Optimisation of Laboratory Methods for Whole Transcriptomic RNA Analyses in Human Left Ventricular Biopsies and Blood Samples of Clinical Relevance

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2019 Mar 15

PMID 30870483

Citations 8

Authors

Kerrie L Ford

Maryam Anwar

Rachael Heys

Eltayeb Mohamed Ahmed

Massimo Caputo

Laurence Game

Barnaby C Reeves

Prakash P Punjabi

Gianni D Angelini

Enrico Petretto

Costanza Emanueli

Affiliations

Soon will be listed here.

Abstract

This study aimed to optimise techniques for whole transcriptome and small RNA analyses on clinical tissue samples from patients with cardiovascular disease. Clinical samples often represent a particular challenge to extracting RNA of sufficient quality for robust RNA sequencing analysis, and due to availability, it is rarely possible to optimise techniques on the samples themselves. Therefore, we have used equivalent samples from pigs undergoing cardiopulmonary bypass surgery to test different protocols for optimal RNA extraction, and then validated the protocols in human samples. Here we present an assessment of the quality and quantity of RNA obtained using a variety of commercially-available RNA extraction kits on both left ventricular biopsies and blood plasma. RNA extraction from these samples presents different difficulties; left ventricular biopsies are small and fibrous, while blood plasma has a low RNA content. We have validated our optimised extraction techniques on human clinical samples collected as part of the ARCADIA (Association of non-coding RNAs with Coronary Artery Disease and type 2 Diabetes) cohort study, resulting in successful whole transcriptome and small RNA sequencing of human left ventricular tissue.

Citing Articles

Small Extracellular Vesicles in the Pericardium Modulate Macrophage Immunophenotype in Coronary Artery Disease.

Ben-Aicha S, Anwar M, Vilahur G, Martino F, Kyriazis P, de Winter N JACC Basic Transl Sci. 2024; 9(9):1057-1072.

PMID: 39444932 PMC: 11494395. DOI: 10.1016/j.jacbts.2024.05.003.

Preanalytical, analytical and postanalytical considerations in circulating microRNAs measurement.

Zendjabil M Biochem Med (Zagreb). 2024; 34(2):020501.

PMID: 38882585 PMC: 11177657. DOI: 10.11613/BM.2024.020501.

Prospective multiparametric CMR characterization and MicroRNA profiling of anthracycline cardiotoxicity: A pilot translational study.

Harries I, Biglino G, Ford K, Nelson M, Rego G, Srivastava P Int J Cardiol Heart Vasc. 2022; 43:101134.

PMID: 36389268 PMC: 9647504. DOI: 10.1016/j.ijcha.2022.101134.

Assessment of RNA extraction protocols from cladocerans.

Razak M, Aris A, Yusoff F, Norhana Balia Yusof Z, Kim S, Kim K PLoS One. 2022; 17(4):e0264989.

PMID: 35472091 PMC: 9041806. DOI: 10.1371/journal.pone.0264989.

Dysregulation of Circulating miR-24-3p in Children with Obesity and Its Predictive Value for Metabolic Syndrome.

Zhang B, Xing L, Wang B Obes Facts. 2021; 14(5):456-462.

PMID: 34428771 PMC: 8546450. DOI: 10.1159/000515720.

References

Vigneron N, Meryet-Figuiere M, Guttin A, Issartel J, Lambert B, Briand M . Towards a new standardized method for circulating miRNAs profiling in clinical studies: Interest of the exogenous normalization to improve miRNA signature accuracy. Mol Oncol. 2016; 10(7):981-92. PMC: 5423189. DOI: 10.1016/j.molonc.2016.03.005. View

Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, Yerushalmi N . Serum microRNAs are promising novel biomarkers. PLoS One. 2008; 3(9):e3148. PMC: 2519789. DOI: 10.1371/journal.pone.0003148. View

Kirschner M, van Zandwijk N, Reid G . Cell-free microRNAs: potential biomarkers in need of standardized reporting. Front Genet. 2013; 4:56. PMC: 3630323. DOI: 10.3389/fgene.2013.00056. View

