Comprehensive Peripheral Immune Profiling by Methylation Cytometry in Men Living with HIV in Latin America

People living with HIV (PLWH) remain at increased risk of inflammation-related comorbidities and cancer despite viral suppression, reflecting persistent immune dysfunction. Most epidemiologic studies rely on surrogate markers of immune health, leaving the broader peripheral immune profile poorly characterized. We applied DNA methylation-based immune cell deconvolution (“methylation cytometry”) to whole-blood specimens from 414 men living with HIV. We estimated counts and proportions of 12 circulating leukocyte subsets and examined associations with nadir CD4+ T cell count, current CD4+ T cell count, and HIV RNA load using linear regression. Men with greater historical immune depletion (nadir CD4+ count < 200 cells/mm3) had significantly higher estimated counts of neutrophils, monocytes, memory CD8+ T cells, and higher neutrophil-to-lymphocyte ratios alongside significantly lower estimated counts of naïve CD4+ T cells, and lower naïve-to-total CD8+ T cell, naïve-to-total T cell and CD4/CD8 ratios. Lower current CD4+ T cell count (<500 cells/mm3) was associated with broad reductions across nearly all leukocyte subsets. Detectable HIV RNA (>50 copies/mL) was associated with higher neutrophil, monocyte, memory CD8+ T cell, and regulatory T cell estimated counts and lower basophil and naïve CD4+ T cell estimated counts. This study observed that markers of HIV disease are associated with persistent immunological alterations and that methylation cytometry provides a scalable approach to comprehensively profile immune cells in large populations and characterize immune reconstitution in PLWH.