Viral rebound with variable kinetics consistently occurs in people living with HIV (PLWH) after the discontinuation of ART during analytical treatment interruptions (ATI). In CD4 T cells, we previously identified candidate host epigenetic DNA methylation (DNAm) states correlating with time to viral rebound during ATI. Whether preexisting host DNAm states in bulk peripheral blood mononuclear cells (PBMCs) of PLWH participating in diverse curative interventions can reveal novel preexisting host epigenetic signatures related to time to viral rebound remains understudied.
Genome-wide DNAm profiling of PBMCs was obtained at study entry from 26 male PLWH on ART who participated in an ATI following combination interventions designed for eradicating residual plasma viremia and decreasing HIV reservoirs (NCT02961829). 15 early rebounding participants ranged in time to viral rebound from 14-24 days, 10 late rebounding participants from 33-102 days, and one exceptional participant (São Paulo Patient) rebounded at 511 days. Differentially methylated loci (DML) associated with the rebound group were identified by comparing early and late groups at a mean difference in methylation greater than 5% (Δβ-value) with FDR correction.
Pre-ATI total HIV DNA at baseline and CD4 count did not significantly associate with time to viral rebound. At baseline study entry visit prior to intervention, we identified 2,694 DML (Δβ-value > |0.05|; P < 0.05) comparing early compared to late rebounding participants (Fig.1). These loci were enriched at intergenic regulatory regions and upstream of CpG islands in the human genome (P=0.001). Gene ontology and pathway enrichment analyses revealed DNAm differences at genes involved in the MHC class II protein complex, interferon-gamma-mediated signaling pathway, platelet activation, and Th17 cell differentiation. Among the top DML associated with rebound group were genes including ADAMTS20 involved in HIV life cycle, MX2 antiviral protein against HIV, epigenetic regulator of plasmacytoid dendritic cells CXXC5, and chemokine gene PF4V1. DNAm states of PRSS50, MX2, ZNF529, and ZNF583 significantly associated with viral load post-ATI.
Fixed epigenetic features of innate and adaptive immune cells in PLWH may predetermine varying viral rebound kinetics during ATI despite multimodal therapies. These findings also suggest that an optimal host epigenetic landscape may exist to control HIV expression and silencing.
Correlogram plot of time to viral rebound, viral load post-ATI, HIV DNA pre-ATI, CD4 count pre-ATI, and pre-ATI DNAm states of host genes.