Single cell characterization of the gastrointestinal HIV reservoir reveals heterogeneous cellular phenotypes.
Human gastrointestinal (GI) tissues are a major site of HIV-1 viral persistence, but the nature of the GI reservoir remains poorly described.  To characterize the GI HIV reservoir, we profiled cells from GI tissue and matched peripheral blood mononuclear cells from ten people with HIV (PWH) on antiretroviral therapy (ART) using single cell RNA sequencing.  We identified distinct compartment-specific patterns of gene expression, highlighting key differences between blood and colon CD4 T cell populations.  vRNA+ cells from both blood and GI tissue were heterogeneous and found in multiple subtypes of CD4 T cells, although vRNA+ cells were particularly enriched in cells with Th17 or Treg17 phenotypes.  Transcriptomic comparison of HIV vRNA+ and vRNA- T cells revealed 116 differentially expressed genes that were associated with HIV infection including ZBED2, MAF and IL17F.  These data provide novel information regarding the GI-resident HIV reservoir and suggest that compartment-specific patterns of gene expression are associated with HIV infection. Overall design: Single cell RNA sequencing of samples derived from 10 HIV seropositive donors and 1 HIV seronegative donor (Donor 11). HIV seropositive participants had been durably suppressed on ART for a median of 12.8 years (IQR 11.2-19.8)  . Samples were derived from the peripheral blood and from the sigmoid region of the colon, optionally isolated with CD4 positive selection, and treated with PMA ionomycin or control conditions. CITE seq using TotalSeqB panel with hash tag oligo (HTO) indexing was performed on peripheral blood samples from three donors (Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3).