Exploratory investigation of hemodialysis membrane–induced differential DNA methylation in patient blood

Abstract

Hemodialysis (HD) patients experience chronic inflammation and immune activation driven by continuous blood contact with synthetic dialysis membranes. Increasing evidence suggests that membrane surface chemistry can modulate immune–epigenetic regulatory mechanisms, including DNA methylation, which influences the expression of inflammation-related genes. However, the fundamental question of how different dialysis membranes acutely induce distinct DNA methylation responses in patient blood remains largely unexplored. This pilot exploratory study investigates the membrane-specific effects of a zwitterionic uremic-metabolite–modified membrane (UM-SB) compared with a standard unmodified hospital-grade membrane. Blood from two HD patients was incubated for four hours with each membrane to isolate acute, chemistry-driven effects independent of in vivo factors. Genome-wide DNA methylation profiling using the Illumina HumanMethylation450 BeadChip identified distinct membrane-induced changes, while functional enrichment (GO, KEGG) and protein–protein interaction (PPI) network analyses were used to identify biological pathways and regulatory hub genes. Inflammatory biomarkers, including CRP, PF4, Serpin C1, Properdin, Complement C5a, IL-1, TNF-α, IL-6, and vWF-A2, were quantified using multiplex immunoassays. Fibrinogen adsorption, as a measure of hemocompatibility, was assessed using synchrotron micro-CT imaging. Across both patients, seventy-two differentially methylated genes (DMGs) exhibited consistent directional changes, suggesting reproducible membrane-specific epigenetic signatures within this pilot cohort. Many of these DMGs were located within promoter and enhancer regions, and functional enrichment analysis identified pathways related to immune regulation, vascular remodeling, neuronal signaling, and PI3K-Akt signaling, all of which are relevant to long-term HD complications. Key regulatory genes such as PEG10, WNT3A, GATA4, PCAT7, and FOXG1 exhibited methylation changes that, based on their genomic location and previously reported biological roles, may represent potentially favorable regulatory responses under UM-SB exposure, consistent with the observed reduction in inflammatory biomarkers and the reported biological roles of these genes. Biomarker analysis supported these findings, with UM-SB demonstrating lower complement activation and platelet stimulation, including reductions in PF4, Properdin, and C5a. Synchrotron micro-CT imaging further confirmed improved hemocompatibility of UM-SB through reduced and more uniform fibrinogen adsorption compared with the hospital membrane. Collectively, these molecular, biochemical, and biophysical results suggest that dialysis membrane chemistry plays a fundamental role in shaping acute DNA methylation responses, and that the UM-SB membrane was associated with a potentially more favorable, less inflammatory blood–material interaction profile. These pilot findings suggest that the UM-SB membrane may have the potential to improve long-term biocompatibility in HD, although this requires validation in larger longitudinal studies.