, including two pericyte subsets (one characterized by CSPG4+CD44+ expression, and another additionally expressing high CCL2), vascular smooth muscle cells (VSMCs; TAGLN+CNN1+MYL9+), and mesenchymal-like PVL cells (MGP+COL1A1+)

summary:
In Homo sapiens breast cancer, vascular smooth muscle cells are marked by TAGLN, CNN1, and MYL9 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:687b1217ab8a19c4c170
claim_id: claim:687b1217ab8a19c4c170
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
PVL cells were classified into four groups, including two pericyte subsets (one characterized by CSPG4+CD44+ expression, and another additionally expressing high CCL2), vascular smooth muscle cells (VSMCs; TAGLN+CNN1+MYL9+), and mesenchymal-like PVL cells (MGP+COL1A1+)

summary:
In Homo sapiens breast cancer, mesenchymal-like perivascular-like cells are marked by MGP and COL1A1 expression.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:2ee48b8eab400580344f
claim_id: claim:2ee48b8eab400580344f
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
Functional annotation revealed that SPP1+ macrophages (Mac1_SPP1) were strongly associated with an immunosuppressive tumor microenvironment (TME), promoting EMT and metastatic dissemination.

summary:
In Homo sapiens breast cancer, SPP1-positive macrophages (Mac1_SPP1) are marked by SPP1 expression and are associated with an immunosuppressive tumor microenvironment.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:12702baa4dca615b45c9
claim_id: claim:12702baa4dca615b45c9
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
span_literal:
In contrast, CXCL9+ macrophages (Mac2_CXCL9) were more likely to participate in antitumor immunity and were significantly enriched in patients with increased tumor-infiltrating lymphocytes and those achieving pathological complete response (pCR).

summary:
In Homo sapiens breast cancer, CXCL9-positive macrophages (Mac2_CXCL9) are marked by CXCL9 expression and are associated with antitumor immunity.


claim_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3:claim:c1bf7a61afdba6199e05
claim_id: claim:c1bf7a61afdba6199e05
paper_key: biorxiv:824fd1db-6db8-1014-aa73-9a84848dcec3
summary: In Homo sapiens breast cancer, polyclonally expanded T cells upregulate CXCL13 expression.
span_literal:
Polyclonally expanded T cells upregulated CXCL13, while non-expanded T cells preferentially expressed JUN and ZFP36L2


claim_key: biorxiv:83575146-7136-1014-babd-f8bef1289909:claim:1d60e1a7e0bc08c13e6f
claim_id: claim:1d60e1a7e0bc08c13e6f
paper_key: biorxiv:83575146-7136-1014-babd-f8bef1289909
span_literal:
A recent study by Okuda et al found no ionocytes (defined as FOXI1-positive, CFTR-expressing cells previously detected in mouse and human airways) in human terminal bronchioles, which has important implications for CFTR function (Okuda et al., 2020).

summary:
In Homo sapiens, ionocytes in human airways are defined as FOXI1-positive and CFTR-expressing cells, and were not detected in human terminal bronchioles.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:eece0d4a4bc153a21abb
claim_id: claim:eece0d4a4bc153a21abb
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
4 PIT1 lineage (PIT1.Pro, Somato, Lacto, Thyro), 2 SF1 lineage (Gonado, Gonado.PIT), 1 TPIT lineage (Cortico), 3 immune cells (Macrophages, Monocytes, CD8+ T cells), 1 stem cells (Stem), 2 stroma cells (Endothelial cells, Fibroblasts)

summary:
In Homo sapiens adult pituitary gland, somatotroph cells belong to the PIT-1 lineage defined by POU1F1 expression.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:71ebc372c2aa618cbb24
claim_id: claim:71ebc372c2aa618cbb24
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
4 PIT1 lineage (PIT1.Pro, Somato, Lacto, Thyro), 2 SF1 lineage (Gonado, Gonado.PIT), 1 TPIT lineage (Cortico), 3 immune cells (Macrophages, Monocytes, CD8+ T cells), 1 stem cells (Stem), 2 stroma cells (Endothelial cells, Fibroblasts)

summary:
In Homo sapiens adult pituitary gland, lactotroph cells belong to the PIT-1 lineage defined by POU1F1 expression.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:5fcf3211e0efc368ed4e
claim_id: claim:5fcf3211e0efc368ed4e
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
4 PIT1 lineage (PIT1.Pro, Somato, Lacto, Thyro), 2 SF1 lineage (Gonado, Gonado.PIT), 1 TPIT lineage (Cortico), 3 immune cells (Macrophages, Monocytes, CD8+ T cells), 1 stem cells (Stem), 2 stroma cells (Endothelial cells, Fibroblasts)

summary:
In Homo sapiens adult pituitary gland, thyrotroph cells belong to the PIT-1 lineage defined by POU1F1 expression.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:368b2819187fb8a19d19
claim_id: claim:368b2819187fb8a19d19
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
summary:
In Homo sapiens adult pituitary gland, corticotroph cells belong to the TPIT lineage defined by TBX19 expression.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:91b8c7b65a71e1532e2c
claim_id: claim:91b8c7b65a71e1532e2c
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
summary: In Homo sapiens, red blood cells were identified using HBB, HBA1, HBG2, and HBA2 as marker genes.
span_literal:
Red blood cells were identified by calculating RBC_score, with HBB, HBA1, HBG2, HBA2 used as marker genes.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:3e2c77518fe24b10cad6
claim_id: claim:3e2c77518fe24b10cad6
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
The key transcription factors for development of mature corticotroph and gonadotroph pituitary lineages are TPIT (encoded by TBX19 gene) and SF-1 (NR5A1), respectively.

summary:
In Homo sapiens, the key transcription factor for development of the mature corticotroph pituitary lineage is TPIT encoded by TBX19, and for the gonadotroph pituitary lineage is SF-1 encoded by NR5A1.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:ea13d12ea763bf85a382
claim_id: claim:ea13d12ea763bf85a382
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
The key transcription factors for development of mature corticotroph and gonadotroph pituitary lineages are TPIT (encoded by TBX19 gene) and SF-1 (NR5A1), respectively.

summary:
In Homo sapiens, the key transcription factor for development of the mature gonadotroph pituitary lineage is SF-1 encoded by NR5A1.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:9bf480bc3ab34a7efa98
claim_id: claim:9bf480bc3ab34a7efa98
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
In turn, PIT-1 (PUO1F1) transcription factor was found pivotal in maturation of somatotroph, lactotroph and tyrotroph cells.

summary:
In Homo sapiens, POU1F1 (PIT-1) transcription factor is pivotal in the maturation of somatotroph cells, lactotroph cells, and thyrotroph cells.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:ae0d06e2a70e096036ff
claim_id: claim:ae0d06e2a70e096036ff
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
In turn, PIT-1 (PUO1F1) transcription factor was found pivotal in maturation of somatotroph, lactotroph and tyrotroph cells.

summary:
In Homo sapiens, POU1F1 (PIT-1) transcription factor is pivotal in the maturation of lactotroph cells.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:ec9d5aa50f45ba10ba32
claim_id: claim:ec9d5aa50f45ba10ba32
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
In turn, PIT-1 (PUO1F1) transcription factor was found pivotal in maturation of somatotroph, lactotroph and tyrotroph cells.

summary:
In Homo sapiens, POU1F1 (PIT-1) transcription factor is pivotal in the maturation of thyrotroph cells.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:e98fa3f4547d99d53f21
claim_id: claim:e98fa3f4547d99d53f21
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
This showed NKX2-2 activity was the most specific (AUC 0.98) confirming the previous suggestion that this TF may serve as reliable marker for this specific transcriptomic subtype [50].

summary:
In Homo sapiens, NKX2-2 transcription factor activity is the most specific marker for PIT-1/SF-1 positive somatotroph pituitary neuroendocrine tumor (Subtype 1).


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:59eeadfbeb7aac712fdf
claim_id: claim:59eeadfbeb7aac712fdf
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
Interestingly, the genes specific to somatotroph cells as GH1, GH2 and GHRHR were annotated with the regulon of NKX2-2 (Fig. 2B).

summary:
In Homo sapiens, genes specific to somatotroph cells include GH1, GH2, and GHRHR, which are annotated within the regulon of NKX2-2.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:025a99347ecab2c11f6b
claim_id: claim:025a99347ecab2c11f6b
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
summary: In Homo sapiens, normal pituitary somatotroph cells are negative for GIPR expression.
span_literal:
expression of this gene distinguishes the tumor cells of these subtype from normal pituitary somatotropes, which are GIPR-negative.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:f7dcc9aa6ceece48d77a
claim_id: claim:f7dcc9aa6ceece48d77a
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
Basically, the lineage of corticotroph cells is characterized by the expression of TPIT transcription factor, gonadotroph cells express SF-1 TF and PIT-1-positive lineage includes somatotropes, lactotropes and tyreotropes.

summary:
In Homo sapiens, the corticotroph cell lineage is characterized by expression of TPIT (TBX19), gonadotroph cells express SF-1 (NR5A1), and the PIT-1 (POU1F1)-positive lineage includes somatotroph cells, lactotroph cells, and thyrotroph cells.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:c9c24671addf0bba9676
claim_id: claim:c9c24671addf0bba9676
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
PIT-1/SF-1 sPitNETs are characterized by activity of TFs known to be involved in development of PIT-1, not SF-1 lineage as POU1F1, PROP1, CEBPD or FOXO1 [55].

summary:
In Homo sapiens, PIT-1/SF-1 somatotroph pituitary neuroendocrine tumors are characterized by activity of POU1F1, PROP1, CEBPD, and FOXO1, transcription factors involved in PIT-1 lineage development.


claim_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02:claim:8cb69a9adfe18f4ec043
claim_id: claim:8cb69a9adfe18f4ec043
paper_key: biorxiv:83c8ac0b-6e16-1014-a00e-d78ba7f4ca02
span_literal:
Beside the activity of SF-1 (NR5A1), these tumors do not show the activity of the other known gonadotroph lineage-related TFs as GATA2 or GATA3 [56].

summary:
In Homo sapiens, PIT-1/SF-1 somatotroph pituitary neuroendocrine tumors do not show activity of the gonadotroph lineage-related transcription factors GATA2 or GATA3.


claim_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e:claim:a54d8b9e288fd0a7abe8
claim_id: claim:a54d8b9e288fd0a7abe8
paper_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e
span_literal:
Examining downstream targets of MITF that are activated in each subclass (see Supplementary Text 8), we identified that GPNMB, MLANA, PMEL, and TYR are shared between two subclasses, whereas ACP5, CDK2, CTSK, DCT, KIT, OCA2 and TRPM1/P1 are unique to subclass C.

summary:
In Homo sapiens, GPNMB, MLANA, PMEL, and TYR are MITF downstream target markers shared between melanoma tumor subclass B and melanoma tumor subclass C, whereas ACP5, CDK2, CTSK, DCT, KIT, OCA2, and TRPM1 are markers unique to melanoma tumor subclass C.


claim_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e:claim:54f4a0ad8032bfd45f40
claim_id: claim:54f4a0ad8032bfd45f40
paper_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e
span_literal:
Examining downstream targets of MITF that are activated in each subclass (see Supplementary Text 8), we identified that GPNMB, MLANA, PMEL, and TYR are shared between two subclasses, whereas ACP5, CDK2, CTSK, DCT, KIT, OCA2 and TRPM1/P1 are unique to subclass C.

summary:
In Homo sapiens, GPNMB, MLANA, PMEL, and TYR are MITF downstream target markers shared between melanoma tumor subclass B and melanoma tumor subclass C.


claim_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e:claim:1761808b4ded6eb2cb8c
claim_id: claim:1761808b4ded6eb2cb8c
paper_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e
span_literal:
Besides MITF and SOX10, there are 38 other factors identified for subclass B and 17 other factors for subclass C. In particular, well-known oncogenes TP53 and MYC are differentially activated in subclass B and subclass C, respectively.

summary:
In Homo sapiens, the well-known oncogene TP53 is differentially activated in melanoma tumor subclass B, while MYC is differentially activated in melanoma tumor subclass C.


claim_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e:claim:1dac88ca62b0aa376668
claim_id: claim:1dac88ca62b0aa376668
paper_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e
span_literal:
Besides MITF and SOX10, there are 38 other factors identified for subclass B and 17 other factors for subclass C. In particular, well-known oncogenes TP53 and MYC are differentially activated in subclass B and subclass C, respectively.

summary:
In Homo sapiens, the well-known oncogene MYC is differentially activated in melanoma tumor subclass C.


claim_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e:claim:ab302d853e363147a606
claim_id: claim:ab302d853e363147a606
paper_key: biorxiv:84e54dbc-6c17-1014-b8ff-c69d804e210e
summary: In Homo sapiens, TP53 and MITF are used as characteristic biomarkers for melanoma tumor subclass B.
span_literal:
Thus, we use both TP53 and MITF as characteristic biomarkers for subclasses B and both MYC and MITF for subclass C.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:e89066b7b74c12e3d285
claim_id: claim:e89066b7b74c12e3d285
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
HSC/MPPs showed high expression of MLLT3, a crucial regulator of human HSC maintenance (Calvanese et al., 2019), HLF, a TF involved in preserving quiescence in HSCs (Komorowska et al., 2017) and MEIS1, a TF involved in limiting oxidative stress in HSCs, which is necessary for quiescence (Unnisa et al., 2012) (Wang et al., 2018).

summary:
In Homo sapiens, haematopoietic stem cells/multipotent progenitors show high expression of MLLT3, HLF, and MEIS1.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:ee2581859f13420c264e
claim_id: claim:ee2581859f13420c264e
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
Cells in this cluster also expressed high levels of surface markers of HSPCs such as CD34, (Morisot et al., 2006), SELL (Ivanovs et al., 2017), and PROM1 (de Wynter et al., 1998) (Saha et al., 2020)

summary:
In Homo sapiens, haematopoietic stem cells/multipotent progenitors express high levels of CD34, SELL, and PROM1.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:24e521d694f45fc22812
claim_id: claim:24e521d694f45fc22812
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
summary: In Homo sapiens, erythroid cells express HBG1, HBA1, GYPA, and ALAS2.
span_literal:
we identified clear transcriptional signatures of erythroid cells (expressing HBG1, HBA1, GYPA, and ALAS2)


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:0b8f2a1b26c557e1b390
claim_id: claim:0b8f2a1b26c557e1b390
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
B cell lineage included pro-B, which showed expression of IGLL1 and RAG1, and pre-B, expressing high levels of CD79B, VPREB1, and CD24

summary:
In Homo sapiens, progenitor B cells show expression of IGLL1 and RAG1, while precursor B cells express high levels of CD79B, VPREB1, and CD24.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:1300fe5c510b7a7308d1
claim_id: claim:1300fe5c510b7a7308d1
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
we identified a cluster of mature B cells, expressing high levels of IGHM and decreased levels of IGLL1, compared to pro/pre B clusters

summary:
In Homo sapiens, mature B cells express high levels of IGHM and decreased levels of IGLL1 compared to progenitor/precursor B cells.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:437306f66500dd48074b
claim_id: claim:437306f66500dd48074b
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
differentially regulated genes in the HSC/MPPs transition to MEMPs included megakaryocyte/erythroid/mast cells lineage-specific genes such as GATA1, ITGA2B, PLEK, KLF1, HDC, and MS4A3,

summary:
In Homo sapiens, megakaryocyte-erythroid-mast progenitors upregulate lineage-specific genes GATA1, ITGA2B, PLEK, KLF1, HDC, and MS4A3 during the transition from haematopoietic stem cells/multipotent progenitors.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:8c6baa5ca286fda2a685
claim_id: claim:8c6baa5ca286fda2a685
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
MEMPs-Cycle population further upregulated erythroid-specific genes such as KLF1, BLVRB, and TFRC compared to MEMPs suggesting their gradual commitment towards erythroid lineage

summary:
In Homo sapiens, cycling megakaryocyte-erythroid-mast progenitors upregulate erythroid-specific genes KLF1, BLVRB, and TFRC compared to megakaryocyte-erythroid-mast progenitors.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:17dccdebd76ba7ac873b
claim_id: claim:17dccdebd76ba7ac873b
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
Cells in this cluster differentially expressed myeloid lineage-specific genes (e.g., AZU1, LYZ, and MPO) compared to HSC/MMPs

summary:
In Homo sapiens, granulocytic progenitors differentially express myeloid lineage-specific genes AZU1, LYZ, and MPO compared to haematopoietic stem cells/multipotent progenitors.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:ea37d70a824441e3fa51
claim_id: claim:ea37d70a824441e3fa51
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
Cells in this cluster expressed genes specific to those lineages, including IGLL1, HMGB2, and CD79B (lymphoid)

summary:
In Homo sapiens, lympho-myeloid progenitors express lymphoid-specific genes IGLL1, HMGB2, and CD79B.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:93828bdb17e2591f9565
claim_id: claim:93828bdb17e2591f9565
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal: upregulated lymphoid genes such as CD81, IGLL1, and HMGN2 compared to HSC/MPP cluster
summary:
In Homo sapiens, lympho-myeloid progenitors upregulate lymphoid genes CD81, IGLL1, and HMGN2 compared to haematopoietic stem cells/multipotent progenitors.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:e9121f15c2f6ffbf4c97
claim_id: claim:e9121f15c2f6ffbf4c97
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
the LMP cluster had higher expression of MPP-related genes such as SPINK2, CD52, and SELL compared to MEMPs, suggesting that these progenitors represent a more immature population compared to MEMPs

summary:
In Homo sapiens, lympho-myeloid progenitors have higher expression of SPINK2, CD52, and SELL compared to megakaryocyte-erythroid-mast progenitors.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:204bc8b26541ace09f19
claim_id: claim:204bc8b26541ace09f19
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
We identified HLF and HOXA9 as main regulons in HSC/MPPs, whereas GATA1, GATA2, and TAL1 were identified in the MEMP branch of the haematopoietic tree

summary:
In Homo sapiens, haematopoietic stem cells/multipotent progenitors have HLF and HOXA9 as main regulons, whereas GATA1, GATA2, and TAL1 are identified in the megakaryocyte-erythroid-mast progenitor branch.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:af4edb598ebe06b6fd42
claim_id: claim:af4edb598ebe06b6fd42
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
We identified HLF and HOXA9 as main regulons in HSC/MPPs, whereas GATA1, GATA2, and TAL1 were identified in the MEMP branch of the haematopoietic tree

summary:
In Homo sapiens, megakaryocyte-erythroid-mast progenitors have GATA1, GATA2, and TAL1 as main regulons.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:1dcd61f6cee48e658e77
claim_id: claim:1dcd61f6cee48e658e77
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
summary: In Homo sapiens, FOXO3 is a highly specific regulon for erythroid cells.
span_literal:
FOXO3 was highly specific for erythroid cells whereas EOMES, OLIG2, and IRF8 for NK cells, monocytes, and pDCs, respectively.


