Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles – from Preanalytical Obstacles to Biomarker Research

Version 1 : Received: 29 May 2023 / Approved: 30 May 2023 / Online: 30 May 2023 (08:23:23 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

Keywords

urinary extracellular vesicles,; exosomes; urine; diabetic kidney disease; reference genes; miRNA; mRNA; sequencing

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Comments (0)

We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.

Leave a public comment
Send a private comment to the author(s)
* All users must log in before leaving a comment
Views 0
Downloads 0
Comments 0


×
Alerts
Notify me about updates to this article or when a peer-reviewed version is published.
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.