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Decoding NEC: epigenetic biomarkers for risk stratification and prognosis

Pediatric Research (2025)Cite this article

Necrotizing enterocolitis (NEC) is a devastating intestinal disease of preterm neonates characterized by inflammatory bowel necrosis of the distal small and the large intestine.1 Even after decades of research, the etiopathogenesis is still unclear but includes immaturity of the gut mucosal barrier, mucosal injury, ischemia, inflammation, and microbial dysbiosis.2,3,4,5 The incidence of NEC in very low birth weight infants (VLBW, babies born at < 1500 g) is about 8%.6 In the clinical setting, about half of all infants with NEC respond to bowel rest, antibiotics, and supportive medical measures, but others develop progressive bowel disease, require surgical intervention; a third of these patients eventually die.7 Although many staging systems exist for grading the severity of illness, modified Bell’s criteria is often followed, which defines disease progression with an early stage of non-specific systemic/gastrointestinal inflammatory response, a more ‘definite’ stage of gastrointestinal disease and localized peritonitis, and finally, an advanced stage with intestinal perforation, diffuse peritonitis and systemic inflammatory response syndrome.1,8,9 NEC is associated with long term morbidity in the form adverse neurodevelopment, short bowel syndrome and intestinal failure.10,11,12 There is an unmet need for biomarkers in NEC that help in risk stratification, and potential prevention.

A biomarker would be highly useful in the following clinical scenarios13: a. Risk assessment of likelihood or probability of NEC in all VLBW infants, b. Early NEC diagnosis, before progression of disease to irreversible intestinal injury, c. Excluding NEC in infants with symptoms suspicious for NEC (i.e., high negative predictive value and specificity) and d. Early NEC prognostication, determining which newborns are likely to have disease progression. Could epigenetic insights provide such biomarkers for NEC?

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References

  1. Patel, R. M., Ferguson, J., McElroy, S. J., Khashu, M. & Caplan, M. S. Defining necrotizing enterocolitis: current difficulties and future opportunities. Pediatr. Res. 88, 10–15 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Pammi, M. et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome 5, 31 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Hodzic, Z., Bolock, A. M. & Good, M. The role of mucosal immunity in the pathogenesis of necrotizing enterocolitis. Front. pediatrics 5, 40 (2017).

    Article  Google Scholar 

  4. Duess, J. W. et al. Necrotizing enterocolitis, gut microbes, and sepsis. Gut microbes 15, 2221470 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Hackam, D. J. & Sodhi, C. P. Toll-like receptor-mediated intestinal inflammatory imbalance in the pathogenesis of necrotizing enterocolitis. Cell. Mol. Gastroenterol. Hepatol. 6, 229–238.e221 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Han, S. M. et al. Trends in incidence and outcomes of necrotizing enterocolitis over the last 12 years: a multicenter cohort analysis. J. Pediatr. Surg. 55, 998–1001 (2020).

    Article  PubMed  Google Scholar 

  7. Moss, R. L. et al. Clinical parameters do not adequately predict outcome in necrotizing enterocolitis: a multi-institutional study. J. Perinatol. : Off. J. Calif. Perinat. Assoc. 28, 665–674 (2008).

    Article  CAS  Google Scholar 

  8. Bell, M. J. et al. Neonatal necrotizing enterocolitis. therapeutic decisions based upon clinical staging. Ann. Surg. 187, 1–7 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Lueschow, S. R., Boly, T. J., Jasper, E., Patel, R. M. & McElroy, S. J. A critical evaluation of current definitions of necrotizing enterocolitis. Pediatr. Res. 91, 590–597 (2022).

    Article  PubMed  Google Scholar 

  10. Zozaya, C. et al. Neurodevelopmental and growth outcomes of extremely preterm infants with necrotizing enterocolitis or spontaneous intestinal perforation. J. Pediatr. Surg. 56, 309–316 (2021).