claim_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e:claim:e4716f555701a1ebc301
claim_id: claim:e4716f555701a1ebc301
paper_key: biorxiv:876ca999-6c0e-1014-8ed9-e7563228589e
span_literal:
DE analysis between HSC/MPPs-Cycle and HSC/MPPs revealed upregulation of genes involved in cell cycle regulation (FOS, PTP4A1, MCL1, and PKN2) in HSC/MPPs-Cycle

summary:
In Homo sapiens, cycling haematopoietic stem cells/multipotent progenitors show upregulation of FOS, PTP4A1, MCL1, and PKN2 compared to haematopoietic stem cells/multipotent progenitors.


claim_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81:claim:10b6e8047c25ed1bf47c
claim_id: claim:10b6e8047c25ed1bf47c
paper_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81
span_literal:
By day 30, a vast majority of hiAs expressed canonical astrocyte markers including Aquaporin 4 (AQP4), CD44, Solute Carrier family 1 member 3 (SLC1A3), S100 calcium binding protein B (S100B) and Vimentin (VIM) by immunofluorescence, paralleling results obtained with human primary astrocytes (hpAs)

summary:
In Homo sapiens, human induced astrocytes express canonical astrocyte markers including Aquaporin 4 (AQP4), CD44, Solute Carrier family 1 member 3 (SLC1A3), S100 calcium binding protein B (S100B), and Vimentin (VIM).


claim_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81:claim:2e2b258518b6099be5e9
claim_id: claim:2e2b258518b6099be5e9
paper_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81
span_literal:
Our scRNAseq analyses further confirmed that hiAs expressed canonical immature astrocytes markers including VIM, GJA1, APOE, CD44, SLC1A3, and ID3

summary:
In Homo sapiens, human induced astrocytes express canonical immature astrocyte markers including VIM, GJA1, APOE, CD44, SLC1A3, and ID3.


claim_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81:claim:185088d76786b454ccd9
claim_id: claim:185088d76786b454ccd9
paper_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81
summary: In Homo sapiens, astrocytes are marked by ID3, CLU, SLC1A3, CD44, APOE, and GJA1.
span_literal:
Dot plot for markers of astrocytes (ID3, CLU, SLC1A3, CD44, APOE, GJA1), oligodendrocytes (SO×10, PLP1, MOG), excitatory neurons (DCX, STMN2, PCP4), and pluripotent stem cells (POU5F1, SOX2).


claim_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81:claim:6bf0a988768056f0140b
claim_id: claim:6bf0a988768056f0140b
paper_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81
summary: In Homo sapiens, immature astrocytes show elevated expression of TOP2A, CENPF, and NUSAP1.
span_literal:
cluster 9 showed elevated expression of immature astrocyte markers such as TOP2A, CENPF and NUSAP1 relative to other clusters


claim_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81:claim:e98f612c8a81e2f293ac
claim_id: claim:e98f612c8a81e2f293ac
paper_key: biorxiv:88b6dd17-6fa5-1014-96e8-90837e572e81
span_literal:
AQP4, ADH1L1, and FGFR3 were more strongly expressed in human adult astrocytes compared to human primary fetal or stem cell derived astrocytes, while VIM was robustly expressed across all datasets

summary:
In Homo sapiens, AQP4, ALDH1L1, and FGFR3 are more strongly expressed in adult astrocytes compared to fetal astrocytes, while VIM is robustly expressed across all astrocyte datasets.


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:238e6e843a421988a138
claim_id: claim:238e6e843a421988a138
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
span_literal:
Utilizing key cellular markers, we identified and confirmed the distribution of specific cell types: CD68 and CD14 for monocytes/macrophages, FCGR3B for neutrophils, CD56 for natural killer (NK) cells, and CD3 for T cells.

summary:
In Homo sapiens, CD68 and CD14 are markers for monocytes/macrophages in bronchoalveolar lavage fluid.


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:cb4f96a34cbde81cfd60
claim_id: claim:cb4f96a34cbde81cfd60
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
summary: In Homo sapiens, neutrophils are marked by high Fc gamma receptor IIIb (FCGR3B) expression.
span_literal:
Neutrophils, marked by high FCGR3B expression, were significantly elevated in severe COVID-19 cases, particularly among those who did not survive (Fig 1C).


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:7e51cd7df0e9ec0e15f1
claim_id: claim:7e51cd7df0e9ec0e15f1
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
summary: In Homo sapiens, natural killer cells are characterized by CD56 expression.
span_literal:
NK cells, characterized by CD56 expression, were generally low across all groups but exhibited a marked decrease in severe cases, suggesting a compromised innate immune response critical for early viral defense.


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:d7cf198e29d3758a787d
claim_id: claim:d7cf198e29d3758a787d
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
summary: In Homo sapiens, T cells are identified by CD3 expression.
span_literal:
T cells, identified by CD3, also showed significant reductions in severe cases, reflecting an impaired adaptive immune response.


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:cdce6e74f82e2a1159aa
claim_id: claim:cdce6e74f82e2a1159aa
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
span_literal:
In severe cases, M1 monocyte-macrophages dominated, indicated by elevated expression of IL1β, TNFα, and IL6, with higher levels in SevereA (Fig 3C).

summary:
In Homo sapiens, M1 monocyte-macrophages are indicated by elevated expression of interleukin 1 beta (IL1β), tumor necrosis factor alpha (TNFα), and interleukin 6 (IL6) in severe COVID-19 cases.


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:63038980edf39e9ef49e
claim_id: claim:63038980edf39e9ef49e
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
span_literal:
Conversely, M2 monocyte-macrophages, characterized by higher expression of MSR1, MRC1, and PPAR-γ, were more prevalent in control and moderate cases.

summary:
In Homo sapiens, M2 monocyte-macrophages are characterized by higher expression of macrophage scavenger receptor 1 (MSR1), mannose receptor C type 1 (MRC1), and peroxisome proliferator-activated receptor gamma (PPAR-γ).


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:6b2ebc6ddc580a59211b
claim_id: claim:6b2ebc6ddc580a59211b
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
span_literal:
In severe cases (SevereA and SevereD), there was an increased presence of LDNs, characterized by elevated expression of C-X-C Motif Chemokine Receptor 4 (CXCR4) and CD274 (increased only in moderate and decreased in severe cases), while HDNs showed reduced activity, as indicated by lower expression levels of C-X-C Motif Chemokine Receptor 2 (CXCR2) and SELL, more so in Severe cases (Fig 2C).

summary:
In Homo sapiens, low-density neutrophils are characterized by elevated expression of C-X-C motif chemokine receptor 4 (CXCR4) and CD274, while high-density neutrophils show lower expression of C-X-C motif chemokine receptor 2 (CXCR2) and SELL in severe COVID-19 cases.


claim_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967:claim:9406f3b742b2467549e6
claim_id: claim:9406f3b742b2467549e6
paper_key: biorxiv:8a79edc5-6e0d-1014-bd87-aa1de4068967
span_literal:
In severe cases (SevereA and SevereD), there was an increased presence of LDNs, characterized by elevated expression of C-X-C Motif Chemokine Receptor 4 (CXCR4) and CD274 (increased only in moderate and decreased in severe cases), while HDNs showed reduced activity, as indicated by lower expression levels of C-X-C Motif Chemokine Receptor 2 (CXCR2) and SELL, more so in Severe cases (Fig 2C).

summary:
In Homo sapiens, high-density neutrophils show reduced activity indicated by lower expression of C-X-C motif chemokine receptor 2 (CXCR2) and SELL compared to low-density neutrophils in severe COVID-19 cases.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:10a708fe554acd403c86
claim_id: claim:10a708fe554acd403c86
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
We identified two distinct clusters of stem cells (SC1 and SC2) marked by the expression of classical stem cell markers LGR5, OLFM4, RGMB, and SMOC2 (Fig. 6A, B).

summary:
In Homo sapiens colon organoids, stem cells (SC1 and SC2) are marked by the expression of LGR5, OLFM4, RGMB, and SMOC2.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:0cdf012dc31214696a8e
claim_id: claim:0cdf012dc31214696a8e
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
Transition to cycling TA cells (TA1) was marked by the transition to exclusively G2/M phase and an enrichment of the proliferation markers MKI67 and TOP2A expression (Fig. 6B and C).

summary:
In Homo sapiens colon organoids, transit-amplifying cells (TA1) are marked by enrichment of the proliferation markers MKI67 and TOP2A.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:ff30fc391c4c54f60784
claim_id: claim:ff30fc391c4c54f60784
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
Canonical colonocytes were marked by the expression of classical absorptive markers SLC26A3, CA2 and FABP1.

summary:
In Homo sapiens colon organoids, canonical colonocytes are marked by the expression of the absorptive markers SLC26A3, CA2, and FABP1.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:532f2c8d170274632493
claim_id: claim:532f2c8d170274632493
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
These markers were absent in the non-canonical colonocytes which were marked by high expression of MMP7, LYZ, IL32 and the IFN response genes ISG15, ISG20 and IFI27 (Fig. 6B).

summary:
In Homo sapiens colon organoids, non-canonical colonocytes are marked by high expression of MMP7, LYZ, IL32, ISG15, ISG20, and IFI27.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:6ade7dd0b8bb0cdd083d
claim_id: claim:6ade7dd0b8bb0cdd083d
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
summary: In Homo sapiens colon organoids, HES1 is an exclusive marker of the absorptive lineage cell.
span_literal:
In addition, we could observe the expression of HES1 an exclusive marker of the absorptive lineage (Fig. 6B).


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:f91e8d6e9d3664cd7204
claim_id: claim:f91e8d6e9d3664cd7204
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
The secretory lineage was characterized by the presence of classical goblet cell markers MUC2, SPINK4, SPDEF and ATOH1.

summary:
In Homo sapiens colon organoids, goblet cells of the secretory lineage are characterized by the expression of MUC2, SPINK4, SPDEF, and ATOH1.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:5df59d06017f50e66031
claim_id: claim:5df59d06017f50e66031
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
Analyzing their gene expression pattern revealed that cluster GC1 had increased expression of AGR2, FCGBP, CLCA1, ERN2 and SPDEF all known to be mucus core proteins or genes involved in mucus biosynthesis64(Fig. 6G).

summary:
In Homo sapiens colon organoids, goblet cell subcluster GC1 is marked by increased expression of AGR2, FCGBP, CLCA1, ERN2, and SPDEF, which are mucus core proteins or genes involved in mucus biosynthesis.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:579cb064930cb4c933bb
claim_id: claim:579cb064930cb4c933bb
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
In contrast to that cluster GC2 was characterized by a higher expression of ZG16 and TFF3 which function as AMP and regulator of mucus viscosity respectively65, 66.

summary:
In Homo sapiens colon organoids, goblet cell subcluster GC2 is characterized by higher expression of ZG16 and TFF3, which function as antimicrobial peptide and regulator of mucus viscosity respectively.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:8258e299d23d0b1f28c0
claim_id: claim:8258e299d23d0b1f28c0
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
Amongst the secretory cell markers were well known goblet cell markers AGR2, TFF3 and SPINK4 as well as CHGA which marks enteroendocrine cells.

summary:
In Homo sapiens colon organoids, AGR2, TFF3, and SPINK4 are well known goblet cell markers, while CHGA marks enteroendocrine cells.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:eed7f5fd1e6ca5f920d7
claim_id: claim:eed7f5fd1e6ca5f920d7
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
With further analysis we were able to identify a small fraction of cells within this GC4 expressing CHGA and POU2F3 indicating the presence of EECs and Tuft cells respectively (Suppl. Fig 6F).

summary:
In Homo sapiens colon organoids, a small fraction of cells within goblet cell subcluster GC4 express CHGA, indicating the presence of enteroendocrine cells.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:b4d3080cd12766927e77
claim_id: claim:b4d3080cd12766927e77
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
With further analysis we were able to identify a small fraction of cells within this GC4 expressing CHGA and POU2F3 indicating the presence of EECs and Tuft cells respectively (Suppl. Fig 6F).

summary:
In Homo sapiens colon organoids, a small fraction of cells within goblet cell subcluster GC4 express POU2F3, indicating the presence of Tuft cells.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:dacdfadddd913fc1601f
claim_id: claim:dacdfadddd913fc1601f
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
BEST2, a marker for goblet cells, was significantly downregulated while markers for enteroendocrine cells (SGC5, GCG, VWA5B2) were upregulated suggesting an alteration in the secretory lineage (Fig. 7E).

summary:
In Homo sapiens descending colon biopsies from systemic lupus erythematosus patients, BEST2, a marker for goblet cells, was significantly downregulated.


claim_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28:claim:04e92062f5f46a14719d
claim_id: claim:04e92062f5f46a14719d
paper_key: biorxiv:8bff4e38-6c13-1014-bcce-e068e3eafd28
span_literal:
BEST2, a marker for goblet cells, was significantly downregulated while markers for enteroendocrine cells (SGC5, GCG, VWA5B2) were upregulated suggesting an alteration in the secretory lineage (Fig. 7E).

summary:
In Homo sapiens descending colon biopsies, SGC5, GCG, and VWA5B2 are markers for enteroendocrine cells.


claim_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23:claim:c37ee9e5f780ad227dd8
claim_id: claim:c37ee9e5f780ad227dd8
paper_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23
span_literal:
Shear stress (15 dynes/cm2) alone increased endothelial characteristics, including homeostatic markers such as CDH5, NOS3, TEK, and S1PR1.

summary:
In Homo sapiens, endothelial cells express homeostatic markers CDH5, NOS3, TEK, and S1PR1 under shear stress conditions.


claim_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23:claim:73f62f5f2cbd109d0599
claim_id: claim:73f62f5f2cbd109d0599
paper_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23
span_literal:
ADM treatment maintained the enhanced level of these markers under shear stress and further improved anti-coagulation by increasing THBD and decreasing F3 expression, and synergistically enhanced the expression of the native lung aerocyte capillary endothelial marker EDNRB.

summary:
In Homo sapiens, EDNRB is a marker of native lung aerocyte capillary endothelial cell, and THBD is increased while F3 is decreased in endothelial cells treated with adrenomedullin under shear stress.


claim_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23:claim:28021ea62f0cdd2e1c74
claim_id: claim:28021ea62f0cdd2e1c74
paper_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23
span_literal:
After 48 hours of exposure to a shear stress of 15 dynes/cm2, HPAECs exhibited increased expression of the mechanotransduction transcription factors KLF2 and KLF4, along with upregulation of canonical endothelial markers CD31, CDH5, NOS3, KDR, TEK, and S1PR1

summary:
In Homo sapiens, canonical endothelial cell markers include CD31, CDH5, NOS3, KDR, TEK, and S1PR1, and mechanotransduction transcription factors KLF2 and KLF4 are upregulated under shear stress in human pulmonary artery endothelial cells.


claim_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23:claim:d65d95ffb64988a1dc2d
claim_id: claim:d65d95ffb64988a1dc2d
paper_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23
span_literal:
Specifically, we assessed the canonical markers for EC subpopulation in the lung vasculature, including EDNRB and HPGD for aCap, CD36 for gCap, SOX17 for arterial, and ACKR1 for venous endothelial cells.

summary:
In Homo sapiens lung vasculature, EDNRB and HPGD are canonical markers for aerocyte capillary endothelial cell, CD36 is a canonical marker for general capillary endothelial cell, SOX17 is a canonical marker for arterial endothelial cell, and ACKR1 is a canonical marker for venous endothelial cell.


claim_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23:claim:25f8d5b8b00dcecd88b9
claim_id: claim:25f8d5b8b00dcecd88b9
paper_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23
span_literal:
Specifically, we assessed the canonical markers for EC subpopulation in the lung vasculature, including EDNRB and HPGD for aCap, CD36 for gCap, SOX17 for arterial, and ACKR1 for venous endothelial cells.

summary:
In Homo sapiens lung vasculature, CD36 is a canonical marker for general capillary endothelial cell.


claim_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23:claim:fe2fc97a047f41f1aa8f
claim_id: claim:fe2fc97a047f41f1aa8f
paper_key: biorxiv:8c2f79d9-6d11-1014-b01f-be5bb307bf23
span_literal:
We found that shear stress alone (15 dynes/cm2) could markedly increase EDNRB expression, a critical marker for aCap cells, and this effect was further enhanced by ADM treatment.

summary:
In Homo sapiens, EDNRB is a critical marker for aerocyte capillary endothelial cells, and its expression is increased by shear stress and further enhanced by adrenomedullin treatment.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:de60b399f8761429d055
claim_id: claim:de60b399f8761429d055
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
span_literal:
SCs marked by PAX7 (Paired Box 7) (Seale et al., 2000), are a prerequisite for skeletal muscle regeneration (Mauro, 1961) and are thought to be the main human muscle stem cells (Hu-MuSCs) of postnatal skeletal muscle.

summary:
In Homo sapiens, satellite cells (the main human muscle stem cells) are marked by PAX7 (Paired Box 7).


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:c184ef7ebee0a1791052
claim_id: claim:c184ef7ebee0a1791052
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
span_literal:
we used FACS to purify HNK1- CD45-CD31- cells co-expressing CD29, CXCR4, and CD56 markers present on human PAX7+ cells (Garcia et al., 2018)

summary:
In Homo sapiens, PAX7-positive human muscle stem cells co-express CD29, CXCR4, and CD56, and are negative for HNK1, CD45, and CD31.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:c3a26c88c5d4219710c2
claim_id: claim:c3a26c88c5d4219710c2
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
summary: In Homo sapiens, human muscle stem cells express intermediate CD56, high PAX7, and low MYOGENIN.
span_literal:
FACS analysis identified intermediate CD56 cells expressing high PAX7 and low MYOGENIN (Figure 3B and Figure 3-figure supplement 1C), consistent with Hu-MuSC expression profiles.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:a3669cb79b410135eaf5
claim_id: claim:a3669cb79b410135eaf5
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
summary: In Homo sapiens, neuronal stem/progenitor cells express EFNB3, SOX2, and ASCL1.
span_literal:
Clusters 0-2, 4-9, and 12 consisted of cells expressing neuronal stem/progenitor cell genes such as EFNB3, SOX2, and ASCL1 (Figure 4D,E and Figure 4-figure supplement 1D,E).


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:0061468f0bc085a860e5
claim_id: claim:0061468f0bc085a860e5
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
summary: In Homo sapiens, mesenchymal cells express PDGFRA, ASPN, and COL1A1.
span_literal:
Mesenchymal genes (PDGFRA, ASPN, and COL1A1) were expressed in cluster 8 (Figure 4D,E and Figure 4-figure supplement 1D,E).


