Single-cell epigenetic, transcriptional, protein, and TCR states of HIV-1-infected cells in gut

Tissue resident memory T cells (TRMs) are essential to mucosal immunity. We postulate that their long-lived tissue residency and restricted effector function promote HIV-1 persistence in human gut. We coupled single-cell-DOGMA-seq and TREK-seq to capture chromatin accessibility, transcriptome, surface proteins, T cell receptor, HIV-1 DNA, and HIV-1 RNA in gut CD4+ and CD8+ T cells from ten aviremic HIV-1+ individuals and five HIV-1- donors. We found that BACH2, a transcription repressor that establishes long-lived memory in T cells, is the leading transcription factor that shapes gut TRMs into long-lived memory and restrains interferon-driven effector function. Colon primary cells from 10 PLWH and five HIV-1 negative donors were processed for DOGMA-seq. For each sample, cells were split into two aliquots, one for CD3+ T cell enrichment (_CD3) and the other for whole gut primary cell sequencing (_whole). Colon cells were processed through dead-cell removal by negative selection. For the whole gut aliquots, cells from each participant were stained by uniquely barcoded TotalSeq-A hashing antibodies and pooled. Cells were then stained with a panel of 154 cell surface proteins and 9 isotype controls included in TotalSeq-A Human Universal Cocktail and with TotalSeq-A CCR7. After staining, cells were permeabilized with 0.01% digitonin. Cells were then loaded into the 10x Genomics Chromium Controller for DOGMA-seq (3’ Single Cell 10x Multiome (ATAC + GEX) with feature barcoding). This resulted in libraries for the single cell epigenome, transcriptome, and surface proteome. Leftover cell-barcoded cDNA libraries were used to perform TREK-seq to enrich and sequence for TCR sequences.