Meeshanthini V. Dogan

The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women

BackgroundRegular smoking is associated with a wide variety of syndromes with prominent inflammatory components such as cancer, obesity and type 2 diabetes. Heavy regular smoking is also associated with changes in the DNA methylation of peripheral mononuclear cells. However, in younger smokers, inflammatory epigenetic findings are largely absent which suggests the inflammatory response(s) to smoking may be dose dependent. To help understand whether peripheral mononuclear cells have a role in mediating these responses in older smokers with higher cumulative smoke exposure, we examined genome-wide DNA methylation in a group of well characterized adult African American subjects informative for smoking, as well as serum C-reactive protein (CRP) and interleukin-6 receptor (IL6R) levels. In addition, complementary bioinformatic analyses were conducted to delineate possible pathways affected by long-term smoking.ResultsGenome-wide DNA methylation analysis with respect to smoking status yielded 910 significant loci after Benjamini-Hochberg correction. In particular, two loci from the AHRR gene (cg05575921 and cg23576855) and one locus from the GPR15 gene (cg19859270) were identified as highly significantly differentially methylated between smokers and non-smokers. The bioinformatic analyses showed that long-term chronic smoking is associated with altered promoter DNA methylation of genes coding for proteins mapping to critical sub-networks moderating inflammation, immune function, and coagulation.ConclusionsWe conclude that chronic regular smoking is associated with changes in peripheral mononuclear cell methylation signature which perturb inflammatory and immune function pathways and may contribute to increased vulnerability for complex illnesses with inflammatory components.

Current and Future Prospects for Epigenetic Biomarkers of Substance Use Disorders

Substance abuse has an enormous impact on economic and quality of life measures throughout the world. In more developed countries, overutilization of the most common forms of substances of abuse, alcohol and tobacco, is addressed primarily through prevention of substance use initiation and secondarily through the treatment of those with substance abuse or dependence. In general, these therapeutic approaches to substance abuse are deemed effective. However, there is a broad consensus that the development of additional tools to aid diagnosis, prioritize treatment selection and monitor treatment response could have substantial impact on the effectiveness of both substance use prevention and treatment. The recent demonstrations by a number of groups that substance use exposure is associated with robust changes in DNA methylation signatures of peripheral blood cells suggests the possibility that methylation assessments of blood or saliva could find broad clinical applications. In this article, we review recent progress in epigenetic approaches to substance use assessment with a particular emphasis on smoking (and alcohol) related applications. In addition, we highlight areas, such as the epigenetics of psychostimulant, opioid and cannabis abuse, which are markedly understudied and could benefit from intensified collaborative efforts to define epigenetic biomarkers of abuse and dependence.

Differential impact of cumulative SES risk on methylation of protein-protein interaction pathways as a function of SLC6A4 genetic variation in African American young adults.

Exposure to cumulative SES risk in childhood may interact with variability at the serotonin transporter linked polymorphic region (5HTTLPR) to alter DNA methylation across interacting sets of proteins. DNA was obtained from 388 African Americans at age 19. Genotype at the 5HTTLPR was determined, and methylation ratios for C-phosphate-G (CpG) residues were assessed. Exposure to cumulative SES risk was determined using repeated parental reports at ages 11-13. At high SES risk, CpG methylation patterns indicated altered cellular stress response in women, but not men, who carried a short allele at the 5HTTLPR. These changes in methylation patterns may lead to increases in mental and physical health risks. No genotype effect emerged for either women or men at low SES risk. Methylation patterns provide guidance in identifying pathways by which genetic susceptibility is transformed into adverse outcomes years later.

Methylomic Aging as a Window onto the Influence of Lifestyle: Tobacco and Alcohol Use Alter the Rate of Biological Aging.

To examine the effect of the relationship between alcohol and cigarette consumption on biological aging using deoxyribonucleic acid methylation‐based indices.

Ethnicity and Smoking-Associated DNA Methylation Changes at HIV Co-Receptor GPR15

Smoking is associated with poorer health outcomes for both African and European Americans. In order to better understand whether ethnic-specific genetic variation may underlie some of these differences, we compared the smoking-associated genome-wide methylation signatures of African Americans with those of European Americans, and followed up this analysis with a focused examination of the most ethnically divergent locus, cg19859270, at the GPR15 gene. We examined the association of methylation at this locus to the rs2230344 SNP and GPR15 gene and protein expression. Consistent with prior analyses, AHRR residue cg05575921 was the most differentially methylated residue in both African Americans and European Americans. However, the second most differentially methylated locus in African Americans, cg19859270, was only modestly differentially methylated in European Americans. Interrogation of the methylation status of this CpG residue found in GPR15, a chemokine receptor involved in HIV pathogenesis, showed a significant interaction of ethnicity with smoking as well as a marginal effect of genotype at rs2230344, a neighboring non-synonymous SNP, but only among African Americans. Gene and protein expression analyses showed that demethylation at cg19859270 was associated with an increase in both mRNA and protein levels. Since GPR15 is involved in the early stages of viral replication for some HIV-1 and HIV-2 isolates, and the prevalence of HIV is increased in African Americans and smokers, these data support a possible role for GPR15 in the ethnically dependent differential prevalence of HIV.

Alcohol and tobacco consumption alter hypothalamic pituitary adrenal axis DNA methylation.