    Article  PubMed  Google Scholar 

  11. Amin, S. C., Pappas, C., Iyengar, H. & Maheshwari, A. Short bowel syndrome in the Nicu. Clin. Perinatol. 40, 53–68 (2013).

    Article  PubMed  Google Scholar 

  12. Jones, I. H. & Hall, N. J. Contemporary outcomes for infants with necrotizing enterocolitis-a systematic review. J. pediatrics 220, 86–92.e83 (2020).

    Article  Google Scholar 

  13. Goldstein, G. P. & Sylvester, K. G. Biomarker discovery and utility in necrotizing enterocolitis. Clin. Perinatol. 46, 1–17 (2019).

    Article  PubMed  Google Scholar 

  14. Waddington, C. H. The Epigenotype. 1942. Int J. Epidemiol. 41, 10–13 (2012).

    Article  CAS  PubMed  Google Scholar 

  15. Turner, B. M. Epigenetic responses to environmental change and their evolutionary implications. Philos. Trans. R. Soc. Lond. B Biol. Sci. 364, 3403–3418 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Marchese, F. P. & Huarte, M. Long non-coding Rnas and chromatin modifiers: their place in the epigenetic code. Epigenetics 9, 21–26 (2014).

    Article  CAS  PubMed  Google Scholar 

  17. Kellermayer, R. Epigenetics and the developmental origins of inflammatory bowel diseases. Can. J. Gastroenterol. 26, 909–915 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Han, M., Jia, L., Lv, W., Wang, L. & Cui, W. Epigenetic enzyme mutations: role in tumorigenesis and molecular inhibitors. Front Oncol. 9, 194 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Tompkins, J. D. et al. Epigenetic stability, adaptability, and reversibility in human embryonic stem cells. Proc. Natl Acad. Sci. USA 109, 12544–12549 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Chan, T. A. & Baylin, S. B. Epigenetic biomarkers. Curr. Top. Microbiol Immunol. 355, 189–216 (2012).

    CAS  PubMed  Google Scholar 

  21. Gunasekara, C. J. et al. Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biol. 24, 2 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Kellermayer, R. Challenges for epigenetic research in inflammatory bowel diseases. Epigenomics 9, 527–538 (2017).

    Article  CAS  PubMed  Google Scholar 

  23. Robertson, K. D. DNA methylation and human disease. Nat. Rev. Genet 6, 597–610 (2005).

    Article  CAS  PubMed  Google Scholar 

  24. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Moore, L. D., Le, T. & Fan, G. DNA methylation and its basic function. Neuropsychopharmacology 38, 23–38 (2013).

    Article  CAS  PubMed  Google Scholar 

  26. Bardhan, K. & Liu, K. Epigenetics and colorectal cancer pathogenesis. Cancers (Basel) 5, 676–713 (2013).

    Article  CAS  PubMed  Google Scholar 

  27. Karatzas, P. S., Gazouli, M., Safioleas, M. & Mantzaris, G. J. DNA methylation changes in inflammatory bowel disease. Ann. Gastroenterol. 27, 125–132 (2014).

    PubMed  PubMed Central  Google Scholar 

  28. Law, C. M., Barker, D. J., Osmond, C., Fall, C. H. & Simmonds, S. J. Early growth and abdominal fatness in adult life. J. Epidemiol. Community Health 46, 184–186 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ding, Y.-X. & Cui, H. Integrated analysis of genome-wide DNA methylation and gene expression data provide a regulatory network in intrauterine growth restriction. Life Sci. 179, 60–65 (2017).

    Article  CAS  PubMed  Google Scholar 

  30. Doan, T. N. A., Akison, L. K. & Bianco-Miotto, T. Epigenetic mechanisms responsible for the transgenerational inheritance of intrauterine growth restriction phenotypes. Front Endocrinol. (Lausanne) 13, 838737 (2022).

