Barreiro, K.; Dwivedi, O.P.; Rannikko, A.; Holthöfer, H.; Tuomi, T.; Groop, P.-H.; Puhka, M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles—From Pre-Analytical Obstacles to Biomarker Research. Genes2023, 14, 1415.
Barreiro, K.; Dwivedi, O.P.; Rannikko, A.; Holthöfer, H.; Tuomi, T.; Groop, P.-H.; Puhka, M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles—From Pre-Analytical Obstacles to Biomarker Research. Genes 2023, 14, 1415.
Barreiro, K.; Dwivedi, O.P.; Rannikko, A.; Holthöfer, H.; Tuomi, T.; Groop, P.-H.; Puhka, M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles—From Pre-Analytical Obstacles to Biomarker Research. Genes2023, 14, 1415.
Barreiro, K.; Dwivedi, O.P.; Rannikko, A.; Holthöfer, H.; Tuomi, T.; Groop, P.-H.; Puhka, M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles—From Pre-Analytical Obstacles to Biomarker Research. Genes 2023, 14, 1415.
Abstract
Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of pre-analytical choices hinder biomarker studies. We aimed to assess how pre-analytical variables (urine storage temperature, isolation workflow) affect diabetic kidney disease (DKD) -linked miRNAs or kidney -linked miRNAs and mRNAs (kidney-RNAs) in uEV isolates and to discover stable reference mRNAs across diverse uEV datasets. We studied nine raw and normalized sequencing datasets including healthy controls and individuals with prostate cancer or type 1 diabetes with or without albuminuria. We focused on kidney-RNAs reviewing literature for DKD-linked miRNAs from kidney tissue, cell culture and uEV/urine experiments. RNAs were analyzed by expression heatmaps, hierarchical clustering and selecting stable mRNAs with normalized counts (>200) and minimal coefficient of variation. Kidney-RNAs were decreased after urine storage at -20°C vs -80°C. Isolation workflows captured kidney-RNAs with different efficiencies. Ultracentrifugation captured DKD -linked miRNAs that separated healthy and diabetic macroalbuminuria groups. Eleven mRNAs were stably expressed across the datasets. Hence, preanalytical choices had variable effects on kidney-RNAs – analyzing kidney-RNAs complemented global correlation, which could fade differences in some relevant RNAs. Replicating prior DKD-marker results and discovery of candidate reference mRNAs encourages further uEV biomarker studies.
Biology and Life Sciences, Biochemistry and Molecular Biology
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