Alcohol and cigarette consumption have profound effects on genome wide DNA methylation and are common, often cryptic, comorbid features of many psychiatric disorders. This cryptic consumption is a possible impediment to understanding the biology of certain psychiatric disorders because if the effects of substance use are not taken into account, their presence may confound efforts to identify effects of other behavioral disorders. Since the hypothalamic pituitary adrenal (HPA) axis is known to be dysregulated in these disorders, we examined the potential for confounding effects of alcohol and cigarette consumption by examining their effects on peripheral DNA methylation at two key HPA axis genes, NR3C1 and FKBP5. We found that the influence of alcohol and smoke exposure is more prominent at the FKBP5 gene than the NR3C1 gene. Furthermore, in both genes, loci that were consistently significantly associated with smoking and alcohol consumption demethylated with increasing exposure. We conclude that epigenetic studies of complex disorders involving the HPA axis need to carefully control for the effects of substance use in order to minimize the possibility of type I and type II errors.

Higher levels of protective parenting are associated with better young adult health: exploration of mediation through epigenetic influences on pro-inflammatory processes

The current investigation was designed to examine the association of parenting during late childhood and early adolescence, a time of rapid physical development, with biological propensity for inflammation. Based on life course theory, it was hypothesized that parenting during this period of rapid growth and development would be associated with biological outcomes and self-reported health assessed in young adulthood. It was expected that association of parenting with health would be mediated either by effects on methylation of a key inflammatory factor, Tumor necrosis factor (TNF), or else by association with a pro-inflammatory shift in the distribution of mononuclear blood cells. Supporting expectations, in a sample of 398 African American youth residing in rural Georgia, followed from age 11 to age 19, parenting at ages 11–13 was associated with youth reports of better health at age 19. We found that parenting was associated with changes in TNF methylation as well as with changes in cell-type composition. However, whereas methylation of TNF was a significant mediator of the association of parenting with young adult health, variation in mononuclear white blood cell types was not a significant mediator of the association of parenting with young adult health. The current research suggests the potential value of examining the health-related effects of parenting in late childhood and early adolescence. Further examination of protection against pro-inflammatory tendencies conferred by parenting appears warranted.

Genetically contextual effects of smoking on genome wide DNA methylation

Smoking is the leading cause of death in the United States. It exerts its effects by increasing susceptibility to a variety of complex disorders among those who smoke, and if pregnant, to their unborn children. In prior efforts to understand the epigenetic mechanisms through which this increased vulnerability is conveyed, a number of investigators have conducted genome wide methylation analyses. Unfortunately, secondary to methodological limitations, these studies were unable to examine methylation in gene regions with significant amounts of genetic variation. Using genome wide genetic and epigenetic data from the Framingham Heart Study, we re‐examined the relationship of smoking status to genome wide methylation status. When only methylation status is considered, smoking was significantly associated with differential methylation in 310 genes that map to a variety of biological process and cellular differentiation pathways. However, when SNP effects on the magnitude of smoking associated methylation changes are also considered, cis and trans‐interaction effects were noted at a total of 266 and 4353 genes with no marked enrichment for any biological pathways. Furthermore, the SNP variation participating in the significant interaction effects is enriched for loci previously associated with complex medical illnesses. The enlarged scope of the methylome shown to be affected by smoking may better explicate the mediational pathways linking smoking with a myriad of smoking related complex syndromes. Additionally, these results strongly suggest that combined epigenetic and genetic data analyses may be critical for a more complete understanding of the relationship between environmental variables, such as smoking, and pathophysiological outcomes.

MTHFR methylation moderates the impact of smoking on DNA methylation at AHRR for African American young adults

Smoking has been shown to have a large, reliable, and rapid effect on demethylation of AHRR, particularly at cg05575921, suggesting that methylation may be used as an index of cigarette consumption. Because the availability of methyl donors may also influence the degree of demethylation in response to smoking, factors that affect the activity of methylene tetrahydrofolate reductase (MTHFR), a key regulator of methyl group availability, may be of interest. In the current investigation, we examined the extent to which individual differences in methylation of MTHFR moderated the association between smoking and demethylation at cg05575921 as well as at other loci on AHRR associated with a main effect of smoking. Using a discovery sample (AIM, N = 293), and a confirmatory sample (SHAPE, N = 368) of young adult African Americans, degree of methylation of loci in the first exon of MTHFR was associated with amplification of the association between smoking and AHRR demethylation at cg05575921. However, genetic variation at a commonly studied MTHFR variant, C677T, did not influence cg05575921 methylation. The significant interaction between MTHFR methylation and the smoking‐induced response at cg05575921 suggests a role for individual differences in methyl cycle regulation in understanding the effects of cigarette consumption on genome wide DNA methylation.

A pilot investigation of the impact of smoking cessation on biological age

BACKGROUND AND OBJECTIVES Smoking is known to increase biological age. However, whether this process is reversible through smoking cessation is not known. In this pilot study, we attempt to determine whether smoking cessation reduces biological age. METHODS We conducted regression analyses of methylation data from 22 subjects, as they entered and exited inpatient substance use treatment, to determine change in biological age, as indicated by the deviation of their methylomic age from chronological age across two time points. RESULTS We found that, as compared to those subjects who did not stop smoking, subjects who significantly decreased their smoking consumption over a 1 month time period exhibited a marked reduction in methylomic age. CONCLUSION The rapid and substantial reversal of accelerated aging associated with successful smoking cessation suggests that it can reverse well-known smoking effects on methylomic aging. This preliminary finding can be readily examined in other, larger data sets, and if replicated, this observation may provide smokers with yet another good reason to quit smoking. SCIENTIFIC SIGNIFICANCE Successful smoking cessation makes patients appear biologically younger than they were at baseline, and to do so quite rapidly. In todays youth driven society, our observations may serve as a powerful impetus for some to quit smoking. (Am J Addict 2017;26:129-135).