Integrated multi-omics analysis reveals dendritic cell centered regulatory networks and therapeutic targets in necrotizing enterocolitis
Source: PubMed Central Open Access, NCBI / U.S. National Library of Medicine
Background Necrotizing enterocolitis (NEC) is a severe inflammatory intestinal disease predominantly affecting premature infants and is characterized by immune dysregulation and epithelial barrier disruption. However, the cellular communication networks and key molecular regulators underlying NEC pathogenesis remain incompletely understood. Methods Single-cell RNA sequencing (scRNA-seq) and transcriptomic datasets of NEC were obtained from the Gene Expression Omnibus (GEO) database and analyzed using R-based bioinformatic workflows to characterize cellular composition, intercellular communication, immune infiltration, pathway activity, and candidate disease-associated genes. The expression of alpha kinase 2 (ALPK2) was validated in NEC intestinal tissues by quantitative real-time PCR, and its potential functional relevance was further investigated using lipopolysaccharide (LPS)-induced intestinal organoids. Results Dendritic cells (DCs) occupied a central position in the NEC intercellular communication network and were enriched in antigen presentation and immune regulatory pathways. Machine learning identified ALPK2, ERICH1, and TMEM123 as candidate NEC-associated genes. Immune infiltration analysis revealed a disturbed immune microenvironment in NEC, with ALPK2 and ERICH1 negatively correlated with DC abundance. Functional enrichment analyses suggested that ALPK2 was predominantly associated with immune and inflammatory pathways, whereas ERICH1 was linked to metabolic and pr
Abstract
Background Necrotizing enterocolitis (NEC) is a severe inflammatory intestinal disease predominantly affecting premature infants and is characterized by immune dysregulation and epithelial barrier disruption. However, the cellular communication networks and key molecular regulators underlying NEC pathogenesis remain incompletely understood. Methods Single-cell RNA sequencing (scRNA-seq) and transcriptomic datasets of NEC were obtained from the Gene Expression Omnibus (GEO) database and analyzed using R-based bioinformatic workflows to characterize cellular composition, intercellular communication, immune infiltration, pathway activity, and candidate disease-associated genes. The expression of alpha kinase 2 (ALPK2) was validated in NEC intestinal tissues by quantitative real-time PCR, and its potential functional relevance was further investigated using lipopolysaccharide (LPS)-induced intestinal organoids. Results Dendritic cells (DCs) occupied a central position in the NEC intercellular communication network and were enriched in antigen presentation and immune regulatory pathways. Machine learning identified ALPK2, ERICH1, and TMEM123 as candidate NEC-associated genes. Immune infiltration analysis revealed a disturbed immune microenvironment in NEC, with ALPK2 and ERICH1 negatively correlated with DC abundance. Functional enrichment analyses suggested that ALPK2 was predominantly associated with immune and inflammatory pathways, whereas ERICH1 was linked to metabolic and proliferative programs. ALPK2 expression was significantly elevated in ileal tissues from NEC patients and experimental NEC mice. In an inflammation model of LPS stimulation using mouse intestinal organoids, TGX221 suppressed inflammatory cytokine induction and partially restored tight junction protein expression. Discussion These findings highlight DCs as central mediators of NEC-associated immune communication and identify ALPK2 as a potential regulator of intestinal inflammation and epithelial barrier dysfunction, supporting ALPK2 as a candidate NEC-associated regulator with potential therapeutic implications.