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:f01839a2310e0d0d705f
claim_id: claim:f01839a2310e0d0d705f
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
summary: In Homo sapiens, muscle cells express PAX7, MYF5, MYOD, and MYOG (MYOGENIN).
span_literal:
Cells expressing muscle markers (PAX7, MYF5, MYOD and MYOG (MYOGENIN)) were found in clusters 3, 10, and 11 (Figure 4D,E and Figure 4-figure supplement 1D,E).


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:8afd96bcbb893b5e4f6e
claim_id: claim:8afd96bcbb893b5e4f6e
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
span_literal:
Cluster 4 expressed higher levels of MYOD, MYOG, SOX8, and MEF2C (markers of differentiated MuSCs/myoblasts/myocytes), while clusters 0-3 expressed higher levels of PAX7 and MYF5 (markers of more quiescent MuSCs) (Figure 5E,F).

summary:
In Homo sapiens, differentiated muscle stem cells/myoblasts/myocytes are marked by MYOD, MYOG, SOX8, and MEF2C.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:eadd0793917f4f439fd5
claim_id: claim:eadd0793917f4f439fd5
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
span_literal:
Quiescence (SPRY1, HEY1, H ES1) and cell cycle (TOP2A or KI67) markers were increased in clusters 0-2 and cluster 3 respectively (Figure 5F,G and Figure 5-figure supplement 1A,B).

summary:
In Homo sapiens, quiescent induced muscle stem/progenitor cells show increased expression of SPRY1, HEY1, and HES1, while proliferating induced muscle stem/progenitor cells show increased expression of TOP2A and KI67.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:ce5b44cbec0a44f2a8f4
claim_id: claim:ce5b44cbec0a44f2a8f4
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
span_literal: Cells expressing APOE and KRT17 defined cluster 0.
summary:
In Homo sapiens, induced muscle stem/progenitor cell cluster 0 is defined by expression of APOE and KRT17.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:47c55f35fff5e547a4f4
claim_id: claim:47c55f35fff5e547a4f4
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
summary: In Homo sapiens, CDH15 is enriched in induced muscle stem/progenitor cell cluster 1.
span_literal:
CDH15, a niche regulator of SCs quiescence (Goel, Rieder, Arnold, Radice, & Krauss, 2017) was enriched in cluster 1.


claim_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1:claim:a54837c79aa3e0fdf3ff
claim_id: claim:a54837c79aa3e0fdf3ff
paper_key: biorxiv:8c3ef8a4-6c0e-1014-9b81-f1618d3e39b1
summary: In Homo sapiens, induced muscle stem/progenitor cell cluster 2 expresses high levels of FOS.
span_literal:
Cluster 2 consisted of cells expressing high levels of FOS (Figure 5F,G and Figure 5-figure supplement 1A).


claim_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223:claim:ade4b479164665e27ab3
claim_id: claim:ade4b479164665e27ab3
paper_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223
span_literal:
Genome browser view of DNA methylation levels at T cell marker genes CD3D, CD3E, and CD3G, which are hypomethylated in the T cell lineage and hypermethylated in other cell types.

summary:
In Homo sapiens, T cell marker genes CD3D, CD3E, and CD3G are hypomethylated in the T cell lineage and hypermethylated in other cell types.


claim_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223:claim:5f796124835979a0b5fc
claim_id: claim:5f796124835979a0b5fc
paper_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223
span_literal:
we plotted the methylation status at T cell marker CD3 genes, which revealed hypomethylation in T cells and hypermethylation in other cell types

summary:
In Homo sapiens, the CD3 genes are hypomethylated in T cells and hypermethylated in other cell types, serving as T cell markers.


claim_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223:claim:529a5f71ff19b6c98e23
claim_id: claim:529a5f71ff19b6c98e23
paper_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223
span_literal:
For instance, TCF motifs were enriched in T cells, while the EBF1 motif showed enrichment in B cells (Figure 2F).

summary:
In Homo sapiens, TCF motifs are enriched in differentially methylated regions of T cells, while the EBF1 motif is enriched in B cells.


claim_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223:claim:e58b9196158bbae3021b
claim_id: claim:e58b9196158bbae3021b
paper_key: biorxiv:8e460cfc-7020-1014-9694-e5bf39316223
summary: In Homo sapiens, naive helper T cells are defined as CD3+, CD4+, CCR7+, CD45RA+.
span_literal:
The sorted cell types included Naive helper T cells (CD3+, CD4+, CCR7+, CD45RA+), Memory helper T cells (CD3+, CD4+, CD45RA-), Naive cytotoxic T cells (CD3+, CD8+, CCR7+, CD45RA+), Memory cytotoxic T cells (CD3+, CD8+, CD45RA-), B cells (CD3-, CD19+), Monocytes (CD3-, CD19-, CD14+), NK cells (CD3-, CD19-, CD14-, CD16+,

CD56+), and other cells (CD3-, CD19-, CD14-, CD16-, CD56-).


claim_key: biorxiv:8ed9ce3f-6c18-1014-9a88-fb4d60bf2f45:claim:d07e53bbd9b38f77bf94
claim_id: claim:d07e53bbd9b38f77bf94
paper_key: biorxiv:8ed9ce3f-6c18-1014-9a88-fb4d60bf2f45
span_literal:
SPTBN1 is highly expressed in the Fibroblasts, Smooth muscle cells, and Tissue stem cells of the Bladder, Esophagus, Heart, Muscle, Rectum, Skin, and Trachea.

summary:
In Homo sapiens, SPTBN1 is highly expressed in fibroblasts of the bladder, esophagus, heart, muscle, rectum, skin, and trachea.


claim_key: biorxiv:8ed9ce3f-6c18-1014-9a88-fb4d60bf2f45:claim:e71dab2de5eb08f6e525
claim_id: claim:e71dab2de5eb08f6e525
paper_key: biorxiv:8ed9ce3f-6c18-1014-9a88-fb4d60bf2f45
span_literal:
SPTBN1 is highly expressed in the Fibroblasts, Smooth muscle cells, and Tissue stem cells of the Bladder, Esophagus, Heart, Muscle, Rectum, Skin, and Trachea.

summary:
In Homo sapiens, SPTBN1 is highly expressed in smooth muscle cells of the bladder, esophagus, heart, muscle, rectum, skin, and trachea.


claim_key: biorxiv:8ed9ce3f-6c18-1014-9a88-fb4d60bf2f45:claim:999458a1a3a9f2734a3a
claim_id: claim:999458a1a3a9f2734a3a
paper_key: biorxiv:8ed9ce3f-6c18-1014-9a88-fb4d60bf2f45
span_literal:
SPTBN1 is highly expressed in the Fibroblasts, Smooth muscle cells, and Tissue stem cells of the Bladder, Esophagus, Heart, Muscle, Rectum, Skin, and Trachea.

summary:
In Homo sapiens, SPTBN1 is highly expressed in tissue stem cells of the bladder, esophagus, heart, muscle, rectum, skin, and trachea.


claim_key: biorxiv:8f45ef4c-6d70-1014-815c-a556cc0c38ce:claim:574d09643652a4f6236e
claim_id: claim:574d09643652a4f6236e
paper_key: biorxiv:8f45ef4c-6d70-1014-815c-a556cc0c38ce
span_literal:
We also investigated known marker genes for specific cell populations, such as for B-cells in PBMC data, finding that ACTIVA generated cells expressed these markers (CD79A, CD19, and MS4A1) in the appropriate clusters (Fig. 4C and other figures not shown here) similar to real data.

summary:
In Homo sapiens, B cells in peripheral blood mononuclear cells are marked by CD79A, CD19, and MS4A1.


claim_key: biorxiv:8f74778a-6c1f-1014-8563-ba83ee46ac17:claim:ff4542ac42d624247e6d
claim_id: claim:ff4542ac42d624247e6d
paper_key: biorxiv:8f74778a-6c1f-1014-8563-ba83ee46ac17
span_literal:
CB1R is highly expressed within the cholecystokinin (CCK) subtype GABAergic inhibitory interneurons within the human cortex

summary:
In Homo sapiens, cannabinoid CB1 receptor (CNR1) is highly expressed in cholecystokinin subtype GABAergic inhibitory interneurons within the cortex.


claim_key: biorxiv:8f74778a-6c1f-1014-8563-ba83ee46ac17:claim:f1324137a800a833d8e1
claim_id: claim:f1324137a800a833d8e1
paper_key: biorxiv:8f74778a-6c1f-1014-8563-ba83ee46ac17
span_literal:
Primary antibodies included monoclonal mouse anti-vGAT antibody (1:500; Synaptic Systems, Göttingen, Germany; product # 131011) – which labels inhibitory boutons; polyclonal guinea pig anti-vGlut1 antibody (1:500; Millipore Sigma, Burlington, MA; product # AB5905) – which labels excitatory boutons

summary:
In Homo sapiens, vGAT (SLC32A1) labels inhibitory boutons and vGlut1 (SLC17A7) labels excitatory boutons.


claim_key: biorxiv:8f74778a-6c1f-1014-8563-ba83ee46ac17:claim:1f4ab9fdba568ddf3ed5
claim_id: claim:1f4ab9fdba568ddf3ed5
paper_key: biorxiv:8f74778a-6c1f-1014-8563-ba83ee46ac17
span_literal:
Current literature supports the predominance of CB1R within CCK-containing interneurons using non-psychiatric postmortem human brain samples, with lower levels of CB1R detected in parvalbumin (PV)-positive cells using rodent studies

summary:
In Homo sapiens, CNR1 (CB1R) is predominantly expressed in cholecystokinin-containing interneurons in postmortem human brain samples.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:074330f64e9985e177f5
claim_id: claim:074330f64e9985e177f5
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
Among the genes consistently upregulated in MRD cells, we identified MS4A1, encoding the B-cell surface antigen CD20.

summary:
In Homo sapiens, MS4A1, encoding the B-cell surface antigen CD20, is a consistently upregulated marker in minimal residual disease cells of B-cell acute lymphoblastic leukemia.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:90696c0e2c3402cea13b
claim_id: claim:90696c0e2c3402cea13b
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
Among them, MS4A1, encoding the B-lymphocyte surface antigen CD20, was the gene for which the up-regulation was found in the most important proportion of cells between untreated and treated cells, from both diagnosis and relapse PDXs (Figure 1H and Table S4).

summary:
In Homo sapiens, MS4A1, encoding the B-lymphocyte surface antigen CD20, is the most prominently upregulated surface marker gene in minimal residual disease cells from B-cell acute lymphoblastic leukemia patient-derived xenografts.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:e6e96a06aa1401b285ae
claim_id: claim:e6e96a06aa1401b285ae
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
the overlap of the 45 up-regulated genes encoding surface markers in MRD cells from patient HB#012 (Figure 1G, left panel) with the up-regulated genes in MRD cells from patient HB#010 (Figures S1F) revealed MS4A1 as a common gene, as well as ITGAM (CD11b) and CD72, that have been implicated for prognosis, treatment response monitoring and MRD detection in pediatric B-ALL (26–28) (Figure S2B).

summary:
In Homo sapiens, MS4A1, ITGAM (CD11b), and CD72 are common upregulated surface marker genes in minimal residual disease cells of pediatric B-cell acute lymphoblastic leukemia.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:7b72abab558b76958fab
claim_id: claim:7b72abab558b76958fab
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
we identified CD34 as the most relevant candidate for which the down-regulation was associated with the resistance of MRD cells (Figure 1I and Figures 2A, B, lower panels).

summary:
In Homo sapiens, CD34 is downregulated in minimal residual disease cells of B-cell acute lymphoblastic leukemia, and its down-regulation is associated with chemoresistance.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:de40a11bb9d85cf2a634
claim_id: claim:de40a11bb9d85cf2a634
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
Interestingly, cluster 10 was the only population within untreated cells, from both diagnosis and relapse PDXs, that expressed MS4A1 and simultaneously repressed CD34 (Figure 2A).

summary:
In Homo sapiens, cluster 10 of B-cell acute lymphoblastic leukemia cells is characterized by expression of MS4A1 and repression of CD34.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:2b2361e280cc98b71ad0
claim_id: claim:2b2361e280cc98b71ad0
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
Unsupervised clustering revealed a phenotypic evolution of MRD cells as compared to untreated cells, characterized by the down-regulation of CD34 and the up-regulation of CD45, CD24 and CD20 (Figures 2C, D), while the expression of CD10 and CD38 markers remained stable (Figure S2G).

summary:
In Homo sapiens, minimal residual disease cells of B-cell acute lymphoblastic leukemia are characterized by downregulation of CD34 and upregulation of CD45, CD24, and CD20, while CD10 and CD38 expression remains stable.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:52d64382abd38eb1b935
claim_id: claim:52d64382abd38eb1b935
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal: MRD-like population exhibiting a mature immunophenotype CD45highCD34lowCD20+
summary:
In Homo sapiens, the minimal residual disease-like population of B-cell acute lymphoblastic leukemia exhibits a mature immunophenotype with high CD45, low CD34, and positive CD20 expression.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:d12f8b40ac826b4cbd43
claim_id: claim:d12f8b40ac826b4cbd43
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
The analysis revealed a significant down-regulation of CD34 and up-regulation of CD45 and CD20, while CD19 expression remained stable (Figure 5A and Table S8), strongly supporting our results in MRD cells from the PDX models (Figures 2C-F and Figures 3B, C).

summary:
In Homo sapiens, minimal residual disease cells from pediatric B-cell acute lymphoblastic leukemia patients show significant downregulation of CD34 and upregulation of CD45 and CD20, while CD19 expression remains stable.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:29816056b93064dc6b4f
claim_id: claim:29816056b93064dc6b4f
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
CHEMO spared persisting MRD cells (Figures 6C-E) that have clearly up-regulated CD20 (Figures 6G, H), as expected.

summary:
In Homo sapiens, persisting minimal residual disease cells of B-cell acute lymphoblastic leukemia clearly upregulate CD20 after chemotherapy.


claim_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b:claim:f7f34554677178586e05
claim_id: claim:f7f34554677178586e05
paper_key: biorxiv:9081da13-83e1-1014-ba34-dc521a45201b
span_literal:
is associated with the presence of persisting leukemic blasts exhibiting the immunophenotype CD45highCD34lowCD20+ (Figures 3B, C and Figure S3F).

summary:
In Homo sapiens, persisting leukemic blasts of B-cell acute lymphoblastic leukemia after chemotherapy exhibit the immunophenotype with high CD45, low CD34, and positive CD20.


claim_key: biorxiv:9143aeff-6c86-1014-8d9c-e6611dda1bec:claim:24c104117e8719f09158
claim_id: claim:24c104117e8719f09158
paper_key: biorxiv:9143aeff-6c86-1014-8d9c-e6611dda1bec
span_literal:
MSMB (beta-microseminoprotein) is consistently downregulated in PRC and has been widely proposed as a diagnostic and prognostic marker

summary:
In Homo sapiens, beta-microseminoprotein (MSMB) is consistently downregulated in prostate cancer and has been widely proposed as a diagnostic and prognostic marker.


claim_key: biorxiv:9143aeff-6c86-1014-8d9c-e6611dda1bec:claim:d7ef713869e128c053c2
claim_id: claim:d7ef713869e128c053c2
paper_key: biorxiv:9143aeff-6c86-1014-8d9c-e6611dda1bec
span_literal:
PARP1, involved in DNA damage repair, is overexpressed in aggressive PRC and targeted by approved therapies

summary:
In Homo sapiens, poly(ADP-ribose) polymerase 1 (PARP1) is overexpressed in aggressive prostate cancer and targeted by approved therapies.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:1fe3a0cb4bb7dd04f440
claim_id: claim:1fe3a0cb4bb7dd04f440
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal:
POU5F1 (also known as OCT4), which encodes a transcription factor critically involved in the self-renewal of undifferentiated pluripotent stem cells (Boyer et al., 2005), was consistently expressed in 98.6% of cells comprising all four subpopulations

summary:
In Homo sapiens, POU5F1 (also known as OCT4) is a positive marker of induced pluripotent stem cells, expressed in 98.6% of cells across all four subpopulations.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:35c305710881472a3189
claim_id: claim:35c305710881472a3189
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal:
Other known markers of pluripotency such as SOX2, NANOG and UTF1 were expressed across the subpopulations

summary:
In Homo sapiens, SOX2, NANOG, and UTF1 are positive markers of pluripotency expressed across induced pluripotent stem cell subpopulations.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:7ecd5edc358cbc0ec6f0
claim_id: claim:7ecd5edc358cbc0ec6f0
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal: In particular, POU5F1, NANOG, and SOX2 are more highly expressed in subpopulation two
summary:
In Homo sapiens, POU5F1, NANOG, and SOX2 are more highly expressed in the proliferative pluripotent subpopulation (subpopulation two) of induced pluripotent stem cells.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:d02f3af744af543f2f0f
claim_id: claim:d02f3af744af543f2f0f
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal:
Among these 49 genes, two key transcription factors and a signaling receptor were significantly higher in subpopulation two than subpopulation one, including SALL4 (Spalt-like transcription factor 4, p-adjusted: 7.0 × 10−5), ZIC1 (Zic family member 1, p-adjusted: 4.3×10−5), and NR6A1 (Nuclear Receptor Subfamily 6 Group A Member 1, p-adjusted: 3.7 × 10−6)

summary:
In Homo sapiens, SALL4 (Spalt-like transcription factor 4), ZIC1 (Zic family member 1), and NR6A1 (Nuclear Receptor Subfamily 6 Group A Member 1) are positive markers of the proliferative pluripotent subpopulation (subpopulation two) compared to the core pluripotent subpopulation (subpopulation one) of induced pluripotent stem cells.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:644e72f80f1702d18eb1
claim_id: claim:644e72f80f1702d18eb1
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal:
Compared to subpopulations one and two, subpopulations three and four represent pluripotent populations with significant down-regulation of key pluripotency network genes (e.g. NANOG and UTF1)

summary:
In Homo sapiens, NANOG and UTF1 are downregulated in the early-primed for differentiation subpopulation (subpopulation three) of induced pluripotent stem cells compared to the core pluripotent and proliferative subpopulations.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:e60b5bd1f17a41027e4d
claim_id: claim:e60b5bd1f17a41027e4d
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal:
Compared to subpopulations one and two, subpopulations three and four represent pluripotent populations with significant down-regulation of key pluripotency network genes (e.g. NANOG and UTF1)

summary:
In Homo sapiens, NANOG and UTF1 are downregulated in the late-primed for differentiation subpopulation (subpopulation four) of induced pluripotent stem cells compared to the core pluripotent and proliferative subpopulations.


