Profiling of Circulating MicroRNAs (miRNAs) Associated with Progression to End Stage Kidney Disease (ESKD) in Diabetes-Preanalytical and Analytical Considerations

Background: miRNAs are short non-coding RNA molecules involved in gene regulation. Previously, we identified 17 plasma miRNAs (8 risk and 9 protective miRNAs) associated with progression to ESKD in diabetes (JASN 2021). Factors that influence the measurement of miRNA concentrations, and thus could impact replication of these findings, including extraction method, miRNA profiling method, and the miRNA source biofluid, have not been investigated. Methods: Plasma and serum were obtained from patients who participated in the Joslin Kidney Study. Extraction-free plasma and serum miRNA profiles were obtained using the HTG EdgeSeq platform. RNA was also extracted from plasma and used to measure miRNAs by RNA sequencing (RNASeq) and quantitative RT-PCR (qRT-PCR). Results: Out of 2,083 miRNAs on the EdgeSeq platform, almost all of them (96%) were detected in plasma without RNA extraction, while only 45% of these miRNAs were detected in RNA extracted from the same plasma specimens. The content of miRNAs detected in extracted RNA was significantly enriched for GC sequences in comparison with miRNAs that were lost during RNA extraction. In the specimens with RNA extracted, significantly lower number of miRNAs were detected by RNASeq or qRT-PCR (31% and 26%, respectively) in comparison with the EdgeSeq platform. Regarding the 17 miRNAs associated with ESKD, many of them had different concentrations in serum samples than in plasma and had lower concentration or were not detected in plasma samples with profiled following RNA extraction. Conclusion: This study demonstrates very strong effects of pre-analytical and analytical factors on concentration of circulating miRNAs. To replicate our findings for 17 circulating miRNAs, it is critical that plasma specimens be used and that miRNAs be measured using the EdgeSeq platform or other platforms that do not require prior extraction of RNA. Disclosure E.Satake: None. Z.Md dom: None. H.Kobayashi: Research Support; Bayer Inc. J.Ricca: None. K.O'neil: None. B.Krolewski: None. M.G.Pezzolesi: Research Support; Renalytix. A.Krolewski: None. Funding National Institutes of Health (DK131061-01)