Association of prenatal exposure to opioids, cannabis, and polysubstance use with cord blood DNA methylation patterns in a multiancestry cohort.

Blood DNA methylation patterns are highly predictive of prenatal exposure to smoking, and differential methylation has been associated with maternal alcohol use. We extended this to determine whether DNA methylation patterns in cord blood are associated with prenatal exposure to opioids, cannabis, and polysubstance use. We also evaluated whether DNA methylation patterns have predictive utility. We examined 932 mother-child pairs in the Boston Birth Cohort between 1998 and 2020 with cord blood DNA methylation data. For each substance self-reported within 72 hr after birth, we performed an adjusted linear regression analysis at 865,859 CpG sites to identify related methylation differences. We generated polyepigenetic scores using summary statistics for each exposure and assessed predictive ability using cross-validation and receiver operating characteristic curves. Specificity of methylation associations was evaluated by assessing overlap across exposure summary statistics and using logistic regression for methylation scores, adjusted for concurrent use. We identified methylation changes at 72, 21, and 1 CpG suggestively associated with prenatal exposure to opioids, cannabis, and polysubstance use, respectively (p < 1e-6), in cord blood, reported for the first time for these exposures. We identified two loci associated at epigenome-wide significance with opioids and one with polysubstance use (p < 1e-8). Methylation scores were highly predictive and exposure-specific, with area under the curve accuracy of 91% for opioids, 90% for cannabis, and 93%-98% depending on polysubstance number. These CpGs provide biologic insights for reducing the impact of substance exposure, and these findings may serve as a biomarker of prenatal substance exposure for future studies and potential clinical utility.