Genome-wide DNA methylation differences in nucleus accumbens of smokers vs. nonsmokers

Abstract

Numerous DNA methylation (DNAm) biomarkers of cigarette smoking have been identified in peripheral blood studies, but their relevance as neurobiological indicators is unknown due to DNAm tissue-specificity. In contrast, blood-based studies may not detect brain-specific smoking-related DNAm differences that may provide greater insight into the neurobiology of smoking behaviors. We report the first epigenome-wide association study (EWAS) of smoking in human postmortem brain, focusing on nucleus accumbens (NAc) as a key brain region in developing addiction. Following Illumina HumanMethylation EPIC array data generation and quality control, 221 decedents ( 120European American [23% current smokers], 101 African American [26% current smokers]) were analyzed. DNAm by smoking (current vs. nonsmoking) was tested using robust linear regression models adjusted for age, sex, cell-type proportion, DNAmderived negative control principal components (PCs), and genotype-derived PCs.Separate ancestry-specific results were combined via meta-analysis, resulting in 7CpGs that exceeded false discovery rate (FDR)<0.05. Using published smoking EWAS results in blood, we extended our NAc findings to identify DNAm smoking effects that are unique (tissue-specific) versus shared between tissues (tissue-shared). Of the 7CpGs identified in NAc, 3 CpGs were located near genes previously indicated with blood-based smoking DNAm biomarkers: ZIC1, ZCCHC24, and PRKDC. The other 4 CpGs are novel for smoking-related DNAm changes: ABLIM3, APCDD1L, MTMR6, and CTCF. Our results provide the first evidence for smoking-related DNAm changes in human NAc, highlighting CpGs that were previously undetected as peripheral biomarkers and may reflect brain-specific processes.

Genetics of substance use disorders: a review

“…For example, Kapoor et al ( 2019 ) performed differential gene expression analysis on prefrontal cortex tissue from 65 AUD cases and 73 controls, identifying relevant genes and molecular pathways including upregulation of pathways related to immune responses. Markunas et al ( 2020 ) conducted the first epigenome-wide association study (EWAS) of smoking in human post-mortem brain tissue (specifically the nucleus accumbens); they identified seven DNA methylation (DNAm) biomarkers, three of which were located near genes previously implicated as blood-based DNAm biomarkers of smoking and four of which were novel ( ABLIM3 , APCDD1L , MTMR6 , and CTCF ). Another recent study (Marees et al, 2020 a ) used GTEx (Genotype-Tissue Expression; Ardlie et al, 2015 ) data to assess the role of eQTLs in six substance use traits; using this approach, they identified novel loci not identified in the original GWAS for five of the traits.…”

“…There is a need for more SUD-specific tissue samples. Evidence from Kapoor et al ( 2019 ) and the Markunas et al ( 2020 ) EWAS further highlight the importance of examining both brain and other tissues (e.g. blood, liver) in substance-specific studies: drugs can have peripheral effects, but brain-specific biomarkers may provide greater insight into the neurobiological effects of substance exposure.…”

Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods

“…For example, cocaine exposure was found to increase DNA methylation, decrease CTCF binding, and inhibit the three-dimensional looping interaction between the Auts2 and Caln1 genes in mouse nucleus accumbens, which was associated with D2-MSN-specific upregulation of Auts2 [ 124 ]. In addition, a smoking-related DNA methylation change was found near the CTCF locus in postmortem NAc tissue [ 125 ]. Our identification of CTCF motif enrichment in NAc D2-MSN-specific UMRs and the recognition of an “alcoholism” pathway within the same UMR category suggests D2-MSN-specific interplay between DNA methylation and higher order chromatin architecture in addiction [ 122 ].…”

TNRC6C Functions as a Tumor Suppressor and Is Frequently Downregulated in Papillary Thyroid Cancer

“…The expression of MMP14 was found significantly increased in thyroid tumor cell lines and PTC samples [ 42 , 43 ] and was associated with the invasiveness of thyroid cancer [ 44 ]. APCDD1L was found to be associated with aortic diseases [ 45 ] and smoking-related DNA methylation in nucleus accumbens [ 46 ], but its effect on cancers was never reported.…”