The DNA methylation signature of smoking: an archetype for the identification of biomarkers for behavioral illness

Abstract

Smoking is perhaps the foremost public health challenge in the United States and in the world. In a series of rapidly emerging studies, we and others have demonstrated that cigarette smoking is associated with changes in the DNA methylation signature of peripheral blood cells. The changes associated with this type of substance use are both dose and time dependent. These changes in DNA methylation are also accompanied by changes in gene transcription and protein expression whose patterns are furthermore indicative of increased vulnerability to other forms of complex illness. In the past, our efforts to translate this knowledge into actionable information has been stymied by a lack of methods through which to systematically to assess these changes. The rapid advance of DNA methylation assessment technologies changes that dynamic and presents the possibility that methylation-based clinical tools to aid the ascertainment of smoking status or effectiveness of treatment can be developed. In this chapter, we will review the latest advances in this field and discuss how these advances allow us insight as to methods through which to prevent smoking and shed insight into optimizing strategies through which to identify biomarkers for other behavioral illnesses which share similar contributions from environmental and gene- environmental interaction effects.

Figure 1

The link between genome methylation and decreased gene expression. DNA methylation is mediated by a family of proteins referred to as DNA Methyltransferases (DNMT 1, 3A, 3B and 3L), Depending on cellular context, these DNMT can transfer methyl groups from methyl donors to CpG residues throughout the genome, including in promoter associated CpG islands. Areas with increased amounts of methylation then attracts a cascade of other proteins, which in turn bundle DNA into tightly packed, transcriptionally inactive chromatin resulting in decreased gene expression from that region.

Figure 2

The role of AHRR in moderating activity in the xenobiotic detoxification pathway. In the unstimulated state, the aryl hydrocarbon receptor (AHR) is found in the cytoplasm bound to a dimer of heat shock proteins (HSP90) and a small group of auxiliary proteins. Poly aromatic hydrocarbons (PAH) and dioxins from cigarette smoke activate the xenobiotic pathway by diffusing into the cell and binding to the PAH domain of AHR. This causes a disassociation of AHR from its binding partners and in turn, heterodimerization with the aryl hydrocarbon receptor nuclear translocator (ARNT). This dimer pair is then transported into the nucleus where it binds to 5 bp DNA motif found immediately upstream of the translation start site of genes critical to the catabolism of xenobiotics. AHRR, whose transcription is induced by AHR, provides negative feedback by competing with AHR for ARNT and by sterically blocking access of AHR to critical xenobiotic pathway genes.

Figure 3

The dose and chronological dependency of DNA methylation at AHRR residue cg05575921 as a function of smoking in three cohorts of subjects age 19 (n=181), 22 (n=107) and 50 years old (n=111). As individuals continue to smoke the difference between methylation at this locus continues to grow from approximately 6% in the 19 year olds to over 15% in the 50-year-old subjects. Please also note that the average methylation at this locus continues to decrease even in non-smokers.