claim_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d:claim:d48963db5c4f04a83542
claim_id: claim:d48963db5c4f04a83542
paper_key: biorxiv:9263ba65-6c09-1014-b701-af82efb9455d
span_literal:
Comparison of transcriptomes between subpopulations revealed a cell proliferation gene network, coordinately regulated by two transcription factors SALL4, ZIC1 and the NR5A1 signaling receptor, together with the well-characterized pluripotency regulators POU5F1, SOX2, and NANOG.

summary:
In Homo sapiens, SALL4, ZIC1, NR5A1, POU5F1, SOX2, and NANOG are positive markers of the proliferative pluripotent subpopulation of induced pluripotent stem cells.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:a79b0ac8f4862b6c5d70
claim_id: claim:a79b0ac8f4862b6c5d70
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
Immunofluorescence analysis of NANOG (epiblast), GATA4 (hypoblast) and GATA3 (trophectoderm, placental progenitor cells) showed that increasing concentrations of FGF4 increased the number of hypoblast cells

summary:
In Homo sapiens blastocysts, NANOG is a marker of epiblast cells, GATA4 is a marker of hypoblast cells, and GATA3 is a marker of trophectoderm cells.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:4dd01c400734b735dd0f
claim_id: claim:4dd01c400734b735dd0f
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
summary: In Homo sapiens blastocysts, SOX2 is used as a marker of epiblast cells.
span_literal:
we stained for pERK in human blastocysts from Days 5 to 6.5, using SOX2 and OTX2 as markers of the epiblast and hypoblast, respectively


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:9ee549ec72d8b1be14f6
claim_id: claim:9ee549ec72d8b1be14f6
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
there is pan-ICM expression of the FGFR1 receptor, while FGF4 is expressed specifically in epiblast cells

summary:
In Homo sapiens, FGF4 is expressed specifically in epiblast cells, while FGFR1 is expressed across inner cell mass cells.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:7fc1f481be51b2a5571a
claim_id: claim:7fc1f481be51b2a5571a
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
ERKi-treated ICM cells downregulated GATA6, GATA4, PDGFRA, HNF4A, SOX17, DAB2, COL4A1, and immediate early FGF responses genes, such as DUSP6, indicating that both signalling and hypoblast-enriched transcripts were perturbed

summary:
In Homo sapiens, GATA6, GATA4, PDGFRA, HNF4A, SOX17, DAB2, and COL4A1 are hypoblast-enriched transcripts that are downregulated in inner cell mass cells following ERK inhibition.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:2667999f4b41740ceeb8
claim_id: claim:2667999f4b41740ceeb8
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
transcripts associated with the pluripotent epiblast or naïve pluripotency such as DNMT3L, DNMT3A, DPPA5, KLF17, KLF3, KLF5, NODAL, POU5F1, PRDM1, PRDM14 and SOX2, were significantly upregulated in ICM cells following ERKi-treatment compared to controls

summary:
In Homo sapiens, DNMT3L, DNMT3A, DPPA5, KLF17, KLF3, KLF5, NODAL, POU5F1, PRDM1, PRDM14, and SOX2 are transcripts associated with the pluripotent epiblast or naïve pluripotency, upregulated in inner cell mass cells following ERK inhibition.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:78f9c288e373bc32a018
claim_id: claim:78f9c288e373bc32a018
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
We confirmed at the protein level that the pluripotent epiblast markers SOX2 and KLF17 are expressed throughout the ICM and that the early hypoblast marker PDGFRA is downregulated following ERKi-treatment

summary:
In Homo sapiens, SOX2 and KLF17 are pluripotent epiblast cell markers, while PDGFRA is an early hypoblast cell marker.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:920ccc8ec3d52b08e578
claim_id: claim:920ccc8ec3d52b08e578
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
immunofluorescence analysis showed they expressed core pluripotency markers OCT4 and SOX2, and naïve pluripotency markers KLF4, KLF17, SUSD2, and TFAP2C31–34

summary:
In Homo sapiens, naïve human embryonic stem cells express core pluripotency markers OCT4 and SOX2, and naïve pluripotency markers KLF4, KLF17, SUSD2, and TFAP2C.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:20c66ebe9df118ef1da8
claim_id: claim:20c66ebe9df118ef1da8
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
the PXGL hPSCs were similar to previously derived naïve hPSCs in their high expression of naïve markers KLF4, KLF17, DNMT3L, and DPPA3, low expression of primed markers ETV4, ETV5 and SALL2 and equivalent level of general pluripotency markers POU5F1, NANOG and SOX2 compared to primed hPSCs

summary:
In Homo sapiens, naïve human pluripotent stem cells show high expression of naïve markers KLF4, KLF17, DNMT3L, and DPPA3, low expression of primed markers ETV4, ETV5, and SALL2, and equivalent levels of general pluripotency markers POU5F1, NANOG, and SOX2 compared to primed human pluripotent stem cells.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:b8bf0bdbca2746ba4f59
claim_id: claim:b8bf0bdbca2746ba4f59
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
the UXGL hESC lines had characteristic domed shaped morphology and expressed expressed SOX2, NANOG and OCT4 in addition to naïve pluripotency markers KLF4, KLF5, KLF17, TFAP2C and DNMT3L

summary:
In Homo sapiens, naïve human embryonic stem cell lines express SOX2, NANOG, and OCT4 in addition to naïve pluripotency markers KLF4, KLF5, KLF17, TFAP2C, and DNMT3L.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:604c4f997836247b655f
claim_id: claim:604c4f997836247b655f
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal: formative/primed pluripotency such as ETV5, FGF5 and WNT7B
summary:
In Homo sapiens, ETV5, FGF5, and WNT7B are markers of formative/primed pluripotency that are downregulated in ERK inhibitor-treated epiblast cells compared to controls.


claim_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9:claim:22511057c3533d03cfb6
claim_id: claim:22511057c3533d03cfb6
paper_key: biorxiv:9338c4d5-712d-1014-b47b-dc1970abe2d9
span_literal:
ERKi embryos lost the early hypoblast marker GATA6 and retained high levels of pluripotency epiblast markers NANOG and OCT4

summary:
In Homo sapiens, GATA6 is an early hypoblast cell marker, while NANOG and OCT4 are pluripotency epiblast cell markers.


claim_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3:claim:ea8868aa6941887b109c
claim_id: claim:ea8868aa6941887b109c
paper_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3
span_literal: CYP4F3, H2AB1, PGR3, FCGR3B and PHF24 were allocated to the neutrophil expression cluster.
summary:
In Homo sapiens, CYP4F3, H2AB1, PGR3, FCGR3B, and PHF24 are markers allocated to the neutrophil expression cluster.


claim_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3:claim:fa6c62f3b931394d7cca
claim_id: claim:fa6c62f3b931394d7cca
paper_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3
span_literal:
ALOX15 and RNASE3 were associated with the eosinophil expression cluster and PGR2 was localized in the basophil expression cluster, while both expression clusters were shared for RAB44 and RNASE2.

summary:
In Homo sapiens, ALOX15 and RNASE3 are markers associated with the eosinophil expression cluster. In Homo sapiens, RAB44 and RNASE2 are markers shared between the eosinophil and basophil expression clusters.


claim_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3:claim:81a3ae7a9a9a1cfc05cd
claim_id: claim:81a3ae7a9a9a1cfc05cd
paper_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3
span_literal:
ALOX15 and RNASE3 were associated with the eosinophil expression cluster and PGR2 was localized in the basophil expression cluster, while both expression clusters were shared for RAB44 and RNASE2.

summary:
In Homo sapiens, PGR2 is a marker localized in the basophil expression cluster. In Homo sapiens, RAB44 and RNASE2 are markers shared between the eosinophil and basophil expression clusters.


claim_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3:claim:100775d96faa1058153b
claim_id: claim:100775d96faa1058153b
paper_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3
span_literal:
An association with the monocyte expression cluster was identified for CLEC6A, MPO, MYO1G and SIGLEC1.

summary:
In Homo sapiens, CLEC6A, MPO, MYO1G, and SIGLEC1 are markers associated with the monocyte expression cluster.


claim_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3:claim:45d39536f6b06ec39442
claim_id: claim:45d39536f6b06ec39442
paper_key: biorxiv:936f1a11-6c21-1014-8f5e-c76664c0d7e3
summary: In Homo sapiens, ATP6V1G2 and SEPTIN1 are markers belonging to the B cell expression cluster.
span_literal:
Few identified genes belonged to B-cell (ATP6V1G2 and SEPTIN1) and T-cell (STAP1) expression clusters and group enrichment was found for LRRC25, LY9 and PADI4 (Fig. 6D).


claim_key: biorxiv:93f05b2d-72a8-1014-8450-ae3deb621084:claim:2e74b4f75ce0ca12ab22
claim_id: claim:2e74b4f75ce0ca12ab22
paper_key: biorxiv:93f05b2d-72a8-1014-8450-ae3deb621084
span_literal:
Within the ventral prostate, we also uncovered two additional androgen-responsive luminal epithelial cell types, marked by Pbsn or Spink1 expression, which align with human luminal subsets and may define the origin of distinct prostate cancer subtypes.

summary:
In Homo sapiens, luminal epithelial cells of the prostate align with mouse ventral prostate luminal epithelial cell types marked by PBSN or SPINK1 expression.


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:ab0363f29e690a1948e1
claim_id: claim:ab0363f29e690a1948e1
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
summary: In Homo sapiens, naïve-like T cells and central memory T cells express SELL, TCF7, LEF1, and CCR7.
span_literal:
naïve-like T cells (TN, CD4_cluster0) and central memory T cells (TCM, CD4_cluster1) expressing SELL, TCF7, LEF1, and CCR7 genes


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:f178c1f5bf8d5a6aa75d
claim_id: claim:f178c1f5bf8d5a6aa75d
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
summary: In Homo sapiens, tissue-resident memory T cells express NR4A1, MYADM, and PTGER4.
span_literal:
tissue-resident memory T cells (TRM, CD4_clusters3, 5, 6) expressing NR4A1, MYADM, and PTGER4 genes were abundant in most samples


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:f344f658fdc81c513bef
claim_id: claim:f344f658fdc81c513bef
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
summary: In Homo sapiens, regulatory T cells express FOXP3, CTLA4, ICOS, and BATF.
span_literal:
Regulatory T cells (Treg, CD4_cluster2) with FOXP3, CTLA4, ICOS, and BATF expression were also abundant


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:a075f852b5f6a1f2897e
claim_id: claim:a075f852b5f6a1f2897e
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
summary: In Homo sapiens, CD8+ effector memory T cells express PRF1 and IFNG.
span_literal:
effector memory T cells (TEM), effector T cells (TEFF), effector memory CD45RA positive cells (TEMRA) (CD8_clusters0, 2, 3, 8) expressing PRF1 and IFNG were dominant over TN/TCM (CD8_clusters4, 5) types


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:c71fb3c896d71b96b311
claim_id: claim:c71fb3c896d71b96b311
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
summary: In Homo sapiens, exhausted T cells express HAVCR2, PDCD1, PRF1, IFNG, CXCR3, and CXCL13.
span_literal:
Exhausted T cells (TEX, CD8_clusters1, 12) expressed multiple checkpoint genes (HAVCR2 and PDCD1) along with high levels of PRF1, IFNG, CXCR3, and CXCL13


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:2e8b051d42c069188dd5
claim_id: claim:2e8b051d42c069188dd5
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
summary: In Homo sapiens, active natural killer cells express PRF1, TNF, and IFNG.
span_literal:
Active NK cells expressed the highest level of PRF1, TNF, and IFNG, reflecting a cytotoxic effector function.


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:df3162ac0c4cbd0f428d
claim_id: claim:df3162ac0c4cbd0f428d
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
span_literal:
Alveolar macrophages (Alveolar Mac, Myeloid_cluster0) expressed well-defined marker genes such as MARCO, FABP4, and MCEMP1 along with anti-inflammatory genes such as CD163, APOE, and C1QA/B/C

summary:
In Homo sapiens, alveolar macrophages express the marker genes MARCO, FABP4, MCEMP1, CD163, APOE, and C1QA/B/C.


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:26c8e71f59779dce0365
claim_id: claim:26c8e71f59779dce0365
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
span_literal:
Dendritic cells were categorized as CD1c+ (Myeloid_cluster8, CD1C and ITGAX), activated (Myeloid_cluster17, CCR7 and LAMP3), and CD141+ (Myeloid_cluster19, CLEC9A and XCR1) subclusters.

summary:
In Homo sapiens, CD1c+ dendritic cells express CD1C and ITGAX, activated dendritic cells express CCR7 and LAMP3, and CD141+ dendritic cells express CLEC9A and XCR1.


claim_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a:claim:3b4fdd92f9da1f43eef7
claim_id: claim:3b4fdd92f9da1f43eef7
paper_key: biorxiv:96c0ca44-7598-1014-bd6e-c97aae1f298a
span_literal:
CD14+CD16-classical monocytes (Myeloid_clusters1,6) were predominantly found over non-classical CD14loCD16+ types (Myeloid_cluster15)

summary:
In Homo sapiens, classical monocytes are CD14-positive and CD16-negative, whereas non-classical monocytes are CD14-low and CD16-positive.


claim_key: biorxiv:971fc928-7029-1014-9faa-c9d63a921f72:claim:0af755bb43b437abcf42
claim_id: claim:0af755bb43b437abcf42
paper_key: biorxiv:971fc928-7029-1014-9faa-c9d63a921f72
span_literal:
We found 12 intersecting genes (EXT1, FBN1, FOSB, GNAO1, GRB10, MMP9, NFE2, PRF1, SLC25A23, SNAI1, ST6GALNAC3 and STX11), which expression pattern in the GSE151371 dataset is characterized by an increasing dysregulation as SCI severity increases

summary:
In Homo sapiens, a twelve-gene signature including EXT1, FBN1, FOSB, GNAO1, GRB10, MMP9, NFE2, PRF1, SLC25A23, SNAI1, ST6GALNAC3, and STX11 in blood serves as severity-associated biomarker genes for spinal cord injury, with increasing dysregulation as injury severity increases.


claim_key: biorxiv:971fc928-7029-1014-9faa-c9d63a921f72:claim:9a275f2b834e77f2287f
claim_id: claim:9a275f2b834e77f2287f
paper_key: biorxiv:971fc928-7029-1014-9faa-c9d63a921f72
span_literal:
Kwon et al. (48) described a significant correlation between elevated MMP9 levels and worsened neurological recovery in human patients.

summary:
In Homo sapiens, elevated MMP9 levels in spinal cord injury patients correlate with worsened neurological recovery, supporting MMP9 as a severity biomarker in blood.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:bac342075deb00fe84ae
claim_id: claim:bac342075deb00fe84ae
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
Integrative transcriptomic analyses identified the upregulated serine/cysteine protease inhibitor, SERPINB3 (squamous cell carcinoma antigen 1, SCCA1) in basal-like/squamous PDAC using discovery and validation approaches.

summary:
In Homo sapiens, SERPINB3 (serine/cysteine protease inhibitor family B member 3, also known as squamous cell carcinoma antigen 1) is upregulated in basal-like/squamous pancreatic ductal adenocarcinoma.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:730358d053fae26cbc1c
claim_id: claim:730358d053fae26cbc1c
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
Among them, SERPINB3 was ranked one of the top and robustly upregulated genes in the basal-like/progenitor subtype (Supplementary Table 2).

summary:
In Homo sapiens, SERPINB3 is one of the top upregulated genes in the basal-like/squamous subtype of pancreatic ductal adenocarcinoma.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:59adfe6e86f145288608
claim_id: claim:59adfe6e86f145288608
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
Tumors defined as basal-like/squamous subtype showed upregulation of SERPINB3 mRNA expression and associated with worse patient survival (Figure 2A).

summary:
In Homo sapiens, tumors of the basal-like/squamous subtype of pancreatic ductal adenocarcinoma show upregulation of SERPINB3 mRNA expression.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:7835ce6215a1fe48d540
claim_id: claim:7835ce6215a1fe48d540
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
SERPINB3 is also known as squamous cell carcinoma antigen (24–27), associates with hypoxia (28,29), and promotes MYC activation (30,31), cancer stemness (32,33), metabolic reprogramming (28), and inflammation (34–36).

summary:
In Homo sapiens, SERPINB3 (squamous cell carcinoma antigen) promotes MYC activation in squamous cell carcinoma.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:52389af91bf81e004561
claim_id: claim:52389af91bf81e004561
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
Serine/cysteine protease inhibitor family B member 3 (SERPINB3, also known as squamous cell carcinoma antigen 1, SCCA1) was initially described as a tumor-specific antigen in squamous cell carcinoma of the uterine cervix (24).

summary:
In Homo sapiens, SERPINB3 (serine/cysteine protease inhibitor family B member 3, also known as squamous cell carcinoma antigen 1) was initially described as a tumor-specific antigen in squamous cell carcinoma of the uterine cervix.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:a8795b655ec5cfd5f64f
claim_id: claim:a8795b655ec5cfd5f64f
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
immunostaining of endothelial marker CD31 and the reactive oxygen species, 8-OHdG, revealed that angiogenesis and oxidative stress are upregulated in the tumor xenografts of SERPINB3-overexpressing AsPC-1 in orthotopic model (Figure 4F and 4G).

summary:
In Homo sapiens, CD31 is a marker of endothelial cells, as shown by immunostaining in pancreatic ductal adenocarcinoma xenografts.


claim_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883:claim:20cb5de84f982a6e5d30
claim_id: claim:20cb5de84f982a6e5d30
paper_key: biorxiv:987080be-6c4e-1014-9a81-e7554d23c883
span_literal:
The density of microvessels in the orthotopic tumor xenografts was assessed using CD31 expression in endothelial cells.

summary:
In Homo sapiens, CD31 expression is used to identify endothelial cells for assessing microvessel density in tumor xenografts.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:010a0f208fa00aa2d5c3
claim_id: claim:010a0f208fa00aa2d5c3
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
SMCs of C0 and C1 displayed a fibromyocyte signature (e.g., FN1, COL1A1, DCN), with C1 having higher expression of inflammatory genes (e.g., CCL2, PTGS2, CXCL1).

summary:
In Homo sapiens, fibromyocyte smooth muscle cells (cluster C0) are marked by positive expression of FN1, COL1A1, and DCN.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:a36b5682091bcbf30f73
claim_id: claim:a36b5682091bcbf30f73
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
SMCs of C0 and C1 displayed a fibromyocyte signature (e.g., FN1, COL1A1, DCN), with C1 having higher expression of inflammatory genes (e.g., CCL2, PTGS2, CXCL1).

summary:
In Homo sapiens, inflammatory smooth muscle cells (cluster C1) display a fibromyocyte signature with FN1, COL1A1, and DCN, and have higher expression of inflammatory genes CCL2, PTGS2, and CXCL1.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:487b69dc6ed31f6f282e
claim_id: claim:487b69dc6ed31f6f282e
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
C2, C4, and C5 had features of proliferating SMCs, with C2 being enriched for markers of the M-phase (e.g., MKI67, CDK1, CCNB1), and C4 being enriched in markers of the S-phase (e.g., CDK2, PCNA, MCM3).

