Multi-Omics Clustering Differentiates the Total and Intact HIV Reservoirs and Related Host Immune Mechanisms

Abstract

HIV reservoirs are heterogeneous across individuals, yet host determinants of this variability remain unclear. Applying multi-omics clustering to 1,230 people with HIV, integrating omics and functional data from circulating immune cells (transcriptomics, DNA methylation, immune phenotyping, ex-vivo cytokine production capacity), plasma proteomics, and CD4+ T-cell reservoir measurements (total and intact HIV-DNA copies), revealed three immunologically distinct endotypes: All Low (low total/low intact reservoir size), All High (high total/high intact reservoir size) and Mixed (high total/low intact reservoir size). Per endotype, distinct immune landscapes were noticed in single-layer analyses as well as differences in clinical signatures. Applying non-linear machine learning across all layers, key predictors not captured by linear single-layer approaches showed IFN-{gamma} production and TCF7/AK5 expression across T-cell and NK-cell populations as well as IL-1{beta}/MCP-1 production after 24h stimulation and MAN1C1/EDAR expression on T-cell populations, linked to intact and total reservoir size, respectively. This host-virus integrative multi-omics framework provides a systems-level resource that may help to personalize reservoir-reducing intervention studies aiming for HIV cure and/or comorbidity reductions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/734029v4_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@16fded7org.highwire.dtl.DTLVardef@18f2e69org.highwire.dtl.DTLVardef@12ffc9borg.highwire.dtl.DTLVardef@17127cc_HPS_FORMAT_FIGEXP M_FIG a) Multi-omics clustering of 1,230 virally suppressed PLHIV identified three immunologically distinct endotypes: All Low (n=428), Mixed (n=483), and All High (n=280), with distinct total and intact HIV reservoir sizes. b) Single-layer analyses reveal characteristic immune landscapes: All Low Th1-skewed, naive T cells (immunophenotyping), high IFN-{gamma} production (7-day), downregulated Type I IFN pathways (bulk transcriptome); Mixed intermediate Th1/Th2, CD8 and CD4 effector memory T cells (immunophenotyping), IL-5 production (7-day), downregulated Type I IFN pathways (bulk transcriptome); All High Th2-skewed, CD4 effector memory T cells (immunophenotyping), high IL-5 production (7-day), upregulated Type I IFN pathways (bulk transcriptome). c) Endotypes carry distinct comorbidity burdens: All Low lower carotid plaque, AIDS-defining malignancies, and residual viremia; Mixed intermediate burden; All High highest carotid plaque, AIDS-defining malignancies, opportunistic infections, and residual viremia. d) Non-linear classification models (XGBoost) prioritize top host predictive markers: IFN-{gamma} response (7-day), TCF7 and AK5 expression in CD4/CD8 T-cells and NK-cells (characterize All Low; IL-1 response (24-hour), MAN1C1 and EDAR in CD4/CD8 T-cells, and MCP1 response (24-hour) characterize All High. Created in BioRender. C_FIG