Urinary MicroRNA Analysis Indicates an Epigenetic Regulation of Chronic Kidney Disease of Unknown Etiology in Sri Lanka

Abstract

Background: Chronic kidney disease of unknown etiology (CKDu) is reported among male paddy farmers in the dry zone of Sri Lanka. The exact cause of this disease remains undeter-mined. Genetic susceptibility is identified as a major risk factor for CKDu. Objectives: In this study, small urinary RNAs were characterized in CKDu patients, healthy endem-ic and non-endemic controls. Differently expressed urinary miRNAs and their associated pathways were identified in the study population. Methods: Healthy and diseased male volunteers (n = 9) were recruited from Girandurukotte (en-demic) and Mawanella (non-endemic) districts. Urinary small RNAs were purified and sequenced using Illumina MiSeqTM. The sequence trace files were assembled and analyzed. Differentially ex-pressed miRNAs among these three groups were identified and pathway analysis was conducted. Results: The urine samples contained 130,623 sequence reads identified as non-coding RNAs, PIWI-interacting RNAs (piRNA), and miRNAs. Approximately four percent of the total small RNA reads represented miRNA, and 29% represented piRNA. A total of 409 miRNA species were ex-pressed in urine. Interestingly, both diseased and endemic controls population showed significantly low expression of miRNA and piRNA. Regardless of the health status, the endemic population ex-pressed significantly low levels of miR-10a, miR-21, miR-148a, and miR-30a which have been linked with several environmental toxins. Conclusion: Significant downregulation of miRNA and piRNA expression in both diseased and healthy endemic samples indicates an epigenetic regulation of CKDu involving genetic and envi-ronmental interaction. Further studies of specific miRNA species are required to develop a miRNA panel to identify individuals susceptible to CKDu.