DNA methylation in cocaine use disorder–An epigenome-wide approach in the human prefrontal cortex

Abstract

BackgroundCocaine use disorder (CUD) is characterized by a loss of control over cocaine intake and is associated with structural, functional, and molecular alterations in the human brain. At the molecular level, epigenetic alterations are hypothesized to contribute to the higher-level functional and structural brain changes observed in CUD. Most evidence of cocaine-associated epigenetic changes comes from animal studies while only a few studies have been performed using human tissue.MethodsWe investigated epigenome-wide DNA methylation (DNAm) signatures of CUD in human post-mortem brain tissue of Brodmann area 9 (BA9). A total of N = 42 BA9 brain samples were obtained from N = 21 individuals with CUD and N = 21 individuals without a CUD diagnosis. We performed an epigenome-wide association study (EWAS) and analyzed CUD-associated differentially methylated regions (DMRs). To assess the functional role of CUD-associated differential methylation, we performed Gene Ontology (GO) enrichment analyses and characterized co-methylation networks using a weighted correlation network analysis. We further investigated epigenetic age in CUD using epigenetic clocks for the assessment of biological age.ResultsWhile no cytosine-phosphate-guanine (CpG) site was associated with CUD at epigenome-wide significance in BA9, we detected a total of 20 CUD-associated DMRs. After annotation of DMRs to genes, we identified Neuropeptide FF Receptor 2 (NPFFR2) and Kalirin RhoGEF Kinase (KALRN) for which a previous role in the behavioral response to cocaine in rodents is known. Three of the four identified CUD-associated co-methylation modules were functionally related to neurotransmission and neuroplasticity. Protein-protein interaction (PPI) networks derived from module hub genes revealed several addiction-related genes as highly connected nodes such as Calcium Voltage-Gated Channel Subunit Alpha1 C (CACNA1C), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), and Jun Proto-Oncogene, AP-1 Transcription Factor Subunit (JUN). In BA9, we observed a trend toward epigenetic age acceleration (EAA) in individuals with CUD remaining stable even after adjustment for covariates.ConclusionResults from our study highlight that CUD is associated with epigenome-wide differences in DNAm levels in BA9 particularly related to synaptic signaling and neuroplasticity. This supports findings from previous studies that report on the strong impact of cocaine on neurocircuits in the human prefrontal cortex (PFC). Further studies are needed to follow up on the role of epigenetic alterations in CUD focusing on the integration of epigenetic signatures with transcriptomic and proteomic data.

Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder

“…c Integrated visualization of functional genomic datasets for ZBTB4 and INPP5E gene loci. CUD-associated genomic variants (SNPs p<0.05 from 30 ), CUD-associated CpG sites (p<0.05 from 22 ), RNA-seq data and intron clusters (q<0.05) from the present study were visualized together with ENCODE ChIP-seq data for different chromatin marks in human dorsolateral prefrontal cortex.…”

“…Convergence of CUD association signals at the pathway level was evaluated by pathway enrichment analysis for GO terms using the enrichGO function on the GO "BP" ontology in the compareCluster functionality of clusterProfiler. A total of 10 gene lists were included in the input dataset: 1) CUDassociated CpG sites (N=394, p>0.001) from the EWAS of CUD 22 , genes in the CUD-associated WGCNA methylation modules 2) blue (N=9,201), 3) steelblue (N=390), 4) brown (N=5,268), 5) brown4 (N=205), 6) nominally significant DEGs (N=1,057,p<0.05), 7) genes in the CUD-associated WGCNA expression module yellow (N=2,517), 8) AS genes (N=98, q<0.05), 9) MOFA methylation weights factor…”

“…CUD-associated co-expression networks were enriched for GTPase signaling and neurotransmitter secretion. Regarding epigenomic alterations in the PFC, we were previously able to identify 20 CUD-associated DMRs in Brodmann Area 9, a subregion of the PFC, and further detected that co-methylation networks in CUD were enriched for synaptic signaling processes 22 .…”

“…CUD-associated co-expression networks were enriched for GTPase signaling and neurotransmitter secretion. Regarding epigenomic alterations in the PFC, we were previously able to identify 20 CUD-associated DMRs in Brodmann Area 9, a subregion of the PFC, and further detected that co-methylation networks in CUD were enriched for synaptic signaling processes 22 . Although epigenetics represents an important regulatory mechanism for transcription, the co-regulation of DNAm and gene expression in the same brain samples has not yet been investigated in CUD, limiting the comparability of results between epigenetic and gene expression studies.…”

Divergent gene expression patterns in alcohol and opioid use disorders lead to consistent alterations in functional networks within the Dorsolateral Prefrontal Cortex

“…Moreover, just as this study aimed to expand upon and explore the current understanding of the genetic underpinnings of SUD by utilizing transcriptomics, epigenomics offers a way to examine factors influencing alterations in the transcriptome. Research has begun to examine candidate genes of SUD that have been identified in GWAS for potential post-translational modifications [59, 60, 61, 62]. By investigating epigenetic mechanisms, such as methylation, acetylation, histone modifications, and chromosome remodeling, to name a few, we may be able to identify molecular mechanisms that drive changes in gene transcription and lead to aberrant neuroadaptations and circuitry seen in SUD.…”