summary:
In Homo sapiens, proliferative M-phase smooth muscle cells (cluster C2) are enriched for MKI67, CDK1, and CCNB1.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:dd2b03d901ec16b8db76
claim_id: claim:dd2b03d901ec16b8db76
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
C2, C4, and C5 had features of proliferating SMCs, with C2 being enriched for markers of the M-phase (e.g., MKI67, CDK1, CCNB1), and C4 being enriched in markers of the S-phase (e.g., CDK2, PCNA, MCM3).

summary:
In Homo sapiens, proliferative S-phase smooth muscle cells (cluster C4) are enriched for CDK2, PCNA, and MCM3.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:25edefde6afbeb6d2cb0
claim_id: claim:25edefde6afbeb6d2cb0
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
C5 displayed expression associated with both the M- and S-phase, though to a lesser extent, and additionally had an increased expression of cell adhesion molecules (e.g., EFEMP1, TINAGL1, MCAM).

summary:
In Homo sapiens, proliferative M-S-phase smooth muscle cells (cluster C5) have increased expression of cell adhesion molecules EFEMP1, TINAGL1, and MCAM.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:ef24da1d60f7961c1fc0
claim_id: claim:ef24da1d60f7961c1fc0
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
C3 (intermediate SMCs) shared the high inflammatory gene expression characteristics of C1, but also displayed higher expression of cell adhesion and migration-associated genes (e.g., TGM2, IGFBP3, TGFB2), showing similarities with C5.

summary:
In Homo sapiens, intermediate smooth muscle cells (cluster C3) display higher expression of cell adhesion and migration-associated genes TGM2, IGFBP3, and TGFB2.


claim_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400:claim:bfa0afb80ebf66cbd3a8
claim_id: claim:bfa0afb80ebf66cbd3a8
paper_key: biorxiv:98d19bc0-7b12-1014-9641-857e081ce400
span_literal:
SMCs of the small C6 showed the highest expression of contractile genes (e.g., ACTA2, TAGLN, MYL9), suggesting that this cluster represents the population more closely related to mature vascular SMCs found in healthy aorta.

summary:
In Homo sapiens, contractile smooth muscle cells (cluster C6) show the highest expression of contractile genes ACTA2, TAGLN, and MYL9.


claim_key: biorxiv:99010971-6d4e-1014-a10e-acd0232efb79:claim:195803fbb9afaa062951
claim_id: claim:195803fbb9afaa062951
paper_key: biorxiv:99010971-6d4e-1014-a10e-acd0232efb79
summary: In Homo sapiens, NOLC1 is used as a nucleolar marker in endometrial organoids.
span_literal:
we cross-referenced the same organoids following immunofluorescence staining with antibodies against NOLC1.


claim_key: biorxiv:99010971-6d4e-1014-a10e-acd0232efb79:claim:063037393fe69326ef5f
claim_id: claim:063037393fe69326ef5f
paper_key: biorxiv:99010971-6d4e-1014-a10e-acd0232efb79
summary: In Homo sapiens, LMNB1 is a positive marker of the nuclear lamina in endometrial organoid cells.
span_literal:
we further stained the nuclear lamina using an antibody against LAMINB1 (LMNB1), a structural component of the nuclear envelope


claim_key: biorxiv:99010971-6d4e-1014-a10e-acd0232efb79:claim:4be39a03b0f36f72815c
claim_id: claim:4be39a03b0f36f72815c
paper_key: biorxiv:99010971-6d4e-1014-a10e-acd0232efb79
span_literal:
To directly assess the proliferative response to progesterone, we evaluated Ki67 expression—a well-established marker of cell proliferation—in organoids derived from both individuals.

summary:
In Homo sapiens, Ki67 is a well-established marker of cell proliferation in endometrial organoid cells.


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:9bfed2479b675f159a2f
claim_id: claim:9bfed2479b675f159a2f
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
summary: In Homo sapiens, JUN is a positively active driver in B cells and T cells in severe COVID-19 cases.
span_literal:
We discovered that the most active drivers in severe cases were JUN (B/T cells) and TIMP1 (all PBMCs except B cells and NKs).


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:b61186a36b16c5ae2255
claim_id: claim:b61186a36b16c5ae2255
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
span_literal:
We discovered that the most active drivers in severe cases were JUN (B/T cells) and TIMP1 (all PBMCs except B cells and NKs).

summary:
In Homo sapiens, TIMP1 is a positively active driver in peripheral blood mononuclear cells (except B cells and natural killer cells) in severe COVID-19 cases.


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:01488a6ce12950d6efa5
claim_id: claim:01488a6ce12950d6efa5
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
summary: In Homo sapiens, PTEN is a positively active driver in monocytes in non-severe COVID-19 cases.
span_literal:
In contrast, in non-severe cases, it was PTEN (monocytes and platelets) and ACAA1 (all PBMCs but especially B cells).


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:f307cc8c71af7a78dabd
claim_id: claim:f307cc8c71af7a78dabd
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
span_literal:
In contrast, in non-severe cases, it was PTEN (monocytes and platelets) and ACAA1 (all PBMCs but especially B cells).

summary:
In Homo sapiens, ACAA1 is a positively active driver in peripheral blood mononuclear cells, especially B cells, in non-severe COVID-19 cases.


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:612cdd658713ddcc85a7
claim_id: claim:612cdd658713ddcc85a7
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
summary:
In Homo sapiens, ACAA1 is a positively active driver especially in B cells in non-severe COVID-19 cases.


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:cb94925cd96bc9b85f26
claim_id: claim:cb94925cd96bc9b85f26
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
summary: In Homo sapiens, CKAP4 is a positive marker of monocytes in non-severe COVID-19 cases.
span_literal:
Like ACAA1, which opposed its proteomic counterpart, CKAP4 was also increased in non-severe cases (monocytes).


claim_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278:claim:616aae82ba33b1818a54
claim_id: claim:616aae82ba33b1818a54
paper_key: biorxiv:9912495b-7074-1014-acf9-d95bb2127278
span_literal:
Other active genes in all non-severe PBMCs were FLT3LG, BAX, LYN and TNFSF10, while NCF2 was mainly in severe monocytes

summary:
In Homo sapiens, FLT3LG, BAX, LYN, and TNFSF10 are positively active genes in peripheral blood mononuclear cells in non-severe COVID-19 cases, while NCF2 is a positive marker of monocytes in severe COVID-19 cases.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:150431acd904686d9100
claim_id: claim:150431acd904686d9100
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal: Expression of MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes was predictive of SD.
summary:
In Homo sapiens, expression of MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes was predictive of severe dengue.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:10f6f1d08134554985c5
claim_id: claim:10f6f1d08134554985c5
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
The majority of DENV-associated cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and antiviral genes, followed by monocytes.

summary:
In Homo sapiens, naive IgM B cells associated with dengue virus express the CD69 and CXCR4 receptors.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:7f61a89b19278226a1dd
claim_id: claim:7f61a89b19278226a1dd
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
the first expressed markers of plasmablasts and plasma cells, whereas the second showed high expression of TYROBP, a transmembrane signalling protein that has been implicated in B cell proliferation

summary:
In Homo sapiens, a cluster of B cells showed high expression of TYROBP, a transmembrane signalling protein implicated in B cell proliferation.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:c9484fc20c6496e844c2
claim_id: claim:c9484fc20c6496e844c2
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
DENV-associated B cells were enriched but not exclusive to IgM/IGD isotypes as well as other markers of naive B lymphocytes, such as the transcription factor TCL1A (see Supplementary Fig. 5 for more markers)

summary:
In Homo sapiens, dengue virus-associated B cells were enriched for markers of naive B lymphocytes, including the transcription factor TCL1A.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:19d826df54c2d30b194b
claim_id: claim:19d826df54c2d30b194b
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
The surface receptors CD69, FCRL1, and CXCR4 that signal B cell activation and tissue-specific homing, and IRF1 that encodes an interferon related protein were also upregulated

summary:
In Homo sapiens, dengue virus-associated B cells showed upregulation of the surface receptors CD69, FCRL1, and CXCR4 that signal B cell activation, and IRF1 that encodes an interferon related protein.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:9b037657e855b722738d
claim_id: claim:9b037657e855b722738d
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
We computed differential gene expression between these bystanders and B cells from healthy controls and identified a strong antiviral response via interferon stimulated genes IFI6, IFI44L, and IFIT3

summary:
In Homo sapiens, bystander B cells from dengue patients showed a strong antiviral response via interferon stimulated genes IFI6, IFI44L, and IFIT3 compared with B cells from healthy controls.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:cbfa344f5ea75e6b0d93
claim_id: claim:cbfa344f5ea75e6b0d93
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
Distribution-level statistics and dimensionality reduction indicated that IgM positive, naive B cells expressing the surface markers CD69 and CXCR4 are the subset of PBMCs that most commonly associate with DENV in vivo, although other B cells of other isotypes were also represented.

summary:
In Homo sapiens, IgM positive naive B cells expressing the surface markers CD69 and CXCR4 are the subset of peripheral blood mononuclear cells that most commonly associate with dengue virus in vivo.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:dec887289c439cdef282
claim_id: claim:dec887289c439cdef282
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
Our data suggests the expression of MX2 within naive B cells and of CD163 within CD14+ CD16+ monocytes is greaty upregulated prior to the development of SD (Fig. 3E).

summary:
In Homo sapiens, expression of MX2 within naive B cells is greatly upregulated prior to the development of severe dengue.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:dcc4b82bc7c962c17284
claim_id: claim:dcc4b82bc7c962c17284
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
span_literal:
Our data suggests the expression of MX2 within naive B cells and of CD163 within CD14+ CD16+ monocytes is greaty upregulated prior to the development of SD (Fig. 3E).

summary:
In Homo sapiens, expression of CD163 within CD14+ CD16+ monocytes is greatly upregulated prior to the development of severe dengue.


claim_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03:claim:7b9637ee23b12831d8ce
claim_id: claim:7b9637ee23b12831d8ce
paper_key: biorxiv:99e5c433-6bf4-1014-a840-83babdf09f03
summary: In Homo sapiens, CD163 shows double specificity for both severe dengue and monocytes.
span_literal:
A number of genes show double specificity for both severe dengue and a single cell type, for instance CD163 in monocytes.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:b6efc5e3b9c95879de1d
claim_id: claim:b6efc5e3b9c95879de1d
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
Two NK cell populations have been described in humans based on their expression of CD56 and CD16 [34].

summary:
In Homo sapiens, natural killer cells are defined by their expression of CD56 and CD16, with two populations described based on these markers.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:f189a48599d2f58d41bd
claim_id: claim:f189a48599d2f58d41bd
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
In the septum, we identified both CD56dim CD16+ NK cells and CD56bright CD16- NK cells in similar frequencies, two subsets of B cells (CD19+ CD27- CD38- CD11c- T-bet- and CD19+ CD27- CD38- CD11c+ T-bet+) and another of antibody-secreting cells (ASCs; CD19+ CD27+ CD38+)

summary:
In Homo sapiens septum, CD56dim CD16-positive natural killer cells are identified by high CD16 expression, while CD56bright CD16-negative natural killer cells lack CD16.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:f88a88da7214551b75ff
claim_id: claim:f88a88da7214551b75ff
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
In the septum, we identified both CD56dim CD16+ NK cells and CD56bright CD16- NK cells in similar frequencies, two subsets of B cells (CD19+ CD27- CD38- CD11c- T-bet- and CD19+ CD27- CD38- CD11c+ T-bet+) and another of antibody-secreting cells (ASCs; CD19+ CD27+ CD38+)

summary:
In Homo sapiens septum, CD56bright CD16-negative natural killer cells are identified by bright CD56 expression and absence of CD16.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:be41c04c30420296f5aa
claim_id: claim:be41c04c30420296f5aa
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
In the septum, we identified both CD56dim CD16+ NK cells and CD56bright CD16- NK cells in similar frequencies, two subsets of B cells (CD19+ CD27- CD38- CD11c- T-bet- and CD19+ CD27- CD38- CD11c+ T-bet+) and another of antibody-secreting cells (ASCs; CD19+ CD27+ CD38+)

summary:
In Homo sapiens septum, one B cell subset is identified as CD19-positive, CD27-negative, CD38-negative, CD11c-negative, and T-bet-negative.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:ab8ebf07abce099bd5ef
claim_id: claim:ab8ebf07abce099bd5ef
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
summary:
In Homo sapiens septum, a second B cell subset is identified as CD19-positive, CD27-negative, CD38-negative, CD11c-positive, and T-bet-positive.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:4ddc90df6116a454e300
claim_id: claim:4ddc90df6116a454e300
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
summary:
In Homo sapiens septum, antibody-secreting cells are identified as CD19-positive, CD27-positive, and CD38-positive.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:d2a4916377d360e81ef8
claim_id: claim:d2a4916377d360e81ef8
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
We defined CD56bright NK cells as CD45+ NKp46+ GrK+ GrB- and CD56dim NK cells as CD45+ NKp46+ GrK- GrB+

summary:
In Homo sapiens, CD56bright natural killer cells are defined as CD45-positive, NKp46-positive, granzyme K-positive, and granzyme B-negative.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:4828bbfaaa28338a9aed
claim_id: claim:4828bbfaaa28338a9aed
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
We defined CD56bright NK cells as CD45+ NKp46+ GrK+ GrB- and CD56dim NK cells as CD45+ NKp46+ GrK- GrB+

summary:
In Homo sapiens, CD56dim natural killer cells are defined as CD45-positive, NKp46-positive, granzyme K-negative, and granzyme B-positive.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:8e1be4cfbf9cadc44138
claim_id: claim:8e1be4cfbf9cadc44138
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
CD56bright NK cells are known by their immunoregulatory properties and were also detected in the blood of the same MS donors with a migratory and activated phenotype, similarly to those in the brain.

summary:
In Homo sapiens, CD56bright natural killer cells are known for their immunoregulatory properties and are characterized by CD56 bright expression.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:b93b6555ee132468f5bf
claim_id: claim:b93b6555ee132468f5bf
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
summary: In Homo sapiens, granzyme K expression is typical of the CD56bright natural killer cell subset.
span_literal:
NK cells expressing granzyme K, typical of the CD56bright subset, are enriched in MS lesions and the choroidal tissue from MS donors.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:699b47c9232631d947ca
claim_id: claim:699b47c9232631d947ca
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
Contrarily, the expression of CD45RA and T-bet, markers of immature and cytotoxic NK cells respectively [6, 56], was lower in NK cells from MS donors compared to both control groups.

summary:
In Homo sapiens, CD45RA is a marker of immature natural killer cells and T-bet is a marker of cytotoxic natural killer cells.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:adb7949347ed3b929086
claim_id: claim:adb7949347ed3b929086
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
There are two main NK cell subsets based on the expression of CD56 and CD16: CD56bright NK cells express low levels of CD16 and are specialised immunoregulators, while CD56dim NK cells have a potent cytolytic capacity, which may be mediated by CD16 [34].

summary:
In Homo sapiens, CD56bright natural killer cells express low levels of CD16, while CD56dim natural killer cells have potent cytolytic capacity mediated by CD16.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:f8b0d8c70bbbe772d6b2
claim_id: claim:f8b0d8c70bbbe772d6b2
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
There are two main NK cell subsets based on the expression of CD56 and CD16: CD56bright NK cells express low levels of CD16 and are specialised immunoregulators, while CD56dim NK cells have a potent cytolytic capacity, which may be mediated by CD16 [34].

summary:
In Homo sapiens, CD56dim natural killer cells have potent cytolytic capacity which may be mediated by CD16.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:406babb323d4ae28fbf4
claim_id: claim:406babb323d4ae28fbf4
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
summary: In Homo sapiens, CD56 and NKp46 are used as markers to identify natural killer cells.
span_literal:
Importantly, we relied on the markers CD56 and NKp46 to identify human NK cells by CyTOF and immunohistochemistry, respectively.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:ad58ee05c77dce490f3c
claim_id: claim:ad58ee05c77dce490f3c
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal: Particularly, certain subsets of ILC3s share the expression of CD56 with NK cells [57].
summary:
In Homo sapiens, certain subsets of innate lymphoid cell type 3 share the expression of CD56 with natural killer cells.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:effa21c0c7c7521c625a
claim_id: claim:effa21c0c7c7521c625a
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
Moreover, we observed higher expression of the ligand PDL1 in CD56bright NK cells from MS brains compared to those from non-neurological controls, suggesting an involvement of the PD1-PDL1 axis.

summary:
In Homo sapiens, CD56bright natural killer cells from multiple sclerosis brains show higher expression of PDL1 compared to those from non-neurological controls.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:f133bd59062b2f5489d3
claim_id: claim:f133bd59062b2f5489d3
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
CD56bright NK cells in MS donors expressed higher levels of adhesion molecules (CD49d, CD54 and CD31), ligand PDL1, costimulatory molecule CD86, and lower levels of CD45RA and T-bet relative to controls

summary:
In Homo sapiens, CD56bright natural killer cells in multiple sclerosis donors express higher levels of CD49d, CD54, CD31, PDL1, and CD86, and lower levels of CD45RA and T-bet relative to controls.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:828b1a3b6d3ea7a9d7fb
claim_id: claim:828b1a3b6d3ea7a9d7fb
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
NK cells from the MS choroid plexus expressed higher levels of the IL-2 receptor α-chain CD25 and of adhesion molecule CD54 relative to those from controls

summary:
In Homo sapiens, natural killer cells from the multiple sclerosis choroid plexus express higher levels of CD25 (interleukin-2 receptor alpha-chain) and CD54 relative to controls.


claim_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027:claim:b274c55c1e5a7c55e09f
claim_id: claim:b274c55c1e5a7c55e09f
paper_key: biorxiv:9a5466f2-6c88-1014-bd5d-ff8513618027
span_literal:
PDL1 is an NK cell activation marker associated with enhanced cytotoxicity [11] and binds the T cell co-inhibitory molecule PD1 inducing suppression of PD1+ autoreactive T cells [44].

