Background: The renal allograft is exposed to a milieu of environmental/metabolic stimuli that trigger epigenetic modifications and thereby gene expression patterns which influence function and pathogenesis. The study aimed to understand the intricacies of molecular crosstalk in chronic renal allograft injury (CRAI) with interstitial fibrosis and tubular atrophy (IFTA) by a multiomics integrative approach.

Methods: Graft biopsies (n=70) were evaluated. Whole DNA methylation (DNAm), gene and miRNA expression assays were done for biopsies from (1) normal functioning allografts (NFA) (>24 months post-kidney transplantation (KT) and (2) grafts with continuos decrease in graft function and IFTA at >24 months post-KT. Also, DNAm analysis for pre-implant (PI) biopsies (n=39) from progressors and non-progressors to CRAI with IFTA was done and compared to NFAs. Arrays were analyzed and probe sets with FDR <0.01 were considered significant. For DNAm arrays an additional [Delta]β ≥0.20 cutoff was used. Integrative analyses were done and genes with concerted dysregulation at DNAm and gene/miRNA expression level were further validated in independent sets.

Results: Differentially methylated CpGs were strongly enriched in regions that were variably methylated among tissues implying very high tissue specificity in their regulatory impact. Gene expression data, for which corresponding CpG methylation pattern matched, were related to immune response (activated state) and nephrogenesis (inhibited state). Multiomics integration analysis revealed that genes involved in metabolic function, especially of the tubular epithelial cells (BHMT2, CLCN5, G6PC, NTRK2, CLCNKB, PPM1H, AHCYL1) were repressed and were targets of 3 miRNA that were differentially expressed and methylated in the promoter regions of their genes. Top disease functions associated with these genes were dysgenesis, cell death, growth failure and hypoplasia (Z activation score > 2.6). Co-expression analyses were done for validation of the identified pathways. Comparison of DNAm patterns of PI biopsies with post-KT biopsies revealed that the methylation changes post-KT were IFTA-specific and denovo.

Conclusions: The findings show DNAm of CpG sites as a possible cause for exacerbated immune mediated damage and decreased metabolism, maintaining the continuum of damage, inhibition of repair, and organogenesis processes during CRAI with IFTA progression.

CITATION INFORMATION: Bontha V, Maluf D, Dozmorov M, Archer K, Gallon L, Mas V. Epigenetic Modifications in the Progression to Chronic Renal Allograft Injury. Am J Transplant. 2017;17 (suppl 3).

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