Gene × environment interaction by a longitudinal epigenome-wide association study (LEWAS) overcomes limitations of genome-wide association study (GWAS)

Abstract

The goal of genome-wide association studies is to identify SNPs unique to disease. It usually involves a single sampling from subjects' lifetimes. While primary DNA sequence variation influences gene-expression levels, expression is also influenced by epigenetics, including the 'somatic epitype' (G(SE)), an epigenotype acquired postnatally. While genes are inherited, and novel polymorphisms do not routinely appear, G(SE) is fluid. Furthermore, G(SE) could respond to environmental factors (such as heavy metals) and to differences in exercise, maternal care and dietary supplements - all of which postnatally modify oxidation or methylation of DNA, leading to altered gene expression. Change in epigenetic status may be critical for the development of many diseases. We propose a 'longitudinal epigenome-wide association study', wherein G(SE) are measured at multiple time points along with subjects' histories. This Longitudinal epigenome-wide association study, based on the 'dynamic' somatic epitype over the 'static' genotype, merits further investigation.

Figure 1. Comparison of the genome-wide association study (surveying genes) and other end point association assays versus the longitudinal epigenome/envirome-wide association study (measuring somatic epitype over time)

(A) Kinetic workflow of LEWAS. Expression of a gene or genes that are ‘pathogenic’ is schematically indicated by the line graph. This model presumes a ‘disease of excess’. However, a ‘disease of defciency’ could also be accounted for. Before an epigenetic event, GWAS would show alleles of genes while LEWAS would show somatic epitypes in a ‘fundamental’ state. After an H₁ that could occur before a specific developmental threshold, such as formation of the blood–brain barrier in early life, GWAS would show genes in the same state as before, while LEWAS would indicate a somatic epitype or epitypes have been altered. After (possibly optional) H_n and a final H_T, which leads to disease state, GWAS would still show genes in the same state as when there was no pathology, except for disorders associated with somatic mosaic mutations, while LEWAS would show changes in somatic epitypes corresponding to disease state. Detecting the changes over time would be critical to determining which somatic epitypes are important for a given disease. (B–E) Comparison of LEWAS versus other assays, highlighting specific elements of ‘organism’/biological substrate and ‘environment’ addressed by each. (B) GWAS. The genome is directly measured. Environmental input and epigenetic status are ignored: ‘genotype determines phenotype’. (C) EgWAS. Epigenomic status is directly measured. Genomic variation is measured or inferred. Environmental effects are inferred as contributing to epigenetic status. Single-time epigenotype determines phenotype. (D) EWAS. Chemical and biochemical traces of specific suspected exposures are directly measured. Environmental effects are partially inferred from circulating (bio)chemicals. Genomic and epigenomic effects might be partially inferred. Current (nonlatent) single-time evidence of past exposures correlates with phenotype. (E) LEWAS. Genomic analysis is combined with measuring epigenetic (oxidomic, methylomic, hydroxymethylomic and histone) status and ‘exposure’, which includes chemicals, previous infections and social influences. Sampling is performed at more than one time point to detect specific changes in an individual that correlate with disease state rather than indirectly infer such changes by comparing currently healthy with currently affected individuals. Changes in the somatic epitype lead to changes in phenotype, including idiopathic disorders. EgWAS: Epigenome-wide association study; EWAS: Environment-wide association study; G_SE: Somatic epitype; GWAS: Genome-wide association study; Hit₁: Initial hit; Hit_n: Intermediate hit; Hit_T: Triggering hit; LEWAS: Longitudinal epigenome/envirome-wide association study.