Change name to Mast Cells.
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Change name to Mast Cells.
Should be labeled Mast cells....homogenously positive for KIT, TPSAB1, TPSB2...
I suggest to rename Granulocytes Mast Cells into Mast cells (example: https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1494025/full)
It could make sense to broadly split the resident macs into homeostatic/steady state macs (involved in phagocytosis, tissue housekeeping that would comprise L1 cluster 6 and 7) and inflammatory/cytokine producing macs (that would comprise L1 clusters 1 + 8). Re the distinct L1 cluster 14, I see that others here may have interesting data on that phenotype - so perhaps a separate cluster is warranted :)
"Tissue resident" is too broad and it should include also: M0, FOLR2, LYVE1, PLA2G2D macrophages. M0 (https://doi.org/10.1038/s41467-023-40156-6) are resident macs (expressing all canonical mac markers C1QA, C1QB, C1QC, SELENOP, RNASEL1, CD163, etc, but lacking the "M2" markers FOLR2, CD209, CD163L1, MAF, STAB1, etc). I would suggest merging clusters 7 and 6 with cluster 8 Leiden L1 (all FOLR2 macrophages), cluster 1 as M0, and cluster 14 as PLA2G2D macrophages. the latter not formally described yet in human. We have 2 oral presentations at ECCO and a MS in preparation describing this as a distinct population of macrophages detected in isolated lymphoid structures. They have been described in mice previously ( https://doi.org/10.1084/jem.20121887).
Cluster 14 in Leiden: PLA2G2D+ macrophages are an independent group of macrophages characterised by the expression of PLA2G2D, PTGDS, MMP9, described in Gudiño V et al. DOP87: Pathologic fibroblasts and macrophages in colonic Crohn’s disease via spatial transcriptomics. J Crohns Colitis. 2024;18(Suppl 1):i235–i236. Manuscript in process. Clusters 1, 6 and 7 would then be the tissue resident macrophages
Myeloid cluster 5 contains classical monocytes (or could consider naming them monocyte-related macs?) whereas myeloid cluster 16 contains non-classical (FCGRA+ etc) - should be split
CD14, VCAN, S100...
M2 is outdated and this cluster "belongs" to the resident macrophage supercluster. This could be split into L1 cluster 9 as Submucosal or perivascular macs (LYVE1++, COLEC12+, C1Q, MRC1.., ref PMID: 35139155) and L1 cluster 8 (C1Q, FOLR2).
M2 is outdated. I would suggest FOLR2 as a better marker for resident macrophages. I would divide into the lyve1+ (cluster 9 in Leiden L1) and lyve1- folr2+ (cluster 8 in Leiden L1). Lyve1+ are considered perivascular. Also, C1Q genes, as well as SELENOP, etc are general markers of macrophages (not of the "M2").
Considering the Leiden clustering, I would split M2 macs into clusters 8 and 9, with 8 being FOLR2+ and 9 being FOLR2+LYVE1+. FOLR2+LYVE1+ macrophages may be perivascular macrophages, whereas FOLR2+ macrophages may be found predominantly at the lamina propria.
I suggest to rename Macrophages M2 into C1q+ macrophages. They are driven by C1Q+ genes. Nomenclature M2 is outdated. Here u have example https://www.sciencedirect.com/science/article/abs/pii/S2405803322000425
This seems a contamination cluster with lymphocytes, mostly composed of T cells. Check out top-hits. E.g. different CD3-related genes. Also some B cells/plasma cells, e.g. MZB1 is also a top hit. Remove from this object?
Normally named as myeloid cycling, however, I agree they are more macrophage profile. Classic cycling markers TOP2A, MKI67... (Melon-Ardanaz, E)
Only L2 cluster 12_0 encompass migratory DCs (CCR7. LAMP3 etc) ....12_2 12_2 and 12_3 are dublets and 12_1 appears to be a subset of cDC2 (CD1C+, CD207+, CLEC10A+ and lacking monocytic markers)
Agree with this being FDCs, but also that they are not of myeloid origin (and should be merged with stromal compartment).
I agree that these are clearly follicular dendritic cells (FDCs). CR1, CR2, FDCSP, CXCL13 etc. https://rupress.org/jem/article/221/1/e20221220/276440/Protective-fibroblastic-niches-in-secondary HOWEVER: This is - despite of the confusing name - a fibroblast subset and should be integrated with the stromal cell object, where they will most likely cluster together with the other fibroblastic reticular cells. These cells have very little in common with myeloid cells.
They are granulocytes; however, I think it can be refined to be eosinophils as they express CLC (top marker), IL4... (Melon-Ardanaz, E 2025).