summary:
In Homo sapiens, PDL1 is a natural killer cell activation marker associated with enhanced cytotoxicity.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:7d45fde24446b4618ca2
claim_id: claim:7d45fde24446b4618ca2
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: we have confirmed that mCL0 and mCL2 were stromal cells (NR2F2+TCF21+PDGFRA+)
summary:
In Homo sapiens fetal testis, stromal cells are marked by positive expression of NR2F2, TCF21, and PDGFRA.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:c51ffaea881bcff5c54c
claim_id: claim:c51ffaea881bcff5c54c
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: mCL5 were proliferating stromal cells (NR2F2+TOP2A+MKI67+)
summary:
In Homo sapiens fetal testis, proliferating stromal cells are marked by positive expression of NR2F2, TOP2A, and MKI67.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:becd7d1e1c00f2a4748f
claim_id: claim:becd7d1e1c00f2a4748f
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: mCL3 and mCL4 were stromal precursor cells from 6-7WPF (NR2F2+TCF21+PDGFRA+)
summary:
In Homo sapiens fetal testis, stromal precursor cells are marked by positive expression of NR2F2, TCF21, and PDGFRA.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:3cf67ee569f61f5a50a4
claim_id: claim:3cf67ee569f61f5a50a4
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: mCL10 were Sertoli precursor cells from 6-7WPF (AMH+SOX9+)
summary:
In Homo sapiens fetal testis, Sertoli precursor cells are marked by positive expression of AMH and SOX9.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:2caf0e280959ccac2b20
claim_id: claim:2caf0e280959ccac2b20
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: mCL14 were Sertoli interstitial precursor cells (AMH+SOX9+NR2F2+)
summary:
In Homo sapiens fetal testis, Sertoli interstitial precursor cells are marked by positive expression of AMH, SOX9, and NR2F2.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:ad9505a9ecfd71232df7
claim_id: claim:ad9505a9ecfd71232df7
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: mCL16 were nephric cells showing expression of podocyte markers NPHS2, PTPRO and CLIC5
summary:
In Homo sapiens fetal testis, nephric cells show expression of podocyte markers NPHS2, PTPRO, and CLIC5.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:5380e1fd25ca0ecda5ba
claim_id: claim:5380e1fd25ca0ecda5ba
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
Interestingly, rete testis epithelial cell markers PAX8 and KRT19 were mainly expressed in cells from mCL7

summary:
In Homo sapiens fetal testis, rete testis epithelial cells are marked by positive expression of PAX8 and KRT19.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:c0cfd51aac79da21ac2f
claim_id: claim:c0cfd51aac79da21ac2f
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
We observed that the top 20 DEGs of R2, including PODXL, ALDH1A2 and PDPN were also highly expressed in R4

summary:
In Homo sapiens fetal testis, surface epithelial cells (R2 and R4) express PODXL, ALDH1A2, and PDPN.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:c0aa4f1e3940676a40fa
claim_id: claim:c0aa4f1e3940676a40fa
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
the top 20 DEGs of R3 included known Sertoli cell markers, such as AMH, GATM, INHA, GSTA1 and ALDH1A1

summary:
In Homo sapiens fetal testis, Sertoli cells are marked by positive expression of AMH, GATM, INHA, GSTA1, and ALDH1A1.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:a97111a7dd072a9bf342
claim_id: claim:a97111a7dd072a9bf342
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
Cells in R3 showed specific enrichment for DMRT1, NR5A1 and SOX9 as well as high levels of KRT8 and WT1, while CDH1 was not detected

summary:
In Homo sapiens fetal rete testis, Sertoli-like cells (R3) show enrichment for DMRT1, NR5A1, SOX9, KRT8, and WT1, while CDH1 was not detected.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:e574e708efdcefe811bf
claim_id: claim:e574e708efdcefe811bf
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: clusters meCL6, meCL7 and meCL11 showed similarities with nephric epithelial cells (PAX2+LHX1+)
summary:
In Homo sapiens fetal mesonephros/epididymis, nephric epithelial cells are marked by positive expression of PAX2 and LHX1.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:f292fa9089ca8a2b5210
claim_id: claim:f292fa9089ca8a2b5210
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: meCL15 were endothelial cells (PECAM1+)
summary:
In Homo sapiens fetal mesonephros/epididymis, endothelial cells are marked by positive expression of PECAM1.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:90cb6bcf3a3be450ff37
claim_id: claim:90cb6bcf3a3be450ff37
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: meCL4 were Sertoli cells (AMH+) from 7WPF
summary:
In Homo sapiens fetal mesonephros/epididymis, Sertoli cells are marked by positive expression of AMH.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:7fb887f2e4e05b772981
claim_id: claim:7fb887f2e4e05b772981
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: meCL14 showed cells with similarities with nephric podocytes (PODXL+CLIC5+)
summary:
In Homo sapiens fetal mesonephros/epididymis, nephric podocytes are marked by positive expression of PODXL and CLIC5.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:36067aed3cb641f94138
claim_id: claim:36067aed3cb641f94138
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
The stromal compartment was represented by 9 clusters (meCL0, meCL1, meCL2, meCL3, meCL5, meCL8, meCL10, meCL12 and meCL13), expressing high levels of DLK1 and NR2F2

summary:
In Homo sapiens fetal mesonephros/epididymis, the stromal compartment is marked by positive expression of DLK1 and NR2F2.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:61349e28381ef8c02c13
claim_id: claim:61349e28381ef8c02c13
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
SOX17 was specifically expressed in meCL11 (Figure 3F) and immunofluorescence SOX17 revealed the Müllerian duct in the male mesonephros at 8WPF and the regressing Müllerian duct in the epididymis of 17WPF testis

summary:
In Homo sapiens fetal mesonephros/epididymis, Müllerian duct epithelial cells are marked by positive expression of SOX17.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:02a9a63b0020580fb4eb
claim_id: claim:02a9a63b0020580fb4eb
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
summary: In Homo sapiens fetal testis, PCP4 is a specific marker of rete testis tubule epithelial cells.
span_literal:
PCP4 not only colocalized with PAX2 in the tubules of the epididymis at 17WPF, but it proved to be a specific marker of the tubules in rete testis


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:f3202087c84c62c28dad
claim_id: claim:f3202087c84c62c28dad
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
cells in fCL1 and fCL3 were stromal cells (DCN+) and fCL3 contained proliferating stromal cells (DCN+MKI67+TOP2A+)

summary:
In Homo sapiens fetal ovary, stromal cells are marked by positive expression of DCN, and proliferating stromal cells are marked by DCN, MKI67, and TOP2A.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:b4f471d0841b1c43a7f5
claim_id: claim:b4f471d0841b1c43a7f5
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
cells in fCL1 and fCL3 were stromal cells (DCN+) and fCL3 contained proliferating stromal cells (DCN+MKI67+TOP2A+)

summary:
In Homo sapiens fetal ovary, proliferating stromal cells are marked by positive expression of DCN, MKI67, and TOP2A.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:90a6ce6fe986b6b282ee
claim_id: claim:90a6ce6fe986b6b282ee
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: cells in fCL2 were surface epithelial cells (PODXL+KRT18+)
summary:
In Homo sapiens fetal ovary, surface epithelial cells are marked by positive expression of PODXL and KRT18.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:74776484f6ccf2ed07bc
claim_id: claim:74776484f6ccf2ed07bc
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: cells in fCL0 were pre-granulosa cells (FOXL2+KITLG+KRT18+)
summary:
In Homo sapiens fetal ovary, pre-granulosa cells are marked by positive expression of FOXL2, KITLG, and KRT18.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:72bea93d5624ee9ef7e4
claim_id: claim:72bea93d5624ee9ef7e4
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we noticed high levels of expression of PAX8, PCP4 and KRT19 in a group of cells from fCL0 (pre-granulosa cells), that could correspond to rete ovarii cells

summary:
In Homo sapiens fetal ovary, rete ovarii cells are marked by positive expression of PAX8, PCP4, and KRT19.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:00909ac9dd7a9f2a6c01
claim_id: claim:00909ac9dd7a9f2a6c01
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal: as in males, the female surface epithelium cells (fCL2) were KRT19+PAX8-
summary:
In Homo sapiens fetal ovary, surface epithelium cells are marked by positive expression of KRT19 and negative expression of PAX8.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:4b77f305fd608cb0b7d2
claim_id: claim:4b77f305fd608cb0b7d2
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we identified sub-cluster G4, with expression of several genes, such as LYPD1, IGFBP3, PCP4, PLAU, PAX8, that were previously identified as DEGs in the rete testis epithelial cells

summary:
In Homo sapiens fetal ovary, rete ovarii epithelial cells (G4) express LYPD1, IGFBP3, PCP4, PLAU, and PAX8.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:72e8a3351695ce964b24
claim_id: claim:72e8a3351695ce964b24
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we have shown that GATA2 was expressed in the mesenchyme of the epididymis, SOX17 marked the Müllerian duct epithelial cells and PAX2 marked all epithelial cells of the mesonephros and epididymis

summary:
In Homo sapiens, GATA2 is expressed in the mesenchyme of the epididymis, SOX17 marks Müllerian duct epithelial cells, and PAX2 marks all epithelial cells of the mesonephros and epididymis.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:06e1f8367b7debac6541
claim_id: claim:06e1f8367b7debac6541
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
our analysis has revealed striking similarities between human rete testis epithelial cells and mesonephric/epididymis epithelial cells, including high expression of PAX8, KRT19, PCP4, PERP, LYPD1 and BCAM, perhaps suggesting a common origin

summary:
In Homo sapiens, rete testis epithelial cells show high expression of PAX8, KRT19, PCP4, PERP, LYPD1, and BCAM.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:41c3f3d5bc1a02e93d75
claim_id: claim:41c3f3d5bc1a02e93d75
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
our analysis has revealed striking similarities between human rete testis epithelial cells and mesonephric/epididymis epithelial cells, including high expression of PAX8, KRT19, PCP4, PERP, LYPD1 and BCAM, perhaps suggesting a common origin

summary:
In Homo sapiens, mesonephric/epididymis epithelial cells show high expression of PAX8, KRT19, PCP4, PERP, LYPD1, and BCAM.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:c4497fdb0083ac91a7e0
claim_id: claim:c4497fdb0083ac91a7e0
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we have identified genes, such as CDH2 and WT1 that are common between Sertoli cells and rete testis epithelial cells, but absent from mesonephric/epididymis epithelial cells

summary:
In Homo sapiens, CDH2 and WT1 are expressed in Sertoli cells and rete testis epithelial cells but absent from mesonephric/epididymis epithelial cells.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:cabf7cc972f7c885b332
claim_id: claim:cabf7cc972f7c885b332
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we have identified genes, such as CDH2 and WT1 that are common between Sertoli cells and rete testis epithelial cells, but absent from mesonephric/epididymis epithelial cells

summary:
In Homo sapiens, CDH2 and WT1 are expressed in rete testis epithelial cells but absent from mesonephric/epididymis epithelial cells.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:81d87b42679bfa02f80e
claim_id: claim:81d87b42679bfa02f80e
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we also identified a small population of human cells at the interface between the seminiferous tubes and the rete testis expressing PAX8, as well as Sertoli cell markers such as AMH, SOX9 and NR5A1

summary:
In Homo sapiens, cells at the interface between the seminiferous tubes and the rete testis express PAX8 as well as Sertoli cell markers AMH, SOX9, and NR5A1.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:84dd0b0413343174d365
claim_id: claim:84dd0b0413343174d365
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
we have detected high levels of CDH2 in both Sertoli cells and rete testis epithelial cells in human, suggesting speciesspecific differences

summary:
In Homo sapiens, CDH2 is expressed at high levels in both Sertoli cells and rete testis epithelial cells.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:6e9e5ad4173d12b90993
claim_id: claim:6e9e5ad4173d12b90993
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
span_literal:
In human female gonads, both pre-granulosa cells, surface epithelial cells and rete ovarii cells expressed KRT19, but rete ovarii cells could be distinguished by the coexpression of PAX8

summary:
In Homo sapiens female gonads, rete ovarii cells are distinguished from pre-granulosa cells and surface epithelial cells by coexpression of KRT19 and PAX8.


claim_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f:claim:bf6f03133feb0aac33ec
claim_id: claim:bf6f03133feb0aac33ec
paper_key: biorxiv:9aa22010-6e01-1014-bc26-9535140d955f
summary: In Homo sapiens adult rete testis, rete testis cells specifically express PAX8 and KRT19.
span_literal:
According to previous studies, PAX8 and KRT19 were specifically expressed in human adult rete testis


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:ed4634c89826e602ac39
claim_id: claim:ed4634c89826e602ac39
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
widespread adoption of a correspondingly constrained 3 or 4-plex ‘canonical definition’ of CTC identity: DAPI or Hoechst (nuclear)-positive; Cytokeratin and/or EpCAM (epithelial)-positive; CD45 (immune cell marker)-negative

summary:
In Homo sapiens, circulating tumor cells are canonically defined as DAPI-positive, Cytokeratin and/or EpCAM-positive, and CD45-negative, where CD45 is an immune cell marker.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:5d4b4701a7d719e3307c
claim_id: claim:5d4b4701a7d719e3307c
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
CTCs are canonically defined as being DAPI-positive, EpCAM and/or cytokeratin-positive, and CD45-negative67.

summary:
In Homo sapiens, circulating tumor cells are canonically defined as being EpCAM and/or cytokeratin-positive and CD45-negative.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:1e04f066f423f83e8720
claim_id: claim:1e04f066f423f83e8720
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
The 10 markers with the highest proportion of important features were EpCAM (0.225), AR (0.067), PSA (0.024), EGFR (0.022), pAKT(308) (0.018), HER-2 (0.013), PD-L1 (0.009), Cytokeratin (0.009), active β-catenin (0.004) and DLX1 (0.004)

summary:
In Homo sapiens, the top markers for identifying circulating tumor cells include EpCAM, androgen receptor, prostate-specific antigen, epidermal growth factor receptor, phosphorylated AKT(308), human epidermal growth factor receptor 2, programmed death-ligand 1, Cytokeratin, active beta-catenin, and DLX1.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:470a5bf51f3842236fbd
claim_id: claim:470a5bf51f3842236fbd
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
22 features were selected in over 90% of (2000) training iterations, and all of these were from either EpCAM (16) or AR (6). This highlights these two markers as invaluable for CTC identification in the PCa patient samples here assessed

summary:
In Homo sapiens, EpCAM and androgen receptor are the most important markers for circulating tumor cell identification in prostate cancer patient samples.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:e77a48452a755bd1f021
claim_id: claim:e77a48452a755bd1f021
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
including AR permitted identification of non-canonical CD45-positive CTCs that have been reported to evade immune responses and promote metastasis22, and are here defined in part by AR expression that is generally absent from normal blood cells91

summary:
In Homo sapiens, non-canonical CD45-positive circulating tumor cells are identified in part by androgen receptor expression, which is generally absent from normal blood cells.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:a856b97f2be1dee18545
claim_id: claim:a856b97f2be1dee18545
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
A threshold of normalised mean intensity (rescaled from 0-99 percentiles) at 0.4 of key cell state markers of vimentin, membrane NCAM, nuclear p-p53, nuclear Ki67 and CD44 allows (F) phenotypic characterization of CTCs as mesenchymal, neuroendocrine, proliferative, apoptotic or cancer stem-cells, respectively.

summary:
In Homo sapiens, circulating tumor cells with high vimentin are classified as mesenchymal, those with high membrane NCAM as neuroendocrine, those with high nuclear Ki67 as proliferative, those with high nuclear phosphorylated p53 as apoptotic, and those with high CD44 as cancer stem cells.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:8df1ce4a903ed3d1c8e2
claim_id: claim:8df1ce4a903ed3d1c8e2
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
A threshold of normalised mean intensity (rescaled from 0-99 percentiles) at 0.4 of key cell state markers of vimentin, membrane NCAM, nuclear p-p53, nuclear Ki67 and CD44 allows (F) phenotypic characterization of CTCs as mesenchymal, neuroendocrine, proliferative, apoptotic or cancer stem-cells, respectively.

summary:
In Homo sapiens, circulating tumor cells with high membrane NCAM expression are classified as neuroendocrine circulating tumor cells.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:a3c76a97e42225194b61
claim_id: claim:a3c76a97e42225194b61
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
A threshold of normalised mean intensity (rescaled from 0-99 percentiles) at 0.4 of key cell state markers of vimentin, membrane NCAM, nuclear p-p53, nuclear Ki67 and CD44 allows (F) phenotypic characterization of CTCs as mesenchymal, neuroendocrine, proliferative, apoptotic or cancer stem-cells, respectively.

summary:
In Homo sapiens, circulating tumor cells with high nuclear Ki67 expression are classified as proliferative circulating tumor cells.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:83f8fab698052a88036b
claim_id: claim:83f8fab698052a88036b
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
summary:
In Homo sapiens, circulating tumor cells with high nuclear phosphorylated p53 expression are classified as apoptotic circulating tumor cells.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:8f2c864c6a952b2792d0
claim_id: claim:8f2c864c6a952b2792d0
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
summary:
In Homo sapiens, circulating tumor cells with high CD44 expression are classified as cancer stem cells.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:7a555cd0538d73fec7c6
claim_id: claim:7a555cd0538d73fec7c6
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
Patient 4 CTCs displayed high membrane PSMA, the direct binding target of Lutetium-177 PSMA (Lu-PSMA) therapy, indicating the potential efficacy of this targeted radio-ligand treatment80 (Fig. 6E-F). Conversely, responder patient 5 CTCs displayed virtually no surface PSMA

summary:
In Homo sapiens, circulating tumor cells from non-responder patient 4 displayed high membrane prostate-specific membrane antigen expression, while circulating tumor cells from responder patient 5 displayed virtually no surface prostate-specific membrane antigen.


claim_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4:claim:3ff4057915a8b0f342ec
claim_id: claim:3ff4057915a8b0f342ec
paper_key: biorxiv:9b741001-784a-1014-b0c0-93f88f9233f4
span_literal:
Therapy non-responsive patient 4 had CTCs with high membrane PSMA, as well as a striking neuroendocrine phenotype with increased expression of NCAM, CD276 and CXCR4

summary:
In Homo sapiens, circulating tumor cells from therapy non-responsive patient 4 displayed a neuroendocrine phenotype with increased expression of prostate-specific membrane antigen, NCAM, CD276, and CXCR4.


claim_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a:claim:6c0d9934264b2b581b2a
claim_id: claim:6c0d9934264b2b581b2a
paper_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a
summary: In Homo sapiens, glucagon (GCG) expression was used to identify alpha cells in pancreatic islets.
span_literal:
the location of pancreatic hormone genes (GCG, INS, PPY and SST) expression was used to determine Alpha (α), β, PP, and delta cell clusters, respectively


claim_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a:claim:48fa897e77f3d5d347f6
claim_id: claim:48fa897e77f3d5d347f6
paper_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a
span_literal:
the location of pancreatic hormone genes (GCG, INS, PPY and SST) expression was used to determine Alpha (α), β, PP, and delta cell clusters, respectively

summary:
In Homo sapiens, pancreatic polypeptide (PPY) expression was used to identify PP cells in pancreatic islets.


claim_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a:claim:237a1fe5efcd069061d6
claim_id: claim:237a1fe5efcd069061d6
paper_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a
summary:
In Homo sapiens, somatostatin (SST) expression was used to identify delta cells in pancreatic islets.


claim_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a:claim:86593dfe3fcfbf994e08
claim_id: claim:86593dfe3fcfbf994e08
paper_key: biorxiv:9bdb3107-6c43-1014-b168-b2ab3b1b366a
summary: In Homo sapiens, endothelial cells in pancreatic islets were identified based on PECAM1 expression.
span_literal:
We also found endothelial cells, duct cells, and acinar cells based on PECAM1, SPP1, and PRSS1 expression localization (Figure 1A, C, D).


