Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach

Abstract

Progressive fibrosis of the interstitium is the dominant final pathway in renal destruction in native and transplanted kidneys. Over time, the continuum of molecular events following immunological and non-immunological insults lead to interstitial fibrosis and tubular atrophy (IFTA) and culminate in kidney failure. We hypothesize that these insults trigger changes in DNA methylation (DNAm) patterns which in turn could exacerbate injury and slow down the regeneration processes, leading to fibrosis development and graft dysfunction. Herein, we analyzed biopsy samples from kidney allografts collected after 24-months post transplantation and used an integrative multi-omics approach to understand the underlying molecular mechanisms. The role of DNAm and microRNAs on the graft gene expression was evaluated. Enrichment analyses of differentially methylated CpG sites were performed using GenomeRunner. CpGs were strongly enriched in regions that were variably methylated among tissues implying high tissue specificity in their regulatory impact. Corresponding to this methylation pattern, gene expression data were related to immune response (activated state) and nephrogenesis (inhibited state). Preimplantation biopsies showed similar DNAm patterns to normal allograft biopsies at 2-years post-transplantation. Our findings demonstrate for the first time a relationship among epigenetic modifications and development of interstitial fibrosis, graft function, and inter-individual variation on long-term outcomes.

Recent Advances on Biomarkers of Early and Late Kidney Graft Dysfunction

“…Another area of active research is that of epigenetic modifications of immunity genes on progression to IFTA: epigenetic mechanisms such as hypomethylation could directly enhance their expression and also indirectly modulate it by regulating miRNAs [ 164 ].…”

Ischemia-Induced DNA Hypermethylation during Kidney Transplant Predicts Chronic Allograft Injury

“…Other medical conditions are, however, also characterized by long-lasting oxygen shortage, but in these affected tissues, they are far less proliferative, raising the questions of whether DNA demethylation activity is impaired and whether this similarly results in the hypermethylation driving disease progression. 9 However, other than the report on DNA methylation changes affecting RASAL1 and one other report showing a relationship between epigenetic modifications and graft fibrosis, 10 DNA methylation is only poorly characterized in the context of kidney transplantation. Specifically, epigenome-wide studies assessing the effects of ischemia on kidneys have never been performed, and also, the potential link between renal ischemia, epigenetic changes, and kidney allograft injury has never been addressed.…”

Unveiling the Role of DNA Methylation in Kidney Transplantation: Novel Perspectives toward Biomarker Identification

“…Its pathogenesis is complex and comprises both immune- and non-immune-mediated mechanisms, culminating in interstitial fibrosis, tubular atrophy, and progressive loss of graft function. Similar to wound repair, fibrosis is triggered by an injury and characterized by the deposition of extracellular matrix through activated fibroblasts but conversely it can progress even after the injury has disappeared [80]. Fibrogenesis is the result of complex interactions among the different involved cell types which is coordinated by an extensive network of growth factors and signalling pathways [81].…”