Fig. 4: Pep-Groups associate with different T cell phenotypes. | Nature Communications

Fig. 4: Pep-Groups associate with different T cell phenotypes.

From: APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Fig. 4

a Illustration of the mapping of peptide physicochemical properties on to T cell gene expression profiles. Created in BioRender59. CD8 T cells were captured by SCT-dextramers from 62 HLA-matched COVID-19 participants for scRNAseq and TCR sequencing. Gene expression UMAP (GEX-UMAP) was generated based on scRNAseq. We used the SCT identity to connect Pep-Groups with gene expression. b GEX-UMAP of SARS-CoV-2-specific CD8 T cells with different phenotypes color-encoded (legend on the top), and then color-coded by expression levels of selected mRNA transcripts. c GEX-UMAP, color-coded by (left) the polarity of exposed peptide antigen residues; (middle) all T cells specific to a given antigen; and (right) SARS-CoV-2 specific T cells from two study participants. d Top: GEX-UMAP color-coded with T cell densities specific for antigens from each Pep-Group. Bottom: Bar plot of the relative abundance of phenotypes for T cells associated with each Pep-Group. Note that the UMAP densities in the original were calculated as an odds ratio. e Top enriched biological pathways of genes significantly elevated in cells captured by PG3 relative to PG2. Adjusted p-values are generated by EnrichR.

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