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:8180e44540e565c9106f
claim_id: claim:8180e44540e565c9106f
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
CD27-CD38- cells gradually lose expression of B cell signature genes PAX5 and BACH2 upon acquisition of CD27 and/or CD38 expression with CD27++CD38++ cells showing the most downregulated expression of PAX5 and BACH2 and upregulation of ASC signature genes IRF4, XBP1, and PRDM1

summary:
In Homo sapiens, antibody-secreting cells (CD27++CD38++) show downregulated expression of PAX5 and BACH2 and upregulation of IRF4, XBP1, and PRDM1 compared to B cells.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:bc31fc06decf41c2e8dd
claim_id: claim:bc31fc06decf41c2e8dd
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
Clusters 4 and 5 showed a clear ASCs gene signature with a prominent expression of known ASC-specific genes IRF4, XBP1, and PRDM1

summary:
In Homo sapiens, antibody-secreting cells show prominent expression of the ASC-specific genes IRF4, XBP1, and PRDM1.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:61aa9b40e0f2a4ad2332
claim_id: claim:61aa9b40e0f2a4ad2332
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
The other three clusters, (clusters 1-3) still showed a pronounced B cell signature with higher expression of genes known to repress the ASCs state such as PAX5, BACH2, and SPIB

summary:
In Homo sapiens, B cells show higher expression of PAX5, BACH2, and SPIB, which are known to repress the antibody-secreting cell state.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:5cc2677cbc28d6ee0014
claim_id: claim:5cc2677cbc28d6ee0014
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
summary: In Homo sapiens, germinal center B cells are marked by IRF8, BCL6, CD22, and CD83.
span_literal:
genes that mark a germinal center (GC) B cells phenotype, such as IRF8, BCL6, CD22, and CD83 were among the top 30 differentially expressed genes in cluster 2


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:0d78e39e482db6a55b6f
claim_id: claim:0d78e39e482db6a55b6f
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
MYC (Calado et al., 2012; Dominguez-Sola et al., 2012) and E2F (Béguelin et al., 2017) targets, known to promote GC B cell differentiation, were the top 3 significantly enriched gene sets and, in fact, MYC was expressed at its highest in cluster 2 compared to the other clusters

summary:
In Homo sapiens, MYC is expressed at its highest in germinal center-like B cells compared to other clusters.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:86b97861c9e35912e3b3
claim_id: claim:86b97861c9e35912e3b3
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
summary: In Homo sapiens, pre-memory B cells are marked by BANK1 and CCR6.
span_literal:
Among the top differentially expressed genes of cluster 1, we found BANK1, recently identified as a marker of a pre-memory B cell stage (Holmes et al., 2020) together with CCR6 which was also expressed at the highest in cluster 1


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:479a8d3f58d3f836df6a
claim_id: claim:479a8d3f58d3f836df6a
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal: MZB1, identified in the same study as a marker of pre-ASCs, is expressed at its lowest in cluster 1
summary:
In Homo sapiens, MZB1 is a marker of pre-antibody-secreting cells and is expressed at its lowest in the pre-memory B cell cluster.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:f1be8d634d9963aa80ac
claim_id: claim:f1be8d634d9963aa80ac
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
summary: In Homo sapiens, SIGLEC6 and FCRL5 expression is increased in the memory-like B cell cluster.
span_literal:
Likewise, the expression of other genes associated with the CD11c+ phenotype, such as SIGLEC6 and FCRL5, were increased in cluster 1


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:4b2f870db986aecb9a7c
claim_id: claim:4b2f870db986aecb9a7c
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
Finally, HHEX, recently shown to direct B cells away from the GC reaction into memory differentiation (Laidlaw et al., 2020), was also increased in cluster 1

summary:
In Homo sapiens, HHEX is increased in the memory-like B cell cluster, directing B cells away from the germinal center reaction into memory differentiation.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:7ebc6f92857f1c1c0104
claim_id: claim:7ebc6f92857f1c1c0104
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
These transcriptional changes are then followed by surface expression of stage-specific cellular markers, such as CD27, CD38, and CD138 on ASCs, with simultaneous downregulation of the B cell markers CD19 and CD20

summary:
In Homo sapiens, antibody-secreting cells express the surface markers CD27, CD38, and CD138, with simultaneous downregulation of the B cell markers CD19 and CD20.


claim_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8:claim:825599fc93c54deb178b
claim_id: claim:825599fc93c54deb178b
paper_key: biorxiv:9c7f8281-6c21-1014-a6df-b6c543b29cb8
span_literal:
The ASC-specific transcription factors IRF4, XBP1, and BLIMP1 are upregulated only once the B cell-specific transcription factors PAX5, IRF8, and BACH2 are downregulated.

summary:
In Homo sapiens, antibody-secreting cells upregulate the transcription factors IRF4, XBP1, and BLIMP1 once the B cell-specific transcription factors PAX5, IRF8, and BACH2 are downregulated.


claim_key: biorxiv:9ca649fd-6cf8-1014-8427-cac0001a663e:claim:631f79b2bb24ab7aea97
claim_id: claim:631f79b2bb24ab7aea97
paper_key: biorxiv:9ca649fd-6cf8-1014-8427-cac0001a663e
span_literal:
CD14+ monocytes were defined by high expression of CD14 and LYZ, consistent with their established role as classical monocyte markers (Villani et al., 2017).

summary:
In Homo sapiens, CD14+ monocytes are defined by high expression of CD14 and LYZ, which are established classical monocyte markers.


claim_key: biorxiv:9ca649fd-6cf8-1014-8427-cac0001a663e:claim:348e3a04fef5d7c8637e
claim_id: claim:348e3a04fef5d7c8637e
paper_key: biorxiv:9ca649fd-6cf8-1014-8427-cac0001a663e
span_literal:
Memory CD4+ T cells were characterized by expression of IL7R, CCR7, and S100A4, markers widely associated with antigen-experienced T cell populations (Zhang et al., 2005);(Mahnke et al., 2013).

summary:
In Homo sapiens, memory CD4+ T cells are characterized by expression of IL7R, CCR7, and S100A4, which are markers associated with antigen-experienced T cell populations.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:878ebd4845d577125b50
claim_id: claim:878ebd4845d577125b50
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
ALDH+ cells expressed the highest levels of various epithelial markers, including KRT19, CD24, CDH1, EpCAM, and KR18.

summary:
In Homo sapiens, ALDH+ normal breast cells express high levels of the epithelial markers KRT19, CD24, CDH1, EpCAM, and KRT18.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:9a2f18bd7bde8909fc5a
claim_id: claim:9a2f18bd7bde8909fc5a
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
CD44+ were strongly enriched for expression of mesenchymal markers, including CDH2, KRT17, ZEB2, KLF8, CD44, KRT14, and VIM.

summary:
In Homo sapiens, ALDH−CD44+CD24− normal breast cells are enriched for expression of mesenchymal markers CDH2, KRT17, ZEB2, KLF8, CD44, KRT14, and VIM.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:dbb065a75569005ae02a
claim_id: claim:dbb065a75569005ae02a
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
ALDH+ cells also, however, expressed intermediate or highest levels of several mesenchymal markers, including the EMT transcription factors SNAI1, TWIST1, and ZEB2.

summary:
In Homo sapiens, ALDH+ normal breast cells express intermediate or highest levels of the epithelial-to-mesenchymal transition transcription factors SNAI1, TWIST1, and ZEB2.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:ef56742b35c9db75d995
claim_id: claim:ef56742b35c9db75d995
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
The top 3 most overexpressed genes, by magnitude of effect were WNT2 (fold change = 705.3), Insulin-like growth factor 1 (IGF1; fold change = 532.3), and the canonical notch ligand DLL1 (fold change = 502.5).

summary:
In Homo sapiens, ALDH+ normal breast cells overexpress WNT2, insulin-like growth factor 1 (IGF1), and the canonical Notch ligand DLL1 compared to CD24+ cells.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:e6bc3543b0d567da95a7
claim_id: claim:e6bc3543b0d567da95a7
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
summary: In Homo sapiens, ALDH+ normal breast cells overexpress WNT2, RSPO3, SFRP4, MMP7, and FOSL1.
span_literal:
Analyzing the relative expression of other WNT pathway genes showed that, in addition to WNT2, ALDH+ cells also overexpress RSPO3, SFRP4, MMP7, and FOSL1 (Figure 2D).


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:5b5e6e1e731904dd273c
claim_id: claim:5b5e6e1e731904dd273c
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
The expression pattern of Wnt pathway members in CD44+ cells was substantially different than for ALDH+ cells, with the signature of CD44+ cells driven by DKK3, CCND2, PRICKLE2, and DRAXIN (Figure 2H).

summary:
In Homo sapiens, ALDH−CD44+CD24− normal breast cells express a Wnt pathway signature driven by DKK3, CCND2, PRICKLE2, and DRAXIN.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:77536c91db2f54fccb94
claim_id: claim:77536c91db2f54fccb94
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
At the single cell level, ALDH+CD44+CD24− cells overexpress the stem cell genes ID1 and SOX2, the IL-8 receptor CXCR1, and the EMT-associated transcription factors TWIST1 and ZEB2.

summary:
In Homo sapiens, ALDH+CD44+CD24− normal breast cells overexpress the stem cell genes ID1 and SOX2, the interleukin-8 receptor CXCR1, and the epithelial-to-mesenchymal transition-associated transcription factors TWIST1 and ZEB2.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:446aa02b71f98cd1a315
claim_id: claim:446aa02b71f98cd1a315
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
ALDH+CD44+CD24− cells also significantly overexpressed EGFR, CD44, WNT2, and VIM, while expressing HER2 at lower levels.

summary:
In Homo sapiens, ALDH+CD44+CD24− normal breast cells overexpress EGFR, CD44, WNT2, and VIM, while expressing HER2 at lower levels.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:0b6eeae0272702a45259
claim_id: claim:0b6eeae0272702a45259
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
Cluster 4 expressed high levels of epithelial-related genes, including KRT7, CD24, EPCAM, GATA3, and KRT5.

summary:
In Homo sapiens, ALDH+ cluster 4 cells express high levels of epithelial-related genes including KRT7, CD24, EPCAM, GATA3, and KRT5.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:7dcd7b2ba0edfee7a756
claim_id: claim:7dcd7b2ba0edfee7a756
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
Cluster 3 was characterized by expression of mesenchymal-phenotype related genes, including CD44, ZEB2, SLUG, VIM, TWIST1, ZEB1, and TGFB1.

summary:
In Homo sapiens, ALDH+ cluster 3 cells are characterized by expression of mesenchymal-phenotype related genes including CD44, ZEB2, SLUG, VIM, TWIST1, ZEB1, and TGFB1.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:9a77495cf3149d66f9ba
claim_id: claim:9a77495cf3149d66f9ba
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
Cluster 2, which had the highest average expression of ITGA6, CD133, and ALDH1A3, expressed high levels of epithelial-related genes, such as KRT7, KRT8, and CDH1 as well as genes associated with EMT, including IL6, CD44, TM4SF1, and VIM, and the mesenchymal stem cell marker CD146.

summary:
In Homo sapiens, ALDH+ cluster 2 cells express the highest levels of ITGA6, CD133, and ALDH1A3, as well as high levels of epithelial-related genes KRT7, KRT8, and CDH1, epithelial-to-mesenchymal transition-associated genes IL6, CD44, TM4SF1, and VIM, and the mesenchymal stem cell marker CD146.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:c01f9e84ab56ef02fc3b
claim_id: claim:c01f9e84ab56ef02fc3b
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
ALDH1A1+ cells expressed significantly higher levels of mesenchymal associated markers, including TWIST1, ZEB2, IL6, ZEB1, VIM, and TGFB1 and lower levels of epithelial associated markers CDH1, CD24, and EpCAM.

summary:
In Homo sapiens, ALDH1A1-expressing normal breast cells express higher levels of mesenchymal markers TWIST1, ZEB2, IL6, ZEB1, VIM, and TGFB1, and lower levels of epithelial markers CDH1, CD24, and EpCAM.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:3a5e16d29f29b11e7b51
claim_id: claim:3a5e16d29f29b11e7b51
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
ALDH1A1+ cells also expressed significantly higher levels of progesterone receptor (PGR), androgen receptor (AR) and the ATP-binding cassette transporters ABCG2 and ABCB1 (Supplemental Table 6).

summary:
In Homo sapiens, ALDH1A1-expressing normal breast cells express higher levels of progesterone receptor (PGR), androgen receptor (AR), and the ATP-binding cassette transporters ABCG2 and ABCB1.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:e3f9a0062a8f6ae14f7c
claim_id: claim:e3f9a0062a8f6ae14f7c
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
Comparing RNA isolated from bulk ALDH+CD44+CD24− and ALDH+ cells that are not also CD44+CD24−, we identified that ALDH+CD44+CD24− cells expressed lower levels of BAX, CDH3, CDH1, KRT19, and MUC1 (p<0.10; Supplemental Figure 8B; Supplemental Table 4).

summary:
In Homo sapiens, ALDH+CD44+CD24− normal breast cells express lower levels of BAX, CDH3, CDH1, KRT19, and MUC1 compared to ALDH+ cells that are not CD44+CD24−.


claim_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee:claim:f15eac1fea4404be25d8
claim_id: claim:f15eac1fea4404be25d8
paper_key: biorxiv:9d923a25-6c34-1014-a848-e326c14e92ee
span_literal:
Further, CD44+ cells differentially expressed genes involved in PI3K-AKT signaling (FDR=7.0E-5), including CCDN2, PIK3CG, FGF1, and NGF (Supplemental Figure 7).

summary:
In Homo sapiens, ALDH−CD44+CD24− normal breast cells differentially express PI3K-AKT signaling genes including CCND2, PIK3CG, FGF1, and NGF.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:53879a7c442bf041e6c8
claim_id: claim:53879a7c442bf041e6c8
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
We found that characteristic endothelial transcripts Von Willebrand Factor (VWF) and VE-cadherin (CDH5) were highly enriched in the ErgHi+ nuclei (Figure 3E).

summary:
In Homo sapiens, endothelial cells are marked by positive expression of Von Willebrand Factor (VWF) and VE-cadherin (CDH5).


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:4df3eb841d69793ebb3a
claim_id: claim:4df3eb841d69793ebb3a
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
summary: In Homo sapiens, microglia are marked by positive expression of CD45 (PTPRC) and IBA1 (AIF1).
span_literal:
In contrast, microglial transcripts CD45 (PTPRC) and IBa (AIF1) were enriched in the ErgLo+ nuclei (Figure 3F), suggesting that microglia express lower, but detectable levels of Erg.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:48e5d59d19ad66462568
claim_id: claim:48e5d59d19ad66462568
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
Notably, the mural cell marker smooth muscle α−actin (ACTA2) is not enriched in the Erg+ fraction (Figure 3G), and neuronal marker MEG3 is enriched in neuronal cells but not ErgHi+ nuclei (Figure 3H).

summary:
In Homo sapiens, mural cells are marked by positive expression of smooth muscle alpha-actin (ACTA2), while neuronal cells are marked by positive expression of MEG3.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:f85156decab9e9878ffc
claim_id: claim:f85156decab9e9878ffc
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
Notably, the mural cell marker smooth muscle α−actin (ACTA2) is not enriched in the Erg+ fraction (Figure 3G), and neuronal marker MEG3 is enriched in neuronal cells but not ErgHi+ nuclei (Figure 3H).

summary:
In Homo sapiens, neuronal cells are marked by positive expression of MEG3, which is not enriched in endothelial cells.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:5ad8bf3ceb69243f5ae4
claim_id: claim:5ad8bf3ceb69243f5ae4
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
We found that, relative to housekeeping transcript UBC, endothelial transcript CDH5 was enriched ∼30-fold from unsorted nuclei in the ErgHi+ nuclei, but not NeuN+ nuclei (Figure 3A).

summary:
In Homo sapiens, endothelial cells are marked by positive expression of CDH5, which is not enriched in neuronal cells.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:1bb05d5c252d29bd9376
claim_id: claim:1bb05d5c252d29bd9376
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
In contrast, the neuronal marker MAP2 was enriched ∼5 fold in the NeuN+ nuclei, but not the Erg+ nuclei (Figure 3A).

summary:
In Homo sapiens, neuronal cells are marked by positive expression of MAP2, which is not enriched in endothelial cells.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:b75279969263a33879a2
claim_id: claim:b75279969263a33879a2
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
To confirm that isolated nuclei were only from the vascular endothelium and not mural cells adjacent to the endothelium (pericytes or smooth muscle cells), we also examined enrichment of transcripts specific to those cell types. We found that neither PDGFRB (pericyte marker) nor ACTA2 were enriched in the Erg+ or NeuN+ nuclei, relative to the unsorted nuclei (SI Figure 3).

summary:
In Homo sapiens, pericytes are marked by positive expression of PDGFRB, and smooth muscle cells are marked by positive expression of ACTA2; neither marker is enriched in endothelial cells.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:897284bf5585d50bc6ce
claim_id: claim:897284bf5585d50bc6ce
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
To confirm that isolated nuclei were only from the vascular endothelium and not mural cells adjacent to the endothelium (pericytes or smooth muscle cells), we also examined enrichment of transcripts specific to those cell types. We found that neither PDGFRB (pericyte marker) nor ACTA2 were enriched in the Erg+ or NeuN+ nuclei, relative to the unsorted nuclei (SI Figure 3).

summary:
In Homo sapiens, smooth muscle cells are marked by positive expression of ACTA2, which is not enriched in endothelial cells.


claim_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289:claim:28bebcd819de98369567
claim_id: claim:28bebcd819de98369567
paper_key: biorxiv:9df09f81-6df1-1014-bd96-ce3556dd2289
span_literal:
Only a few nuclear markers have been established, NeuN (Rbfox3, a neuronal marker) and Erg, which we establish here as a reliable marker of endothelial cell nuclei by flow.

