Non-invasive analysis of methylated cell free DNA in necrotizing enterocolitis

Project Summary/Abstract
Necrotizing enterocolitis (NEC) is a devastating complication of prematurity that develops suddenly and carries
significant morbidity and a high mortality rate for which no biomarkers exist. The high mortality rate seen in NEC
could likely be prevented if there was a screening method that permitted early disease detection. Predictive and
prognostic tools for NEC are essential to advance our biological insight with a view towards non-invasive
detection and accurate and timely phenotyping. We have developed a NEC Biorepository with a variety of
specimen types and extensive clinical metadata obtained prospectively from premature infants before the
development of NEC. These samples allow us to interrogate the mechanisms that underlie NEC development,
including genetic or environmental factors. These factors include epigenetic mechanisms that regulate important
aspects of cellular differentiation and gut development. Importantly, the epigenetic mechanisms, specifically, at
the level of DNA methylation that take place during neonatal NEC are unknown. Our preliminary epigenomic
data demonstrate that numerous biological pathways are altered during NEC. Based on these findings, we now
hypothesize that non-invasive identification of methylation signatures can identify an infant at risk for necrotizing
enterocolitis. We will test this hypothesis by defining and quantifying the DNA methylation signatures in stool and
blood of premature infants before, during and after the development of NEC. Moreover, we will expand on our
observations that dysregulation of multiple key pathways is a defining pathogenic feature of NEC and use our
mouse model to gain additional mechanistic insights into NEC pathobiology. By the conclusion of the proposal,
we will have generated a considerable amount of genomic data from infants across the time course of
development and manifestation of NEC, and also during the normal extrauterine development of preterm infants.
These studies will advance our understanding of the epigenomic regulation of the pathways involved during NEC
development, and furthermore, may explain the unique susceptibility of the premature infant to NEC and identify
a non-invasive approach to diagnosing this devastating disease.