Epigenetic changes associated with severe necrosis and survival in preterm infants with surgical necrotizing enterocolitis.

Background: We aim to determine the epigenetic changes assessed by DNA methylation associated with necrosis severity and survival in preterm infants with surgical necrotizing enterocolitis (NEC).

Methods: Using Illumina's Infinium EPIC v2.0 BeadChips, the DNA methylation profiles of 46 infants with NEC were generated from intestinal tissue collected during laparotomy. Samples were categorized by disease severity and survival outcome. STRING functional enrichment analyses and MCODE network analyses of the genes found to contain CpG sites with significantly different methylation levels (Benjamini-Hochberg adjusted p-value ≤ 0.01) were used to investigate the biological relevance of the epigenetic differences between sample groups.

Results: 4570 CpG sites showed a significant difference in methylation when comparing survivors (n = 34) and non-survivors (n = 12) of surgical NEC (p < 0.05). 19,518 CpG sites showed a significant difference in methylation when comparing NEC patients with low (n = 18) and high necrosis (n = 28) (p < 0.05). Genes with the greatest number of significant methylation sites include PRDM16, SEPTIN9, FOXP1, POLR1C, and several homeobox genes. NOTCH and Rap1 signaling were two of the major pathways identified.

Conclusion: The DNA methylation profiles of infants with surgical NEC were found to differ, depending on necrosis severity and survival outcome.

Impact: The DNA methylation profiles in surgical necrotizing enterocolitis (NEC) were found to differ depending on necrosis severity and survival outcome. Significant differences in the DNA methylation levels of thousands of genes helped identify molecular pathways that may be epigenetically regulated and involved in disease progression. These genes and molecular pathways are potential therapeutic targets for NEC, an incompletely understood and life-threatening disease.