El-Khoury V, Pierson S, Kaoma T, Bernardin F, Berchem G . Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material. Sci Rep. 2016; 6:19529. PMC: 4726450. DOI: 10.1038/srep19529. View

Brunet-Vega A, Pericay C, Quilez M, Ramirez-Lazaro M, Calvet X, Lario S . Variability in microRNA recovery from plasma: Comparison of five commercial kits. Anal Biochem. 2015; 488:28-35. DOI: 10.1016/j.ab.2015.07.018. View

Robinson M, Oshlack A . A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010; 11(3):R25. PMC: 2864565. DOI: 10.1186/gb-2010-11-3-r25. View

Kumarswamy R, Volkmann I, Thum T . Regulation and function of miRNA-21 in health and disease. RNA Biol. 2011; 8(5):706-13. PMC: 3256347. DOI: 10.4161/rna.8.5.16154. View

Cheng Y, Zhang C . MicroRNA-21 in cardiovascular disease. J Cardiovasc Transl Res. 2010; 3(3):251-5. PMC: 3611957. DOI: 10.1007/s12265-010-9169-7. View

Mitchell P, Parkin R, Kroh E, Fritz B, Wyman S, Pogosova-Agadjanyan E . Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A. 2008; 105(30):10513-8. PMC: 2492472. DOI: 10.1073/pnas.0804549105. View

10.

Chistiakov D, Orekhov A, Bobryshev Y . The role of miR-126 in embryonic angiogenesis, adult vascular homeostasis, and vascular repair and its alterations in atherosclerotic disease. J Mol Cell Cardiol. 2016; 97:47-55. DOI: 10.1016/j.yjmcc.2016.05.007. View

11.

Burgos K, Javaherian A, Bomprezzi R, Ghaffari L, Rhodes S, Courtright A . Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing. RNA. 2013; 19(5):712-22. PMC: 3677285. DOI: 10.1261/rna.036863.112. View

12.

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

13.

Guariguata L, Whiting D, Hambleton I, Beagley J, Linnenkamp U, Shaw J . Global estimates of diabetes prevalence for 2013 and projections for 2035. Diabetes Res Clin Pract. 2014; 103(2):137-49. DOI: 10.1016/j.diabres.2013.11.002. View

14.

Caporali A, Emanueli C . MicroRNA-503 and the extended microRNA-16 family in angiogenesis. Trends Cardiovasc Med. 2012; 21(6):162-6. PMC: 3407871. DOI: 10.1016/j.tcm.2012.05.003. View

15.

Mayr M, Lee R, Kaudewitz D, Zampetaki A, Channon K . Effects of heparin on temporal microRNA profiles. J Am Coll Cardiol. 2013; 63(9):940-1. PMC: 5357045. DOI: 10.1016/j.jacc.2013.07.118. View

16.

Biglino G, Caputo M, Rajakaruna C, Angelini G, Van Rooij E, Emanueli C . Modulating microRNAs in cardiac surgery patients: Novel therapeutic opportunities?. Pharmacol Ther. 2016; 170:192-204. DOI: 10.1016/j.pharmthera.2016.11.004. View

17.

Mateescu B, Kowal E, van Balkom B, Bartel S, Bhattacharyya S, Buzas E . Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles. 2017; 6(1):1286095. PMC: 5345583. DOI: 10.1080/20013078.2017.1286095. View

18.

Vickers K, Palmisano B, Shoucri B, Shamburek R, Remaley A . MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol. 2011; 13(4):423-33. PMC: 3074610. DOI: 10.1038/ncb2210. View

19.

Huang L, Li L, Chen X, Zhang H, Shi Z . MiR-103a targeting Piezo1 is involved in acute myocardial infarction through regulating endothelium function. Cardiol J. 2016; 23(5):556-562. DOI: 10.5603/CJ.a2016.0056. View

20.

Arroyo J, Chevillet J, Kroh E, Ruf I, Pritchard C, Gibson D . Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A. 2011; 108(12):5003-8. PMC: 3064324. DOI: 10.1073/pnas.1019055108. View