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Capturing the Kidne...
Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles—From Pre-Analytical Obstacles to Biomarker Research
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- Barreiro, Karina (author)
- University of Helsinki
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- Dwivedi, Om Prakash (author)
- University of Helsinki
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- Rannikko, Antti (author)
- University of Helsinki
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- Holthöfer, Harry (author)
- University Medical Center Hamburg-Eppendorf,University of Helsinki
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- Tuomi, Tiinamaija (author)
- Lund University,Lunds universitet,Molekylär endokrinologi,Forskargrupper vid Lunds universitet,Diabetiska komplikationer,Molecular Endocrinology,Lund University Research Groups,Diabetic Complications,University of Helsinki,Helsinki University Central Hospital,Folkhälsan Research Center
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- Groop, Per Henrik (author)
- University of Helsinki,Monash University,Folkhälsan Research Center
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- Puhka, Maija (author)
- University of Helsinki
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(creator_code:org_t)
- 2023
- 2023
- English.
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In: Genes. - 2073-4425. ; 14:7
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Abstract
Subject headings
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- Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of preanalytical choices hinder biomarker studies. We aimed to assess how preanalytical 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, pre-analytical 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Urologi och njurmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Urology and Nephrology (hsv//eng)
Keyword
- diabetic kidney disease
- exosomes
- miRNA
- mRNA
- reference genes
- sequencing
- urinary extracellular vesicles
- urine
Publication and Content Type
- art (subject category)
- ref (subject category)
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