Research ExplorerPublicationsComparison of urinary extracellular vesicle isolation method...

Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease

Standard

Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease. / Barreiro, Karina; Dwivedi, Om Prakash; Leparc, German; Rolser, Marcel; Delic, Denis; Forsblom, Carol; Groop, Per-Henrik; Groop, Leif; Huber, Tobias B; Puhka, Maija; Holthofer, Harry.

In: J EXTRACELL VESICLES, Vol. 10, No. 2, 12.2020, p. e12038.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Barreiro, K, Dwivedi, OP, Leparc, G, Rolser, M, Delic, D, Forsblom, C, Groop, P-H, Groop, L, Huber, TB, Puhka, M & Holthofer, H 2020, 'Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease', J EXTRACELL VESICLES, vol. 10, no. 2, pp. e12038. https://doi.org/10.1002/jev2.12038

APA

Barreiro, K., Dwivedi, O. P., Leparc, G., Rolser, M., Delic, D., Forsblom, C., Groop, P-H., Groop, L., Huber, T. B., Puhka, M., & Holthofer, H. (2020). Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease. J EXTRACELL VESICLES, 10(2), e12038. https://doi.org/10.1002/jev2.12038

Vancouver

Barreiro K, Dwivedi OP, Leparc G, Rolser M, Delic D, Forsblom C et al. Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease. J EXTRACELL VESICLES. 2020 Dec;10(2):e12038. https://doi.org/10.1002/jev2.12038

Bibtex

@article{b89547645caf4e20b74d93e158f73f46,
title = "Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease",
abstract = "Urinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of kidney damage, holding potential to replace the conventional invasive techniques including kidney biopsy. However, comprehensive studies characterizing uEV isolation methods with patient samples are rare. Here we compared performance of three established uEV isolation workflows for their subsequent use in transcriptomics analysis for biomarker discovery in diabetic kidney disease. We collected urine samples from individuals with type 1 diabetes with macroalbuminuria and healthy controls. We isolated uEV by Hydrostatic Filtration Dialysis (HFD), ultracentrifugation (UC), and a commercial kit- based isolation method (NG), each with different established urine clearing steps. Purified EVs were analysed by electron microscopy, nanoparticle tracking analysis, and Western blotting. Isolated RNAs were subjected to miRNA and RNA sequencing. HFD and UC samples showed close similarities based on mRNA sequencing data. NG samples had a lower number of reads and different mRNA content compared to HFD or UC. For miRNA sequencing data, satisfactory miRNA counts were obtained by all methods, but miRNA contents differed slightly. This suggests that the isolation workflows enrich specific subpopulations of miRNA-rich uEV preparation components. Our data shows that HFD,UC and the kit-based method are suitable methods to isolate uEV for miRNA-seq. However, only HFD and UC were suitable for mRNA-seq in our settings.",
author = "Karina Barreiro and Dwivedi, {Om Prakash} and German Leparc and Marcel Rolser and Denis Delic and Carol Forsblom and Per-Henrik Groop and Leif Groop and Huber, {Tobias B} and Maija Puhka and Harry Holthofer",
note = "{\textcopyright} 2020 The Authors. Journal of Extracellular Vesicles published by Wiley Periodicals LLC on behalf of International Society for Extracellular Vesicles.",
year = "2020",
month = dec,
doi = "10.1002/jev2.12038",
language = "English",
volume = "10",
pages = "e12038",
journal = "J EXTRACELL VESICLES",
issn = "2001-3078",
publisher = "Taylor and Francis Ltd.",
number = "2",

}

RIS

TY - JOUR

T1 - Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease

AU - Barreiro, Karina

AU - Dwivedi, Om Prakash

AU - Leparc, German

AU - Rolser, Marcel

AU - Delic, Denis

AU - Forsblom, Carol

AU - Groop, Per-Henrik

AU - Groop, Leif

AU - Huber, Tobias B

AU - Puhka, Maija

AU - Holthofer, Harry

N1 - © 2020 The Authors. Journal of Extracellular Vesicles published by Wiley Periodicals LLC on behalf of International Society for Extracellular Vesicles.

PY - 2020/12

Y1 - 2020/12

N2 - Urinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of kidney damage, holding potential to replace the conventional invasive techniques including kidney biopsy. However, comprehensive studies characterizing uEV isolation methods with patient samples are rare. Here we compared performance of three established uEV isolation workflows for their subsequent use in transcriptomics analysis for biomarker discovery in diabetic kidney disease. We collected urine samples from individuals with type 1 diabetes with macroalbuminuria and healthy controls. We isolated uEV by Hydrostatic Filtration Dialysis (HFD), ultracentrifugation (UC), and a commercial kit- based isolation method (NG), each with different established urine clearing steps. Purified EVs were analysed by electron microscopy, nanoparticle tracking analysis, and Western blotting. Isolated RNAs were subjected to miRNA and RNA sequencing. HFD and UC samples showed close similarities based on mRNA sequencing data. NG samples had a lower number of reads and different mRNA content compared to HFD or UC. For miRNA sequencing data, satisfactory miRNA counts were obtained by all methods, but miRNA contents differed slightly. This suggests that the isolation workflows enrich specific subpopulations of miRNA-rich uEV preparation components. Our data shows that HFD,UC and the kit-based method are suitable methods to isolate uEV for miRNA-seq. However, only HFD and UC were suitable for mRNA-seq in our settings.

AB - Urinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of kidney damage, holding potential to replace the conventional invasive techniques including kidney biopsy. However, comprehensive studies characterizing uEV isolation methods with patient samples are rare. Here we compared performance of three established uEV isolation workflows for their subsequent use in transcriptomics analysis for biomarker discovery in diabetic kidney disease. We collected urine samples from individuals with type 1 diabetes with macroalbuminuria and healthy controls. We isolated uEV by Hydrostatic Filtration Dialysis (HFD), ultracentrifugation (UC), and a commercial kit- based isolation method (NG), each with different established urine clearing steps. Purified EVs were analysed by electron microscopy, nanoparticle tracking analysis, and Western blotting. Isolated RNAs were subjected to miRNA and RNA sequencing. HFD and UC samples showed close similarities based on mRNA sequencing data. NG samples had a lower number of reads and different mRNA content compared to HFD or UC. For miRNA sequencing data, satisfactory miRNA counts were obtained by all methods, but miRNA contents differed slightly. This suggests that the isolation workflows enrich specific subpopulations of miRNA-rich uEV preparation components. Our data shows that HFD,UC and the kit-based method are suitable methods to isolate uEV for miRNA-seq. However, only HFD and UC were suitable for mRNA-seq in our settings.

U2 - 10.1002/jev2.12038

DO - 10.1002/jev2.12038

M3 - SCORING: Journal article

C2 - 33437407

VL - 10

SP - e12038

JO - J EXTRACELL VESICLES

JF - J EXTRACELL VESICLES

SN - 2001-3078

IS - 2

ER -