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We investigated intestinal molecular alterations associated with NEC and explored candidate diagnostic biomarkers.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n Bulk proteomics of formalin\u2010fixed paraffin\u2010embedded intestinal tissues was integrated with spatial proteomics of an index NEC case, single\u2010cell RNA sequencing, immunohistochemical validation, serum enzyme\u2010linked immunosorbent assays, and a murine NEC model with pharmacological inhibition of Snail\u2010mediated epithelial\u2013mesenchymal transition (EMT).<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Multiomics analyses indicated layer\u2010associated epithelial injury, inflammatory activation, and EMT\u2010like fibroblast\/myofibroblast remodelling during NEC. Single\u2010cell sequencing of six intestinal samples showed reduced epithelial\u2010cell abundance with increased fibroblast and smooth\u2010muscle\u2010cell proportions in NEC. In the murine model, CYD19 treatment was associated with improved intestinal pathology, survival, inflammatory cytokine profiles, and barrier\u2010related readouts. ANXA2, RPL13, RPL23A, and RPS28 were identified as tissue candidate biomarkers and validated by immunohistochemistry. Serum ANXA2 was higher in NEC than in available non\u2010NEC controls (AUC, 0.944) and showed exploratory discrimination between medical NEC and highly suspected cow\u2019s\u2010milk protein allergy; the adjusted AUC was 0.899.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n NEC is associated with inflammation\u2010linked EMT\u2010like intestinal remodelling and epithelial injury. ANXA2 and selected ribosomal proteins are candidate tissue biomarkers, while serum ANXA2 warrants prospective multicentre validation as a blood\u2010based diagnostic and risk\u2010stratification biomarker.<\/jats:p>\n <\/jats:sec>\n \n Key points<\/jats:title>\n \n \n \n NEC was associated with epithelial injury, excessive inflammation, and EMT\u2010like fibroblast\/myofibroblast remodelling, as revealed by integrated bulk proteomics, spatial proteomics, and single\u2010cell sequencing.<\/jats:p>\n <\/jats:list-item>\n \n Pharmacological inhibition of Snail\u2010mediated EMT in a murine NEC model was associated with improved intestinal injury, inflammatory responses, barrier\u2010related readouts, and survival.<\/jats:p>\n <\/jats:list-item>\n \n ANXA2, RPL13, RPL23A, and RPS28 were identified as candidate tissue biomarkers, while serum ANXA2 showed exploratory potential for NEC diagnosis and risk stratification.<\/jats:p>\n <\/jats:list-item>\n <\/jats:list>\n <\/jats:p>\n 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