Cytotoxic CX3CR1+ Vδ1 T cells clonally expand in an interplay of CMV, microbiota, and HIV-1 persistence in people on antiretroviral therapy

We performed a comprehensive characterization of Vδ1 T cells in blood of people with HIV-1 on antiretroviral therapy and HIV-seronegative controls, in a substudy of the ANRS EP61 GALT study (NCT02906137). We deciphered the single-cell transcriptome of Vδ1 cells. Vδ1 T cells were mainly terminally differentiated effectors that expanded in the blood with some trafficking with the gut of people with HIV-1. Most expressed CX3CR1 and displayed a highly cytotoxic profile, but low cytokine production, supported by a transcriptomic shift towards enhanced effector lymphocytes. The increase in Vδ1 T cells observed in people with HIV-1 has multiple triggers, particularly CMV and microbiota, and may in turn contribute to the control of the HIV-1 reservoir. For Vδ1 single-cell RNA sequencing, Vδ1 T cells were sorted after a stainingn step with TotalSeq-B anti-human hashtags (LNH-94; 2M2/BioLegend) directed against CD298 and β2-microglobulin. Sorted Vδ1 T cells were stored on ice and immediately processed for single-cell library generation. Vδ1 cells were sorted from PBMC of 6 PLWH and 6 controls, all CMV seropositive. Single-cell libraries were generated using the Chromium iX Single-Cell Instrument and Chromium Next GEM Single Cell 3′ Kit v3.1, Chip G Single Cell kit, Dual Index kit TT Set A and NT set A, and 3’ Feature Barcode kit (10x Genomics). Sequencing was then performed on a full SP flow cell 100 cycles (2 lanes) on the Illumina NovaSeq 6000 instrument (Illumina, San Diego, USA). *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************