Single-cell epigenetic, transcriptional, and protein states of HIV-1-infected cells [Feature_Barcoding]

The heterogeneity and rarity of HIV-1-infected cells hampers effective cure strategies. We used single-cell DOGMA-seq to simultaneously capture transcription factor accessibility, transcriptome, 156 surface proteins, HIV-1 DNA, and HIV-1 RNA from six HIV-1+ individuals during viremia and after suppressive antiretroviral therapy. We identified 252 transcriptionally inactive (HIV-1 DNA+ RNA–) and 270 transcriptionally active (HIV-1 RNA+) HIV-1-infected cells from 82,549 memory CD4+ T cells. We identified increased transcription factor accessibility in HIV-1 DNA+ RNA– cells (RORC) and HIV-1 RNA+ cells (IRF and AP-1), in addition to CNC and MAF in both. Both HIV-1 DNA+ RNA– and HIV-1 RNA+ cells upregulate IKZF3 (Aiolos) that correlates with proliferation of HIV-1-infected cells. We revealed that the heterogeneous HIV-1-infected T cells comprise four distinct immune programs driven by epigenetic regulators – IRF-activation, Eomes-cytotoxic effector, AP-1-migration, and cell death. Our study revealed the single-cell epigenetic, transcriptional, and protein states of transcriptionally inactive and active HIV-1-infected cells. Overall design: Paired PBMC samples from 6 HIV-1-infected individuals from the Sabes cohort during viremia and after viral suppression and PBMC samples from 4 uninfected controls were processed for DOGMA-seq. Memory CD4+ T cells were isolated from dead-cell removed PBMC by negative selection. Purified memory CD4+ T cells from participants were each stained with uniquely barcoded TotalSeq-A hashing antibodies and pooled. Cells were stained with a panel of 154 cell surface proteins and 9 isotype controls included in TotalSeq-A Human Universal Cocktail. 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. Six DOGMA-seq runs from virally suppressed HIV-1 infection samples (YW1 – YW6); three DOGMA-seq runs from viremic HIV-1 infection (YW8 – YW10); one DOGMA-seq runs from uninfected controls (HD1). Supplementary file “Participant Hashtags” contains the hashtag IDs for each participant in each pooled samples.