    Article  PubMed  Google Scholar 

  31. Good, M. et al. Neonatal necrotizing enterocolitis-associated DNA methylation signatures in the colon are evident in stool samples of affected individuals. Epigenomics 13, 829–844 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Everson, T. M. et al. Serious neonatal morbidities are associated with differences in DNA methylation among very preterm infants. Clin. Epigenetics 12, 151 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Cho, H. Y. et al. Prospective epigenome and transcriptome analyses of cord and peripheral blood from preterm infants at risk of bronchopulmonary dysplasia. Sci. Rep. 13, 12262 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Bulka, C. M. et al. Placental Cpg methylation of inflammation, angiogenic, and neurotrophic genes and retinopathy of prematurity. Investigative Ophthalmol. Vis. Sci. 60, 2888–2894 (2019).

    Article  CAS  Google Scholar 

  35. Everson, T. M. et al. Epigenome-wide analysis identifies genes and pathways linked to neurobehavioral variation in preterm infants. Sci. Rep. 9, 6322 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Hodyl, N. A., Roberts, C. T. & Bianco-Miotto, T. Cord Blood DNA Methylation Biomarkers for Predicting Neurodevelopmental Outcomes. Genes 7 (2016).

  37. LaSalle, J. M. Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder. Mol. psychiatry 28, 1890–1901 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bahado-Singh, R. O. et al. Artificial intelligence analysis of newborn leucocyte epigenomic markers for the prediction of autism. Brain Res. 1724, 146457 (2019).

    Article  CAS  PubMed  Google Scholar 

  39. Gao, L. et al. Association between Axl promoter methylation and lung function growth during adolescence. Epigenetics 13, 1027–1038 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  40. den Dekker, H. T. et al. Newborn DNA-Methylation, Childhood Lung Function, and the Risks of Asthma and Copd across the Life Course. Eur Resp J. 53 (2019).

  41. Reese, S. E. et al. Epigenome-wide meta-analysis of DNA methylation and childhood asthma. J. allergy Clin. Immunol. 143, 2062–2074 (2019).

    Article  CAS  PubMed  Google Scholar 

  42. Radhakrishna, U. et al. Newborn blood DNA epigenetic variations and signaling pathway genes associated with tetralogy of fallot (Tof). PloS one 13, e0203893 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Gagne-Ouellet, V. et al. Mediation analysis supports a causal relationship between maternal hyperglycemia and placental dna methylation variations at the leptin gene locus and cord blood leptin levels. Int. J. Mol. Sci. 21 (2020).

  44. Guay, S.-P. et al. DNA Methylation at Lrp1 gene locus mediates the association between maternal total cholesterol changes in pregnancy and cord blood leptin levels. J. Dev. Orig. Health Dis. 11, 369–378 (2020).

    Article  CAS  PubMed  Google Scholar 

  45. Schaible, T. D., Harris, R. A., Dowd, S. E., Smith, C. W. & Kellermayer, R. Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes. Hum. Mol. Genet. 20, 1687–1696 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mir, S. A. et al. Prenatal methyl-donor supplementation augments colitis in young adult mice. PLoS ONE 8, e73162 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Krishna, M. et al. Maternal lactobacillus reuteri supplementation shifts the intestinal microbiome in mice and provides protection from experimental colitis in female offspring. FASEB Bioadv 4, 109–120 (2022).

    Article  CAS  PubMed  Google Scholar 

  48. Simon, D. A. et al. Developmental windows of environmental vulnerability for inflammatory bowel disease. J. Pediatr. Clin. Pr. 11, 200104 (2024).

    Google Scholar 

  49. Pepke, M. L., Hansen, S. B. & Limborg, M. T. Unraveling Host Regulation of Gut Microbiota through the Epigenome-Microbiome Axis. Trends in microbiology (2024).

