DNA methylation variants in young adult offspring exposed to famine during postnatal life in Bangladesh

Abstract

BackgroundDevelopmental programming via exposure to malnutrition suggests windows of susceptibility during periconceptual, in-utero, and postnatal periods, and might contribute to the missing heritability of complex disease. Metastable epialleles in offspring exposed to periconceptual nutritional deficiency have been identified, as have trimester-specific and sex-specific epigenetic effects. Methylation variation from postnatal exposure to famine has not been described. We aimed to identify whether Bangladeshi adults exposed to famine in utero or in postnatal life display DNA methylation variation compared with those unexposed, on a genome-wide scale or at previously described metastable epialleles. MethodsWe studied a cross-sectional cohort of adults (27–32 years old) exposed to severe famine during 1974–75 in Matlab, Bangladesh. Whole blood DNA was bisulphite converted and hybridised to the Illumina 450k methylation array to access genome-wide DNA methylation. Normalised data were analysed with the limma package and methylation variable positions (MVPs) were identified in two-way group comparisons (t test, leave-one-out cross-validation). Pathway analysis was done with GOstats. Replication of metastable epialleles was done with targeted bisulphite pyrosequencing. Samples were obtained with written consent, under ethics approval and a Material Transfer Agreement. Findings78 participants were included (25 exposed in utero, 29 exposed in postnatal life, and 24 unexposed). Samples from 55 individuals were used for validation. MVPs were identified in the two-way comparisons of postnatal exposure versus unexposed (n=2122), and in-utero exposure versus unexposed (n=1454) but did not reach genome-wide significance. Consistent directionality of methylation difference at MVPs in postnatal exposure versus unexposed was observed in validation samples (r2=0·69, p<0·05). Gene ontology analysis of MVPs suggests their role in growth factor signalling pathways. Preliminary analysis of targeted replication at metastable epialleles on all samples (n=133) showed methylation differences at PAX8 and ZFYVE28 across at least five adjacent CpG sites according to in-utero and postnatal exposure. InterpretationOur data identified DNA methylation differences in young Bangladeshi adults exposed to famine in the postnatal period with putative roles in regulation of growth factor signalling. Preliminary replication using previously described metastable epialleles is reassuring, but requires further analysis. Larger sample sizes are required to control for multiple testing biases and false discovery. Future studies should incorporate the postnatal window of exposure, longitudinal sampling and intervention to establish causation over association, and primary aetiological over secondary pathophysiological epigenomic differences. FundingUK Medical Research Council.