They expressed well-described canonical markers of lamina propria fibs.
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They expressed well-described canonical markers of lamina propria fibs.
I think this is correct. The ADAMDEC1hi, CCL8, CCL13, CCL11 profile is like in the Kinchen et al. paper (2018) and a lot of the following milestone papers.
These are submucosal PI16+CD34+CD55 fibroblasts, previously also described as "adventitial-like" or "universal" (https://pmc.ncbi.nlm.nih.gov/articles/PMC11196929/; ; https://www.nature.com/articles/s41590-025-02267-8) fibroblasts. Also trophocytes (CD81, RSPO3, GREM1...) are likely in here. I think it is much more likely that the very most of these cells come from the submucosa (or possibly to an extent from under the intestinal crypts (https://www.pnas.org/doi/10.1073/pnas.1620059114), i.e. are not subserosal. Check e.g. submucosal fibroblast profiles here: https://www.sciencedirect.com/science/article/pii/S009286742400254X https://www.biorxiv.org/content/10.1101/2025.07.29.667377v2.full.pdf https://academic.oup.com/jimmunol/article-abstract/201/1/215/7952082?redirectedFrom=fulltext&login=false 10.1084/jem.20250471
Markers of subepithelial F3, SOX6 wnt5b expressed by this cluster.
This cluster contains a mix of cells. One of the markers mentioned in the metadata as specific is PLVAP (not expressed by half of the cells in this cluster). I would suggest selectin leiden L1 cluster 14 (as the arterial endothelium using GJA5 and SEMA3G as markers). Cluster 14, however, lacks PLVAP (highly expressed in clusters 3 and 17) which I would annotate as capilary (based on PLVAP expression).
This cluster shows expression of adhesion molecules MADCAM, SELEP and SELE normally described in inflammed endothelium but also described in venular endothelium. It also expresses another marker of venular endothelium lrg1.
My guess would be that this is a mixed cluster of submucosal (or here "subserosal") fibroblasts and ADAMDEC1+ interstitial cells, given the presence of key signature markers such as PI16, CD34, SFRP2 on one hand and ADAMDEC1, CCL11, CCL13 etc on the other hand. Is there any location data for these cells that would prove these would sit in the muscular propria?
this cluster also expressed NRG1, demonstrated to be crypt top (validated in https://doi.org/10.1038/s41467-023-40156-6 by ISH).
These lack classic submucosal and trophocyte markers. CD34, CD55, PI16, CD81, RSPO3, GREM1.... https://academic.oup.com/jimmunol/article-abstract/201/1/215/7952082?redirectedFrom=fulltext&login=false 10.1084/jem.20250471 https://www.sciencedirect.com/science/article/pii/S009286742400254X https://www.biorxiv.org/content/10.1101/2025.07.29.667377v2.full.pdf
Smooth muscle cell signature markers expressed such as ACTA2, ACTG2, TAGLN, MYH11...
Agree with the overall annotation, as PROX1, FLT4 as "lymphatic endothelial cells (LEC)". Although the cell number is low there is heterogeneity in some canonical markers that would suggest the presence of LEC subsets within the cluster annotated now as "Vascular Endothelial Lymphatic". For instance, not all express LYVE1 or CCL21. Indeed, cells lacking expression of these two markers express ACKR4 (Leiden lineage L2 cluster 13_3) could be annotated as Ceiling subcapsular sinus LECs (https://doi.org/10.1016/j.immuni.2019.06.027) . Also clusters 13_0 and 13_1 do express LYVE1, CCL21 as well as CLEC4M marker of medullary sinus LECs (https://doi.org/10.1016/j.immuni.2019.06.027).
Clearly LYVE-1+, PROX1+ lymphatic endothelial cells (LEC). https://www.nature.com/articles/nrgastro.2017.79 But please delete "vascular" as this is indicative that is NOT a lymphatic cell, but a blood endothelial cell (BEC).
T-cell contamination needs to be deleted from this object.
Seems to be mostly T cells with CD2, CD3, CD69?
Clearly a lymphoid tissue FRC cluster. CD24+ CCL19/CCL21+ CLU+ As CXCL13/CXCL14/FDCSP are also on the list, this is likely a T cell zone / B cell zone mixed cluster
Clearly LYVE-1 lymphatic endothelial cells (LEC), also the "Lacteal" label makes sense (LYVE1hi, PROX1hi KDR+...) https://www.nature.com/articles/nrgastro.2017.79 But please delete "vascular" as this is indicative that is NOT a lymphatic cell, but a blood endothelial cell (BEC).
this cluster also expressed NRG1, demonstrated to be crypt top (validated in https://doi.org/10.1038/s41467-023-40156-6 by ISH).
F3+ subepithelial fibroblasts. See Kinchen et al. 2018.
This is for sure a glial cell. PLP1, Sox10, L1CAM. I am not sure this is purely a submucosal glial cell. Check out the expression of all the MHCII-related genes and there are also some interferon response genes. Could this be more a "reactive glia" = activated cluster?
ESAM+CD36+, ACTA2lower than the other pericytes. Absence of endothelial cell markers (e.g. PECAM1) and fibroblast markers (e.g. PDPN)
Definitely containing some enterocytes. CLDN1, CALB2, PDZK1IP1
I think this label is in line with the Elmentaite et al paper (https://www.nature.com/articles/s41586-021-03852-1). However, given that some of the main DEG are e.g. TNFSF11 and CXCL14, I think one could also label them MRC = marginal reticular cells. Especially TNSF11 is a hallmark of MRC from secondary lymphoid tissues such as Peyers patches and isolated lymphoid follicles. (https://www.nature.com/articles/s41590-021-00894-5); (10.1084/jem.20250471)
For real myofibroblasts, I would expect MYH11, ACTA2, ACTG2 etc. expression = genes associated with muscle function. These fibroblasts are CTHRC1 and FAP positive and are most likely small amounts of pro-fibrotic inflammation-associated fibroblasts as described previously. --> Call them "Inflammation-associated fibroblasts" (IAF)? E.g. Bauer-Rowe et al. https://www.sciencedirect.com/science/article/abs/pii/S0092867425010189 Zhang et al. https://www.jci.org/articles/view/179472 Review by Brügger/Basler https://www.cell.com/trends/cell-biology/fulltext/S0962-8924(23)00048-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS096289242300048X%3Fshowall%3Dtrue
Delete
ANPEP+DPP4, FABP1 clear epithelial cells. Remove from this object as there is a separate epithelial lineage object?
Delete.
Surely containing plasma cells (MZB1, JCHAIN, CD79A), but also other lymphocytes (likely incl. T cells IL7R, CD69hi). As this is a stromal cell object, they cluster together. Delete this cluster from this object?