Background
DNA methylation (DNAm) clocks are quantitative markers of biological aging. The first-generation Horvath and Hannum clocks closely track actual age, second-generation clocks such as PhenoAge and GrimAge are sensitive to morbidity and mortality, and the third-generation DunedinPACE model estimates individual longitudinal “pace of aging.” Multiple studies have linked HIV infection with increased DNAm age; however, the clinical relevance of these clocks to brain health in virally suppressed persons with HIV (PWH) is unclear. We hypothesized that second-generation DNAm clocks would be significantly associated with HIV serostatus and would correlate with brain age acceleration (BAA), a machine learning model of overall brain health derived from structural MRI.
Methods
PWH and people without HIV (PWoH) underwent phlebotomy and 3-Tesla brain imaging. DNA was extracted from peripheral blood mononuclear cells, and DNAm levels were quantified using MethylationEPIC 2.0 microarrays (Illumina). The R packages EWAStools, minfi, FlowSorted.Blood and methylclock were used for quality control, normalization, cell type inference, and DNAm age calculation. DeepBrainNet was used to calculate BAA from MRI. Hypotheses were tested using multiple linear regression, with age, sex at birth, and blood cell proportions as co-variates.
Results
Participants included PWH (n=61; sex=39/22 M/F; 34/27 Afr. Amer./White; age=51.7±11.1 yr.) and PWoH (n=50; 22/28 M/F; 28/20/2 A.A./W/other; age=51.3±13.9 yr.). The Horvath and Hannum clocks were not different by serostatus (p=0.51, p=0.053). PhenoAge showed a 4.8-year increase in PWH (p=0.02; left panel), but GrimAge and DunedinPACE did not (p=0.82, p=0.16). A consensus clock averaging all models showed a 1.9-year increase in PWH (p=0.02). The Hannum, PhenoAge, and consensus clocks were positively associated with older brain-predicted age across serostatus (p=0.002, p=0.008, p=0.005; right panel).
Conclusions
These findings indicate that HIV infection is associated with increased DNAm age even in PWH with viral suppression. However, the Dunedin ‘pace of aging’ measure was not faster in these individuals, suggesting that biological aging is stabilized by antiviral therapy. Several DNAm clocks were correlated with older-appearing brain structure, suggesting that DNAm age reflects neurological health. More research is needed to understand the mechanisms linking altered DNAm in leukocytes to brain structural phenotypes, and potentially to neurocognitive impairment.