Differential CpG methylation in the Interferon Gamma (IFNG) promoter correlates with viral load and transcriptional control in people with HIV.

HIV persistence is facilitated by immune evasion strategies that reshape host immune responses. As the Interferon Gamma (IFNG) gene encodes a key immunoregulatory cytokine whose transcriptional competence is governed by promoter CpG methylation, we hypothesized that HIV plasma RNA would track with epigenetic remodeling at the IFNG promoter, altering IFNG mRNA transcription. DNA methylation at the IFNG promoter was quantified by bisulfite sequencing in PBMCs from people with HIV (PWH) with high (n = 16; >5000 copies/µL), medium (n = 18; 500 to 4999 copies/µL), or undetectable (n = 18; ≤50 copies/µL) plasma HIV RNA. Corresponding IFNG mRNA was quantified by RT-qPCR, with a sensitivity analysis adjusting for T cell abundance. High detectable plasma HIV RNA was associated with significant IFNG hypomethylation across 4 out of 5 CpG sites in the IFNG promoter compared to those with medium HIV RNA, while those with undetectable plasma HIV RNA showed no significant differences after adjusting for duration of infection. Accordingly, IFNG mRNA transcription was significantly elevated in participants with high plasma HIV RNA compared to medium (p = 0.037), which strengthened after modeling TCF7 expression as a covariate to account for varying T cell counts (p = 0.02). These findings provide the first in vivo evidence correlating HIV viral load with epigenetic transcriptional control of IFNG in peripheral blood.