Genome-Wide DNA Methylation Profiling Reveals Stage- and Severity-Associated Epigenetic Alterations in Children with Posterior Urethral Valve-Associated Chronic Kidney Disease

Background: Chronic kidney disease (CKD) is an important cause of morbidity in children, particularly in those with congenital anomalies of the kidney and urinary tract. Although epigenetic alterations have been implicated in CKD, stage-associated genome-wide DNA methylation changes remain poorly characterized in posterior urethral valves (PUV). This study aimed to characterize DNA methylation patterns across CKD stages in children with PUV and identify potential methylation markers associated with CKD severity. Methods: Genome-wide DNA methylation profiling was performed on peripheral blood DNA from 20 boys with PUV stratified by CKD stage and 19 age-matched healthy male controls using the Illumina MethylationEPIC v2.0 array. Analyses included a global stage-wise model, stage-specific comparisons against controls and between CKD stages, an overall PUV-associated CKD-versus-control model, functional enrichment analysis, candidate CKD progression gene analysis, and CKD severity-associated methylation analysis. Results: A global stage-wise analysis identified 11,134 CpG sites showing significant methylation variation across controls and PUV-associated CKD. Differential methylation burden was limited in early CKD stages but increased markedly in advanced CKD, with 4734 and 20,242 DMPs identified in Stage 4 and Stage 5, respectively. DMP-associated genes in advanced CKD stages showed enrichment of immune-related, structural remodeling, and intracellular signaling pathways. Candidate gene analysis identified significant methylation changes in previously reported CKD progression-associated genes, with greater representation in advanced CKD stages. CKD severity-associated analysis identified cg16879596_BC21, annotated to CYP3A5, as positively associated with CKD severity (r = 0.74, FDR = 1.32 × 10−5). Methylation at this CpG site increased across CKD stages and showed strong internal discrimination between PUV-associated CKD patients and controls (AUC = 0.947, 95% CI = 0.887–1.000). Conclusions: PUV-associated CKD is characterized by stage-associated DNA methylation changes, with a marked increase in methylation burden in advanced CKD stages. The findings highlight immune, structural remodeling, and signaling pathways associated with advanced CKD and identify CYP3A5 methylation as a potential marker of CKD severity. In future, larger longitudinal studies with independent validation and functional integration are required.