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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
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
Expressing high levels of CD8A and CD8B and not expressing CD4, likely CD8 T cells instead
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 FOXP3, IL10, CTLA4, IKZF2, TIGIT, CCR4, Can be further split into IKZF2 high and IKZF2 low
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
Expressing CD4, not expressing CD8A or CD8B
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?
