Background
Human gastrointestinal (GI) tissues are a major site of HIV-1 viral replication and persistence, but the nature of the persistent HIV-1 reservoir in the GI remains poorly described. Previous study has identified higher levels of viral DNA but lower levels of transcriptional initiation in the colon as compared to the peripheral blood.
Methods
To characterize HIV infected cells in GI tissues from people with HIV (PWH), we developed a protocol to isolate and sequence GI-associated human lymphocytes with 10x Genomics scRNAseq. We analyzed 433,655 high-quality single-cell transcriptomes from GI-associated cells and matched PBMC from eleven PWH on ART.
Results
We identified expected patterns of compartment-specific gene expression in GI tissue resident T cells. Non-stimulated GI resident T cells differentially express surface factors including ITGA1/CD103 and CD69 whereas non-stimulated peripheral blood T cells express SELL/CD62L, CCR7, and S1PR1. Non-stimulated GI resident T cells express distinct transcriptional regulators like RUNX3 and STAT4 whereas non-stimulated peripheral blood T cells express KLF2, LEF1, and TCF7/TCF1. We identified 103 HIV RNA positive cells from the GI samples which exclusively clustered with T cells. We observed that the HIV+ cells from PWH were heterogeneous, but nevertheless, we could observe distinct transcriptomic differences between HIV+ and HIV- T cells. Across all T cells (gut and blood), the HIV+ cells exhibited elevated expression of a set of cytokines including IL-2, IL-21 and CCL20, while the HIV-regulating long non-coding RNA MALAT1 was downregulated. NFKBID and JARID, which encode proteins that repress HIV expression, were also upregulated in HIV+ T cells. Within the HIV+ gut T cells, MTRNR2L1, a negative regulator of apoptosis, was upregulated, suggesting a mechanism by which GI resident HIV+ cells can persist.
Conclusions
By identifying molecular mechanisms of differential transcriptional regulation in GI tissue resident T cells, we generate testable hypotheses that may lead to a better understanding of HIV latency and persistence.
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