ZFP148 is a transcriptional regulator of effector CD8+ T cell differentiation [single-cell_multiome]

Chronic antigen exposure, as seen in persistent viral infections and cancer, drives CD8? T cells to differentiate into diverse subsets: progenitor/stem-like, effector, and exhausted/dysfunctional cells. While genetic and epigenetic factors influencing these subsets are known, the mechanisms regulating their dynamic balance remain unclear. We identified Zinc-Finger Protein 148 (ZFP148) as a novel transcriptional checkpoint in CD8? T cell effector differentiation. Using a genetic approach that deletes ZFP148 specifically in CD8+ T cells, we performed matched single cell RNA-seq and ATAC-seq on antigen-specific CD8+ T cells. Overall design: CD44High GP33-41 tetramer+ CD8+ T cells were FACs-sorted from the spleens of control or ZFP148 KO mice 21 days-post lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl13) infection. After sorting, cells were washed with PBS containing 0.04% BSA, then approximately 10,000 nuclei of either control or ZFP148 KO sample were isolated and processed with the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit following manufacture's manual (10x genomics). Two separate sets of libraries, Gene expression (GEX) and ATAC, were generated from each sample according to manufacturer's instructions. Pre-sequencing quality control was performed using an Agilent Tapestation. GEX libraries and ATAC libraries were sequenced on an Illumina Novaseq X plus platform by Azenta Life Sciences.