summary:
In Homo sapiens, NeuN (RBFOX3) is a marker of neuronal cells, and ERG is a reliable marker of endothelial cells.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:d671ab51d246dd700e53
claim_id: claim:d671ab51d246dd700e53
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
1) Glioblastoma Negative Prognostic (GNP) cells that co-express astrocytic marker S100B and stem-like marker SOX2 and are associated with shorter overall survival times (median survival of 144 days), and 2) Glioblastoma Positive Prognostic (GPP) cells that are characterized by high expression of EGFR and are associated with longer overall survival times (median survival of 836 days).

summary:
In Homo sapiens, glioblastoma negative prognostic cells co-express the astrocytic marker S100B and the stem-like marker SOX2, while glioblastoma positive prognostic cells are characterized by high expression of EGFR.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:0dce195702b64bc8d92d
claim_id: claim:0dce195702b64bc8d92d
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
1) Glioblastoma Negative Prognostic (GNP) cells that co-express astrocytic marker S100B and stem-like marker SOX2 and are associated with shorter overall survival times (median survival of 144 days), and 2) Glioblastoma Positive Prognostic (GPP) cells that are characterized by high expression of EGFR and are associated with longer overall survival times (median survival of 836 days).

summary:
In Homo sapiens, glioblastoma positive prognostic cells are characterized by high expression of EGFR.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:4969a41e29d7cd7015cf
claim_id: claim:4969a41e29d7cd7015cf
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
GNP cells in cluster 1 co- expressed S100B and SOX2 and displayed basal phosphorylation of multiple signaling proteins (MEM: S100B+6 SOX2+5 p-STAT3+4, CyclinB1+3 p-STAT5+3, p-S6+3, p-AKT+2, and p-NFkB+2; Figure 2B).

summary:
In Homo sapiens, glioblastoma negative prognostic cells co-express S100B and SOX2 and display basal phosphorylation of STAT3, CyclinB1, STAT5, S6, AKT, and NFkB.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:c9b9ba48f5a7a42f38c7
claim_id: claim:c9b9ba48f5a7a42f38c7
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal: Cluster 2 expressed a high level of EGFR (MEM: EGFR+7 SOX2+3 GFAP+3 p-NFkB+2 CD44+2).
summary:
In Homo sapiens, glioblastoma positive prognostic cell cluster 2 expresses high levels of EGFR, SOX2, GFAP, NFkB, and CD44.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:2392ec5526a2278b55a1
claim_id: claim:2392ec5526a2278b55a1
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Cluster 3 co-expressed astrocytic markers S100B and GFAP as well as EGFR (MEM: S100B+3 EGFR+3 GFAP+2).

summary:
In Homo sapiens, glioblastoma positive prognostic cell cluster 3 co-expresses the astrocytic markers S100B and GFAP as well as EGFR.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:4e5dacbc05573a4b4931
claim_id: claim:4e5dacbc05573a4b4931
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Cluster 5 displayed high levels of phosphorylation of p- STAT5 and p-NFkB along with EGFR expression (MEM: p-STAT5+9 EGFR+5 p-NFkB+4 S100B+2 CD56+2 SOX2+2 CD44+2 GFAP+2).

summary:
In Homo sapiens, glioblastoma positive prognostic cell cluster 5 displays high levels of phosphorylated STAT5 and NFkB along with EGFR, S100B, CD56, SOX2, CD44, and GFAP expression.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:a536e7cefb9159af9e64
claim_id: claim:a536e7cefb9159af9e64
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Optimization of search input revealed that the key cellular features that distinguished GNP cells from other cells were co- expression of SOX2 and S100B as well as lack of GFAP and p-NFkB expression (F1-measure=0.80; optimized GNP label: SOX2+7 S100B+4 GFAP+1 p-NFkB+0; Supplementary Figure S2B).

summary:
In Homo sapiens, glioblastoma negative prognostic cells are distinguished from other cells by co-expression of SOX2 and S100B as well as lack of GFAP and NFkB expression.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:f8f3a73b60541e0c8b91
claim_id: claim:f8f3a73b60541e0c8b91
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
GPP cells were distinguished by high expression of EGFR and lack of CD49F, p-p38, CD44, and B3TUB (F1- measure=0.90; optimized GPP label: EGFR+7 CD49F+2 p-p38+2 CD44+1 B3TUB+0.

summary:
In Homo sapiens, glioblastoma positive prognostic cells are distinguished by high expression of EGFR and lack of CD49F, p38, CD44, and B3TUB.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:527d0fe555b801cfedc2
claim_id: claim:527d0fe555b801cfedc2
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
CD4+ and CD8+ T cells populations that were statistically lacking from the two patients with GATA2 haploinsufficiency each expressed high levels of CD27 and CCR7 (MEM scores ≥ +6).

summary:
In Homo sapiens, CD4+ T cell populations lacking from patients with GATA2 haploinsufficiency express high levels of CD27 and CCR7.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:4b9880020fa7d2924d55
claim_id: claim:4b9880020fa7d2924d55
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
CD4+ and CD8+ T cells populations that were statistically lacking from the two patients with GATA2 haploinsufficiency each expressed high levels of CD27 and CCR7 (MEM scores ≥ +6).

summary:
In Homo sapiens, CD8+ T cell populations lacking from patients with GATA2 haploinsufficiency express high levels of CD27 and CCR7.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:99df687cb8cdb4b3895c
claim_id: claim:99df687cb8cdb4b3895c
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Conversely, the CD4+ and CD8+ populations that were statistically enriched in the two patients with GATA2 haploinsufficiency expressed very high levels of CD57 (MEM scores ≥ +6).

summary:
In Homo sapiens, CD4+ T cell populations enriched in patients with GATA2 haploinsufficiency express very high levels of CD57.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:108a5665f6f5fe97de67
claim_id: claim:108a5665f6f5fe97de67
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Conversely, the CD4+ and CD8+ populations that were statistically enriched in the two patients with GATA2 haploinsufficiency expressed very high levels of CD57 (MEM scores ≥ +6).

summary:
In Homo sapiens, CD8+ T cell populations enriched in patients with GATA2 haploinsufficiency express very high levels of CD57.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:7aef957816fe7c057f33
claim_id: claim:7aef957816fe7c057f33
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Interestingly, the phenotype of GNP cells share similarity with multiple healthy neuronal cells due to aberrant co-expression of S100B, a marker of astrocytic cells, and SOX2, a Yamanaka factor that is highly expressed in pluripotent stem cells 1,37.

summary:
In Homo sapiens, S100B is a marker of astrocytic cells, and SOX2 is highly expressed in pluripotent stem cells; glioblastoma negative prognostic cells aberrantly co-express both.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:d7d41f0637caf19f2b06
claim_id: claim:d7d41f0637caf19f2b06
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Results suggested a lack of naïve T cell subsets in IEI patients with GATA2 haploinsufficiency and a corresponding enrichment of CD57 T cell subsets; however, additional samples are required to confirm these findings.

summary:
In Homo sapiens, CD57-positive T cell subsets are enriched in inborn errors of immunity patients with GATA2 haploinsufficiency.


claim_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f:claim:0a69d1811f7933b85ac0
claim_id: claim:0a69d1811f7933b85ac0
paper_key: biorxiv:9e5c18fc-76e5-1014-9f81-96148d260e0f
span_literal:
Notably, CD57 cells have been observed in other disease settings. After observing these findings from Velociraptor, we noted a study that also reported that patients with GATA2 haploinsufficiency have reduced numbers of naïve T cells and increased numbers of CD57+ T cells compared to healthy donors that correlated with clinical severity 42.

summary:
In Homo sapiens, patients with GATA2 haploinsufficiency have increased numbers of CD57-positive T cells compared to healthy donors.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:a7fc3bf3f9fe77e61bc1
claim_id: claim:a7fc3bf3f9fe77e61bc1
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Cluster 1 is enriched for CD8 T cells that express Th1 and cytotoxic transcripts such as, TBET, IFN-γ, EOMES, and PRF1 (Figure 4C, Supplemental Table 4).

summary:
In Homo sapiens, CD8 T cells specific for sulfoglycolipid presented by CD1b express T-bet, interferon-gamma, EOMES, and perforin 1, consistent with a Th1 and cytotoxic phenotype.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:73dc216065f7240cdfa4
claim_id: claim:73dc216065f7240cdfa4
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Cluster 2 is characterized by a strong enrichment of CD4 T cells that express a variety of functional transcripts, including Th1 (TNF and IL-12A), Th2 (GATA3), regulatory (CTLA4 and FOXP3), and the TFH transcription factor, BCL6 (Figure 4D, Supplemental Table 4).

summary:
In Homo sapiens, CD4 T cells specific for glycolipid presented by CD1b express tumor necrosis factor, interleukin-12A, GATA3, cytotoxic T-lymphocyte associated protein 4, forkhead box P3, and BCL6, reflecting Th1, Th2, T regulatory, and T follicular helper phenotypes.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:2869c21fd59024da061f
claim_id: claim:2869c21fd59024da061f
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Among SGL-specific T cells, only those expressing the CD4 co-receptor also expressed Ki67, suggesting that they were actively proliferating at the time of sample collection.

summary:
In Homo sapiens, sulfoglycolipid-specific T cells expressing the CD4 co-receptor also expressed Ki-67, suggesting active proliferation, whereas those without CD4 did not.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:d19f1954807fd44a39eb
claim_id: claim:d19f1954807fd44a39eb
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
There was also a significant correlation between CTLA4 and FOXP3, indicating that these two markers are co-expressed by CD4 glycolipid-specific T cells that may have a regulatory function (r = 0.36, p = 0.0001) (Figure 6B).

summary:
In Homo sapiens, CD4 glycolipid-specific T cells co-express cytotoxic T-lymphocyte associated protein 4 and forkhead box P3, indicating a potential regulatory function.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:e4e24c0770b690274aa8
claim_id: claim:e4e24c0770b690274aa8
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
MKI67, which is expressed by actively proliferating cells, was enriched in the same cluster as CD4 (Figure 4D, Figure 6C, Supplemental Table 4)

summary:
In Homo sapiens, MKI67 is enriched in the cluster of CD4-positive glycolipid-specific T cells, indicating active proliferation.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:ac34949142e23f21bb75
claim_id: claim:ac34949142e23f21bb75
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Canonically, T cells that express the CD4 co-receptor can be divided into four major functional subsets: Th1, Th2, Th17, and Treg. These functional lineages are driven by the master transcription factors T-bet, GATA3, ROR-γt, and FOXP3, respectively (Fontenot et al., 2003; Hori et al., 2003; Ivanov et al., 2006; Szabo et al., 2000; Zhen and Flavell, 1997).

summary:
In Homo sapiens, T helper 1 cells are driven by T-bet, T helper 2 cells by GATA3, T helper 17 cells by ROR-gamma-t, and T regulatory cells by forkhead box P3.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:d08dae8085b83c024d7d
claim_id: claim:d08dae8085b83c024d7d
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Conversely, peptide-specific T cells that express the CD8 co-receptor are traditionally cytotoxic T cells, which are defined by the expression of cytolytic effector molecules, such as granzymes and perforin (Apasov et al., 1993).

summary:
In Homo sapiens, cytotoxic T cells expressing the CD8 co-receptor are defined by the expression of granzymes and perforin.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:f8dc6f9ca4cd4d3fba40
claim_id: claim:f8dc6f9ca4cd4d3fba40
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
CD8 MAIT cells express higher levels of granulysin, granzyme B, and perforin, suggesting that they are more potently cytotoxic (Dias et al., 2018).

summary:
In Homo sapiens, CD8 mucosal associated invariant T cells express higher levels of granulysin, granzyme B, and perforin, suggesting more potent cytotoxicity.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:aa0618817544aa1b7f31
claim_id: claim:aa0618817544aa1b7f31
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
DN MAIT cells express less IFN-γ and more IL-17 than CD8 MAIT cells, and have a higher ROR-γt to T-bet ratio, indicative of a Th17 phenotype (Dias et al., 2018).

summary:
In Homo sapiens, double negative mucosal associated invariant T cells express less interferon-gamma and more interleukin-17 than CD8 mucosal associated invariant T cells, with a higher ROR-gamma-t to T-bet ratio indicative of a Th17 phenotype.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:2a570deea2579c44fa9b
claim_id: claim:2a570deea2579c44fa9b
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Mycobacterial glycolipid-specific T cells that express the CD8 co-receptor are broadly cytotoxic T cells and express IFN-γ, TNF, and IL-2.

summary:
In Homo sapiens, mycobacterial glycolipid-specific T cells expressing the CD8 co-receptor are cytotoxic T cells that express interferon-gamma, tumor necrosis factor, and interleukin-2.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:59347ecdfbf9a463b3a9
claim_id: claim:59347ecdfbf9a463b3a9
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
Conversely, T cells that express the CD4 co-receptor are more diverse. They express some Th1 cytokines (TNF), but also can express features of Treg (FOXP3, CTLA4), Th2 (GATA3), and TFH (BCL6) T cell subsets.

summary:
In Homo sapiens, CD4 glycolipid-specific T cells express tumor necrosis factor, forkhead box P3, cytotoxic T-lymphocyte associated protein 4, GATA3, and BCL6, reflecting features of T regulatory, T helper 2, and T follicular helper subsets.


claim_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569:claim:89585a81351e823287d7
claim_id: claim:89585a81351e823287d7
paper_key: biorxiv:9ea3f9c1-6d62-1014-8a0f-e0eee23ad569
span_literal:
The transcription factors RORC and RUNX3, which are canonically expressed by Th17 and cytotoxic peptide-specific T cells, respectively, were ubiquitously expressed (Figure 6A) (Ivanov et al., 2006; Shan et al., 2017).

summary:
In Homo sapiens, RORC is canonically expressed by T helper 17 cells and RUNX3 is canonically expressed by cytotoxic peptide-specific T cells.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:c478363ec2e1918aabfb
claim_id: claim:c478363ec2e1918aabfb
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
an early pre-neuralisation epiblast phase, characterized by markers such as POU5F1, SOX2, HESX1, and ZIC3

summary:
In Homo sapiens, the early pre-neuralisation epiblast phase is characterized by expression of POU5F1, SOX2, HESX1, and ZIC3.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:1044f04f4164041460de
claim_id: claim:1044f04f4164041460de
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
a regional neural progenitor phase, defined by markers such as OTX2, SOX1, SOX2, PAX6, NKX2.1, HOXB1 and FGF17

summary:
In Homo sapiens, the regional neural progenitor phase is defined by markers OTX2, SOX1, SOX2, PAX6, NKX2.1, HOXB1, and FGF17.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:906b27f6bcf5d487dcc7
claim_id: claim:906b27f6bcf5d487dcc7
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal: a postmitotic neuronal phase, indicated by markers such as STMN2, LHX6, ASCL1 and PHOX2B
summary:
In Homo sapiens, the postmitotic neuronal phase is indicated by markers STMN2, LHX6, ASCL1, and PHOX2B.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:688b0d177b7c5b867938
claim_id: claim:688b0d177b7c5b867938
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
Rostral cells were characterised by expression of HESX1 and SHISA2 during pre-neuralisation and PAX6 during early neuralisation, whereas caudal cells expressed FST and HOXA1 during pre-neuralisation and SOX1 as the dominant neuralising factor.

summary:
In Homo sapiens, rostral neural cells are characterised by expression of HESX1 and SHISA2 during pre-neuralisation and PAX6 during early neuralisation.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:86c205c8ed7211441247
claim_id: claim:86c205c8ed7211441247
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
Rostral cells were characterised by expression of HESX1 and SHISA2 during pre-neuralisation and PAX6 during early neuralisation, whereas caudal cells expressed FST and HOXA1 during pre-neuralisation and SOX1 as the dominant neuralising factor.

summary:
In Homo sapiens, caudal neural cells express FST and HOXA1 during pre-neuralisation and SOX1 as the dominant neuralising factor.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:f8e43826d440ae8a2c0a
claim_id: claim:f8e43826d440ae8a2c0a
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
The OTX2+ population showed an early expression wave of HESX1, CYP26A1 and SHISA2, whereas the GBX2+ population in contrast showed a strong induction of ZIC3, SP5 and FST during the first days of patterning

summary:
In Homo sapiens, the OTX2-positive rostral population shows early expression of HESX1, CYP26A1, and SHISA2, whereas the GBX2-positive caudal population shows strong induction of ZIC3, SP5, and FST.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:b370a5c1b2b0bf9275d9
claim_id: claim:b370a5c1b2b0bf9275d9
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
The OTX2+ population showed an early expression wave of HESX1, CYP26A1 and SHISA2, whereas the GBX2+ population in contrast showed a strong induction of ZIC3, SP5 and FST during the first days of patterning

summary:
In Homo sapiens, the GBX2-positive caudal population shows strong induction of ZIC3, SP5, and FST during the first days of patterning.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:d1dd9c63ebc8675e4999
claim_id: claim:d1dd9c63ebc8675e4999
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
while PAX6 emerged as the first neuroepithelial marker appearing in the rostral (OTX2+) domain, SOX1 was simultaneously activated exclusively in the caudal domain (GBX2+)

summary:
In Homo sapiens, PAX6 is the first neuroepithelial marker appearing in the rostral OTX2-positive domain, while SOX1 is activated exclusively in the caudal GBX2-positive domain.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:861b29865f73331dc661
claim_id: claim:861b29865f73331dc661
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
we confirmed a strong activation of OTX2, HESX1, SHISA2, FEZF1 and LHX5 in the forebrain differentiations during the early pre-neuralisation phase from d0-3.

summary:
In Homo sapiens, forebrain cells show strong activation of OTX2, HESX1, SHISA2, FEZF1, and LHX5 during the early pre-neuralisation phase.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:333de167f7ba8a535ddd
claim_id: claim:333de167f7ba8a535ddd
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
In contrast, GBX2, FST, HOXA1 and CRABP2 were strongly upregulated in the hindbrain differentiations during this phase.

summary:
In Homo sapiens, hindbrain cells show strong upregulation of GBX2, FST, HOXA1, and CRABP2 during the pre-neuralisation phase.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:866226bb7fbae59ac8b2
claim_id: claim:866226bb7fbae59ac8b2
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
The pre-neuralisation phase was followed by activation of PAX6 and DLK1 in the forebrain-patterned cells

summary:
In Homo sapiens, forebrain-patterned cells activate PAX6 and DLK1 following the pre-neuralisation phase.


claim_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d:claim:e03e9f8e66db5d9f6386
claim_id: claim:e03e9f8e66db5d9f6386
paper_key: biorxiv:9f961596-7f11-1014-8c2f-a898bdc06a6d
span_literal:
Pluripotent stem cells initially differentiate into two distinct types of regionally patterned epiblasts: late rostral epiblast (expressing OCT4 and OTX2) and late caudal epiblast (expressing OCT4 and GBX2).

summary:
In Homo sapiens, late rostral epiblast cells express OCT4 and OTX2, while late caudal epiblast cells express OCT4 and GBX2.


