Epigenetic priming of the ectodermal mucosal-immune axis: Concurrent hypomethylation of protocadherin and innate immune sensors in edematous severe acute malnutrition

Abstract Background The pathophysiology of edematous severe acute malnutrition (ESAM, or kwashiorkor) is characterized by a paradoxical "double hit": catastrophic epithelial barrier breakdown and systemic innate immune hyper-reactivity. Furthermore, survivors suffer profound, persistent neurodevelopmental deficits. The molecular mechanisms linking these phenotypes remain unknown. We hypothesized that early-life metabolic stress induces a targeted epigenetic scar on the shared ectodermal lineage, concurrently dysregulating physical barrier integrity and mucosal immune sensors. Methods We developed a gold-standard bioinformatics pipeline to analyze raw Illumina IDAT methylation files from the GSE112893 cohort (374 buccal swab samples). Data were processed with Normal-Exponential Out-Of-Band (Noob) background correction, and differential methylation was assessed using limma with empirical Bayes moderation, adjusting for cellular heterogeneity. Results We identified 76 significant differentially methylated positions (DMPs) (false discovery rate [FDR] < 0.05), with 98.7% (75/76) exhibiting hypomethylation in ESAM. Strikingly, these DMPs were not randomly distributed. A targeted sub-analysis revealed concurrent hypomethylation of the protocadherin gamma ( PCDHG ) cluster (22 probes) and key innate immune/mucosal remodelling genes, including promoter-region (TSS1500) hypomethylation of CHI3L1 and C3 , alongside structural barrier genes MACF1 , SDK1 , and ANK3 . Pathway analysis confirmed profound convergence on homophilic cell-cell adhesion (p = 2.93 × 10⁻²⁹) and nervous system development (p = 4.55 × 10⁻¹⁰). Conclusions ESAM is characterized by a coordinated epigenetic dysregulation of the ectodermal mucosal-immune axis. Hypomethylation of the PCDHG cluster and innate immune sensors provides a unified molecular mechanism explaining the simultaneous barrier failure, systemic inflammation, and neurodevelopmental vulnerability observed in kwashiorkor.