  50. Li, Z. et al. Effects of metabolites derived from gut microbiota and hosts on pathogens. Front Cell Infect. Microbiol 8, 314 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Cortese, R., Lu, L., Yu, Y., Ruden, D. & Claud, E. C. Epigenome-microbiome crosstalk: a potential new paradigm influencing neonatal susceptibility to disease. Epigenetics 11, 205–215 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Fofanova, T. Y., Petrosino, J. F. & Kellermayer, R. Microbiome-Epigenome Interactions and the Environmental Origins of Inflammatory Bowel Diseases. J. Pediatr. Gastroenterol. Nutr. 62, 208–219 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Zou, P. et al. Identification of risk factors for necrotizing enterocolitis in twins: a case-control matching analysis of over ten-years’ experience. BMC Pediatr. 24, 744 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Hourigan, S. K. et al. The microbiome in necrotizing enterocolitis: a case report in twins and minireview. Clin. Ther. 38, 747–753 (2016).

    Article  PubMed  Google Scholar 

  55. Hall, N. G. et al. Epigenetic Changes Associated with Severe Necrosis and Survival in Preterm Infants with Surgical Necrotizing Enterocolitis. Pediatric research (2025).

  56. Good, M. et al. Global hypermethylation of intestinal epithelial cells is a hallmark feature of neonatal surgical necrotizing enterocolitis. Clin. epigenetics 12, 190 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Good, M. et al. Selective hypermethylation is evident in small intestine samples from infants with necrotizing enterocolitis. Clin. epigenetics 14, 49 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Klerk, D. H. et al. DNA Methylation of Tlr4, Vegfa, and Defa5 Is Associated with Necrotizing Enterocolitis in Preterm Infants. Front. pediatrics 9, 630817 (2021).

    Article  Google Scholar 

  59. Klerk, D. H. et al. Hypermethylation of Ctdspl2 Prior to Necrotizing Enterocolitis Onset. Epigenomics 15, 479–486 (2023).

    Article  CAS  PubMed  Google Scholar 

  60. Winans, S., Flynn, A., Malhotra, S., Balagopal, V. & Beemon, K. L. Integration of Alv into Ctdspl and Ctdspl2 Genes in B-cell lymphomas promotes cell immortalization, migration and survival. Oncotarget 8, 57302–57315 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  61. Xiao, Y., Chen, Y., Peng, A. & Dong, J. The Phosphatase Ctdspl2 Is Phosphorylated in Mitosis and a Target for Restraining Tumor Growth and Motility in Pancreatic Cancer. Cancer Lett. 526, 53–65 (2022).

    Article  CAS  PubMed  Google Scholar 

  62. Kellermayer, R. Genetic Drift. Physiologic noise obscures genotype-phenotype correlations. Am. J. Med Genet A 143a, 1306–1307 (2007).

    Article  PubMed  Google Scholar 

  63. Philip, A., Krishna, M. & Kellermayer, R. Stochasticity driven limitations for counseling in autoimmune gastrointestinal disease. J. Pediatr. Gastroenterol. Nutr. 77, 695–697 (2023).

    Article  CAS  PubMed  Google Scholar 

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Funding

Dr. Mohan Pammi’s effort is partly supported by funding from NIH (R01HD112886). R.K. was supported by the Gutsy Kids Fund, graciously maintained by Brock Wagner, the Klaasmeyers, the Frugonis, and other generous donor families.

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Authors and Affiliations

  1. Department of Pediatrics, Division of Neonatology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA

    Mohan Pammi

  2. Department of Pediatrics, Division of Pediatric Gastroenterology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA

    Richard Kellermayer

  3. USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA

    Richard Kellermayer

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  1. Mohan Pammi
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  2. Richard Kellermayer
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MP wrote the first draft of the manuscript and RK provided critical intellectual input. Both authors approved the final version of the manuscript to be published.

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Correspondence to Mohan Pammi.

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Pammi, M., Kellermayer, R. Decoding NEC: epigenetic biomarkers for risk stratification and prognosis. Pediatr Res (2025). https://doi.org/10.1038/s41390-025-04620-x

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