Structural and functional changes of the brain are assumed to contribute to excessive cocaine intake, craving, and relapse in cocaine use disorder (CUD). Epigenetic and transcriptional changes were hypothesized as a molecular basis for CUD-associated brain alterations. Here we performed a multi-omics study of CUD by integrating epigenome-wide methylomic (N=42) and transcriptomic (N=25) data from the same individuals using postmortem brain tissue of Brodmann Area 9 (BA9). Of the N=1,057 differentially expressed genes (p<0.05), one gene, ZFAND2A, was significantly upregulated in CUD at transcriptome-wide significance (q<0.05). Differential alternative splicing (AS) analysis revealed N=98 alternatively spliced transcripts enriched in axon and dendrite extension pathways. Strong convergent overlap in CUD-associated expression deregulation was found between our BA9 cohort and independent replication datasets. Epigenomic, transcriptomic, and AS changes in BA9 converged at two genes, ZBTB4 and INPP5E. In pathway analyses, synaptic signaling, neuron morphogenesis, and fatty acid metabolism emerged as the most prominently deregulated biological processes. Drug repositioning analysis revealed glucocorticoid receptor targeting drugs as most potent in reversing the CUD expression profile. Our study highlights the value of multi-omics approaches for an in-depth molecular characterization and provides insights into the relationship between CUD-associated epigenomic and transcriptomic signatures in the human prefrontal cortex.

The authors have declared no competing interest.

Funding supporting this study was provided by the German Federal Ministry of Education and Research (BMBF) within the e:Med research program SysMedSUDs: "A systems-medicine approach toward distinct and shared resilience and pathological mechanisms of substance use disorders" (01ZX01909 to R.S., M.R., A.C.H., and S.H.W.). In addition, by the Deutsche Forschungsgemeinschaft (DFG) through the collaborative research centre TRR265: "Losing and Regaining Control over Drug Intake" (Project ID 402170461 to S.H.W., R.S., A.C.H. and M.R.), the Hetzler Foundation for Addiction Research (to A.C.H.), the ERA-NET program: Psi-Alc (01EZ1908), Spanish Ministerio de Ciencia, Innovacion y Universidades (PID2021-1277760B-I100, to B.C.), Generalitat de Catalunya/AGAUR (2021-SGR-01093, to B.C.), ICREA Academia 2021, Fundacio La Marato de TV3 (202218-31, to B.C.) and from Ministerio de Sanidad, Servicios Sociales e Igualdad/Plan Nacional Sobre Drogas (PNSD-2020I042, to N.F.-C.). The project has been carried out using the Mannheim (CIMH) infrastructure of the German Center for Mental Health (DZPG).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Postmortem human brain tissue was obtained from the Douglas Bell Canada Brain Bank where tissue sampling is performed based on their established ethical guidelines. Our multi-omics study was approved by the Ethics Committee II of the University of Heidelberg, Medical Faculty Mannheim, Germany, under the register number 2021-681.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Raw methylation data is deposited in the European Genome Phenome Archive (EGA) under accession number EGAS00001006828 (https://ega-archive.org/studies/EGAS00001006826). RNA-sequencing data has been uploaded to the EGA will be listed with an accession number by the time of publication.