Interindividual Epigenetic Variation at Birth and Subsequent Risk of Dysbiosis and NEC

PROJECT SUMMARY Necrotizing enterocolitis (NEC) is a devastating intestinal morbidity of preterm infants preceded by microbial dysbiosis and intestinal necrosis. But even after decades of research, the etiopathogenesis is still unclear. The gut epigenome-microbiome axis may determine the phenotype that predisposes to NEC but studying epigenetic variation in the gut is difficult to do non-invasively. Focusing on genomic regions that display systemic interindividual variation in DNA methylation (CoRSIVs) therefore offers great promise. The systemic nature of these stable epigenetic variations means that measuring CoRSIV methylation in blood DNA provides information about epigenetic regulation throughout the body. CoRSIVs are essentially epigenetic polymorphisms, which have been linked to human disease including immune disorders and cancer. The role of CoRSIVs in NEC and preterm pathophysiology has not been investigated. Our overall hypothesis is that interindividual variation in CoRSIV methylation, which is established in the early embryo and maintained in various tissue lineages during differentiation, influences the development of the intestinal microbiome (including microbial dysbiosis) leading to intestinal inflammation and necrosis in NEC. We intend to test our hypothesis by 2 specific aims. Aim 1. Among preterm neonates, determine if CoRSIV methylation in peripheral blood at birth is associated with subsequent diagnosis of NEC. In a pilot nested case-control study design, we have enrolled preterm infants (< 32 weeks or born at < 1500 g) and collected stool and blood samples every week for 4 weeks (11 NEC patients and 22 gestational age matched controls). We will investigate CoRSIVs in peripheral blood leukocytes and perform whole genome sequencing for methylation quantitative loci (mQTL) effects at CoRSIVs. Aim 2: In preterm infants, determine if blood leukocyte CoRSIVs methylation at birth associates with subsequent development of stool microbiome diversity and microbial composition. Animal data supports the hypothesis that individual variation in DNA methylation informs the development of the diversity and composition of the stool microbiome. We will correlate stool microbiome in the first 4 weeks, evaluated by metagenomics with blood leukocyte CoRSIVs methylation at birth. We propose an innovative DNA methylation profiling approach to investigate the role of interindividual epigenetic variation in the pathophysiology of NEC in preterm infants. Our high risk- high reward approach opens the door to a new area of research in preterm infants that has the potential to inform novel preventive strategies, which improve clinical outcomes. The novel data generated in the proposal will seed a future R01 proposal with a large multi-center study and mechanistic studies in organoid models and germ free mice. New knowledge on epigenetic influences on microbiome development is relevant to a broad-spectrum of diseases such as cancer, infection, immunity and growth