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There is a mixture of naive T cells (left cluster) expressing CCR7, LSEL, and not naive ( cluster on the right lacks these two canonical markers of naive lymphocytes) expressing cytokines (IFNG, TNF, tnfsf13B, tnfrsf25, il2, cd40lg etc). This will fit with an effector phenotype.
This cluster contains a mix of CD4 subsets including Naive. e.g. Cells expressing IL12RB2, TBX21, CCL5, IFNG, TNF suggest some Th1. In our data CD45-RO negative and CD45-RA positive CD4 T cells at the CITE-seq level can be distinguished at the RNA level by a lack of expression of genes such as KLRB1, CCR6, CCL5. These cells are also SELL, LEF1, KLF2, CCR7, TCF7 high.
Appears to be a subset expressing CD4 as well
Agree IL23R, IL17A, RORC, IL4I1, KIT
Split into CD8+ naive (CD8A, CCR7, SELL) and the other cluster (negative for CCR7 and SELL) which appears to be jejunal (and accordingly expressing CCR9).
Also these "CD4+ TH1" cells are negative for CD4, but positive for CD8A/B. When comparing to the CD4TH17 cluster, CD4 is actually among the top downregulated genes in the "TH1" cluster. Merge with CD8+ T cells?
I think this is likely the naive B cell cluster. FCER2+, CD27-, Foxo1+, CD24hi, TCL1A+, IL4R+. https://www.science.org/doi/10.1126/sciimmunol.abe6291
Leiden Lineage L2 9_2 cluster is CD8 FGFBP2 (FGFBP2, FCGR3A, ...) (Corridoni, D and Garrido-Trigo A)
Also these "CD4+ TH1" cells are negative for CD4, but positive for CD8A/B. When comparing to the CD4TH17 cluster, CD4 is actually among the top downregulated genes in the "TH1" cluster. Merge with CD8+ T cells?
Expressing high levels of CD8A and CD8B and not expressing CD4, likely CD8 T cells instead
These cells are CD83high, MYChigh, CXCR5high, but lack AICDA and are MKI67 low-ish. --> I would judget them as light zone GC B cells and think that the "cycling B cell" cluster in fact is the real dark zone GC B cell cluster. Check out details e.g. here. https://www.sciencedirect.com/science/article/pii/S1074761321003010?via%3Dihub
This is a heterogeneous cluster, containing at least 3 different subsets. Only 1 of them has the canonical CXCL13, IL21 Tfh. A second subset not expressing these genes but with expression of CXCR5 and CCR6. The third subset has no markers of Tfh, and expresses several heat shock gene markers and CCL20. I would re-annotate this last cluster (number 3_3 in Leiden L2) as Heat shock T cells.
T follicular helper cells (CXCL13 and MAGEH1) (Garrido-Trigo, A)
Agree BCL6, TOX2, CXCR5, CD200
CXCR5, CXCL13, MME indicates TFH
Contains several subsets, including a GMZA, IL23R and IL12RB2 expressing Th1/Th17-like population
I think these are dark zone germinal center B cells. Mostly based on AICDA expression. But also MKI67, EZH2, CD9, PCNA, CDK1 https://rupress.org/jem/article/217/10/e20200483/151908/Single-cell-analysis-of-germinal-center-B-cells
I think there is a couple of problems here with this cluster. I don´t think they are Naive B cells (check out e.g. CD27 expression. Also, the "marginal B cell zone" cluster has a couple of key naive B cell markers FCER2, CD27, Foxo1, CD24hi, TCL1A, IL4R. Lastly, there are a couple of plasmacytoid dendritic cells included in this cluster, the island very far out left of the T cell islands. CLEC4C, IL3RA... And in the myeloid object, pDCs are missing completely. In my opinion, this small pDC island should be removed here and put into the myeloid object. https://www.science.org/doi/10.1126/sciimmunol.abe6291 https://pmc.ncbi.nlm.nih.gov/articles/PMC10470411/
Agree with splitting into IKZF2+ (also expressing CCR8 RTKN2) with a highly suppressive phenotype, and IKZF2- (also IL10+).
Agree FOXP3, IL10, CTLA4, IKZF2, TIGIT, CCR4, Can be further split into IKZF2 high and IKZF2 low
This is contamination from the epithelial compartment and should be removed from here (EPCAM, MUC2...)
CD4pos, CCR7pos, TCF7pos. Naive CD4+ T cells? (Possibly central memory, maybe a T cell person should double check)
Not expressing CD8A or CD8B but is expressing CD4. So not Naive CD8. The Naive CD8 subset is likely a subset of the current CD8 T cluster, specifically the one above the Naive CD4 T cells on the left of the T cell island. This cluster is Tfh like, ICOS, TOX2, CD200
they are the same subset, expressing IL-23R and TNFR25. Actually "ILC2" express more IL22 a marker of ILC3. Merge both into ILC3.
Expressing CD4, not expressing CD8A or CD8B
Annotate as NK cells. they are CD3 negative but expressing NCAM1, KLRD1. Nature Immunology volume 25, pages 1474–1488 (2024)
Delete. This cluster is noise. Has no B cell marker. Markers include secretory epithelial markers ZG16, CLCA1, MUC2.
they are the same subset, expressing IL-23R and TNFR25. Actually "ILC2" express more IL22 a marker of ILC3. Merge both into ILC3.
Top DEG when comparing to the "ILC3" cluster is IL22 (top up). No signs of increased GATA3, IL4, IL13, AREG... Possibly a mix of ILCs?
This is contamination from the epithelial compartment (MUC2, KRT19...) and should be deleted from here.
TRAV, RORC, IL23R Checks out with previous scRNA-seq MAIT T cell profiles. (e.g. here https://www.nature.com/articles/s41590-023-01575-1; this is liver, though)
