PREdictive Value of Inflammatory PaTTerns at Two Years of Successful ART (PRETTY)
This study investigates transcriptomic signatures associated with severe non-AIDS events (SNAEs) in people with HIV (PWH) receiving suppressive antiretroviral therapy (ART). Despite effective viral suppression, PWH remain at increased risk of non-AIDS morbidity, and the biological mechanisms underlying these outcomes are not fully understood.  We performed RNA sequencing (RNA-seq) on peripheral blood mononuclear cells (PBMCs) collected from participants enrolled in the Spanish CoRIS cohort, a large prospective multicenter study of ART-naïve PWH. The study followed a nested case-control design including individuals who initiated ART, achieved virological suppression, and remained free of major clinical events for at least two years. Cases (n=92) subsequently developed SNAEs (including cardiovascular events, non-AIDS-defining malignancies, or non-accidental death) while matched controls (n=95) remained event-free over comparable follow-up. PBMC samples were obtained two years after ART initiation, representing a stable phase of immune reconstitution.  Total RNA was extracted from PBMCs and sequenced using Illumina NovaSeq X Plus (paired-end 150 bp reads), generating approximately 6 Gb of data per sample. Library preparation followed standard protocols including RNA quality control, fragmentation, adaptor ligation, amplification, and size selection. After quality filtering, 155 samples were retained for downstream transcriptomic analyses.  Differential gene expression analysis identified distinct transcriptional profiles associated with subsequent clinical outcomes. Across comparisons, individuals who later developed SNAEs exhibited consistent upregulation of type I interferon-stimulated genes, including USP18, ISG15, SIGLEC1, and IFI27, indicating a persistent interferon-driven immune activation state.  Pathway enrichment analyses confirmed that interferon alpha/beta signaling was the most consistently enriched pathway among individuals with adverse outcomes, suggesting a shared underlying inflammatory axis. Integration with plasma proteomics further demonstrated concordance between interferon-related gene expression and circulating inflammatory markers, including galectin-9 (LGALS9), reinforcing the biological relevance of these pathways.  Overall, this dataset provides a high-resolution transcriptomic resource capturing immune dysregulation during suppressive ART and its association with long-term clinical outcomes. The RNA-seq data highlight a reproducible interferon-associated transcriptional signature that precedes major non-AIDS events, supporting its role as a potential biomarker and mechanistic pathway in treated HIV infection.
This study investigates transcriptomic signatures associated with severe non-AIDS events (SNAEs) in people with HIV (PWH) receiving suppressive antiretroviral therapy (ART). Despite effective viral suppression, PWH remain at increased risk of non-AIDS morbidity, and the biological mechanisms underlying these outcomes are not fully understood.  We performed RNA sequencing (RNA-seq) on peripheral blood mononuclear cells (PBMCs) collected from participants enrolled in the Spanish CoRIS cohort, a large prospective multicenter study of ART-naïve PWH. The study followed a nested case-control design including individuals who initiated ART, achieved virological suppression, and remained free of major clinical events for at least two years. Cases (n=92) subsequently developed SNAEs (including cardiovascular events, non-AIDS-defining malignancies, or non-accidental death) while matched controls (n=95) remained event-free over comparable follow-up. PBMC samples were obtained two years after ART initiation, representing a stable phase of immune reconstitution.  Total RNA was extracted from PBMCs and sequenced using Illumina NovaSeq X Plus (paired-end 150 bp reads), generating approximately 6 Gb of data per sample. Library preparation followed standard protocols including RNA quality control, fragmentation, adaptor ligation, amplification, and size selection. After quality filtering, 155 samples were retained for downstream transcriptomic analyses.  Differential gene expression analysis identified distinct transcriptional profiles associated with subsequent clinical outcomes. Across comparisons, individuals who later developed SNAEs exhibited consistent upregulation of type I interferon-stimulated genes, including USP18, ISG15, SIGLEC1, and IFI27, indicating a persistent interferon-driven immune activation state.  Pathway enrichment analyses confirmed that interferon alpha/beta signaling was the most consistently enriched pathway among individuals with adverse outcomes, suggesting a shared underlying inflammatory axis. Integration with plasma proteomics further demonstrated concordance between interferon-related gene expression and circulating inflammatory markers, including galectin-9 (LGALS9), reinforcing the biological relevance of these pathways.  Overall, this dataset provides a high-resolution transcriptomic resource capturing immune dysregulation during suppressive ART and its association with long-term clinical outcomes. The RNA-seq data highlight a reproducible interferon-associated transcriptional signature that precedes major non-AIDS events, supporting its role as a potential biomarker and mechanistic pathway in treated HIV infection.
Instituto Ramon y Cajal de Investigacion Sanitaria