Background: Multiple genetic and environmental factors interact to determine the risk and trajectory of cocaine dependence, and the expression of addiction-associated genes is likely influenced by environmental factors that leave persistent epigenetic marks on an individual’s genome. Recently, several studies have identified epigenetic mechanisms that are associated with the acquisition of compulsive drug seeking in animal models, but little is known about the role of epigenetics in human cocaine dependence. Of particular interest is DNA methylation as it represents a mitotically stable mark that has been shown to be altered by environmental experience.

Objective: To identify DNA methylation associated with chronic cocaine abuse in humans, in two dopamine dependent brain regions, the dorsal and ventral striatum.

Methods: We used Reduced Representation Bisulfite Sequencing (RRBS) on nucleus accumbens and caudate tissue from 25 dependent cocaine users and 25 drug-free and age-matched controls to detect genome-wide methylation profiles. RRBS is a high throughput sequencing based approach, which enriches for CpG dinucleotides and generates methylation data at base- pair resolution.

Results: This technique identified differentially methylated CpGs between groups and brain areas. All RRBS libraries contained more than 4 million reads at 10X coverage and over 65% of reads in each library were aligned to the human genome. In addition, all libraries were bisulfite converted with over 98% efficiency. Our analyses, corrected for multiple covariates, identified regions of hyper- and hypomethylation that are associated with transcriptional dysregulation in cases versus controls, in both brain areas.

Impact: High throughput discovery of cocaine-associated networks and pathways allow us to investigate the epigenetic changes in brain that accompany the transition from cocaine abuse to chronic cocaine dependence.

Funded by a grant NIDA (DA033684).