Epigenome-wide association study in a large admixture cohort reveals immune and stress response epigenetic alterations in cocaine use disorder

Abstract Cocaine use disorder (CUD) is frequently accompanied by tobacco use, polysubstance exposure and traumatic life events, complicating the interpretation of peripheral epigenetic signatures. We conducted a large epigenome-wide association study of CUD in peripheral blood DNA from 1,250 Brazilian adults, including 563 individuals with CUD and 687 non-using controls. After adjustment for technical factors, ancestry-related methylation structure, sex, age and estimated blood cell composition, 34 CpGs reached epigenome-wide significance (p < 9 × 10⁻⁸), and 79 top-ranked DMPs met FDR < 0.005. Most DMPs showed lower methylation in CUD and included loci annotated to AHRR, FKBP5, SOCS3, RARA and ELMSAN1. Enrichment analyses of hypomethylated DMP-associated genes converged on cytokine/interferon signaling, JAK–STAT regulation, platelet activation, endocytosis, focal adhesion and MAPK/Rap1/PI3K-Akt pathways, indicating a peripheral immune-inflammatory and cell-remodeling methylation profile. Within the CUD group, nicotine sensitivity analysis identified 78 nicotine-associated CpGs, only 12 of which overlapped with CUD-associated DMPs, suggesting that tobacco exposure explains a biologically expected subset, but not the majority, of the CUD methylation signal. Trauma burden and polysubstance-use histories explained partially distinct methylation components, with FKBP5 linked to trauma-associated variance. Blood–brain analyses showed limited global portability but locus-specific convergence in postmortem BA9 for selected CpGs. These findings identify a predominantly hypomethylated peripheral methylation profile in CUD shaped by nicotine exposure, trauma, polysubstance use and immune-stress regulation.