Pre-analytical considerations in quantifying circulating miRNAs that predict end-stage kidney disease in diabetes

Our previous study identified 8 risk and 9 protective plasma miRNAs associated with progression to end-stage kidney disease (ESKD) in diabetes. This study aimed to elucidate pre-analytical factors that influence the quantification of circulating miRNAs. Using the EdgeSeq platform, which quantifies 2,002 miRNAs in plasma, including ESKD-associated miRNAs, we compared miRNA profiles in whole plasma vs. miRNAs profiles in RNA extracted from the same plasma specimens. Less than half of the miRNAs were detected in standard RNA extracted methods from plasma. Detection of individual and concentrations of miRNAs were much lower when RNA extracted from plasma was quantified by RNA sequencing (RNASeq) or RT-qPCR platforms compared to EdgeSeq. Plasma profiles of miRNAs determined by the EdgeSeq platform had excellent reproducibility in assessment, and had no variation with age, sex, HbA1c, BMI, and cryostorage time. The risk ESKD-associated miRNAs were detected and measured accurately only in whole plasma and using the EdgeSeq platform. Protective ESKD-associated miRNAs were detected by all platforms except RT-qPCR, however, correlations among concentrations obtained with different platforms were weak or non-existent. In conclusion, pre-analytical factors have a profound effect on detection and quantification of circulating miRNAs in ESKD in diabetes. Quantification of miRNAs in whole plasma and using the EdgeSeq platform may be the preferable method to study profiles of circulating cell-free miRNAs associated with ESKD, and possibly other diseases. To compare circulating miRNA profiles from plasma with RNA extraction or direct isolation, samples from eight individuals were randomly selected from the Josliln Kidney Study. miRNA expression profilings were performed by the HTG EdgeSeq miRNA sequence, and RNA sequencing of small RNAs, including SeqMatic and LC Sciences platforms. Comparisons of the miRNA expression profilings between EdgeSeq and RNA sequencings were performed. *************************************************************** Raw data file not available because the HTG company went bankrupt ***************************************************************