RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

Rodrigo Coutinho de Almeida; Yolande F M Ramos; Ahmed Mahfouz; Wouter den Hollander; Nico Lakenberg; Evelyn Houtman; Marcella van Hoolwerff; H Eka D Suchiman; Alejandro Rodríguez Ruiz; P Eline Slagboom; Hailiang Mei; Szymon M Kiełbasa; Rob G H H Nelissen; Marcel Reinders; Ingrid Meulenbelt

doi:10.1136/annrheumdis-2018-213882

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

Ann Rheum Dis. 2019 Feb;78(2):270-277. doi: 10.1136/annrheumdis-2018-213882. Epub 2018 Dec 1.

Authors

Rodrigo Coutinho de Almeida^#¹, Yolande F M Ramos^#¹, Ahmed Mahfouz^{2

3}, Wouter den Hollander¹, Nico Lakenberg¹, Evelyn Houtman¹, Marcella van Hoolwerff¹, H Eka D Suchiman¹, Alejandro Rodríguez Ruiz¹, P Eline Slagboom¹, Hailiang Mei⁴, Szymon M Kiełbasa^{1

4}, Rob G H H Nelissen⁵, Marcel Reinders^{1

2}, Ingrid Meulenbelt⁶

Affiliations

¹ Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
² The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
³ Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.
⁴ Sequence Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands.
⁵ Department of Orthopaedics, Leiden University Medical Center, Leiden, The Netherlands.
⁶ Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands i.meulenbelt@lumc.nl.

^# Contributed equally.

Abstract

Objective: To uncover the microRNA (miRNA) interactome of the osteoarthritis (OA) pathophysiological process in the cartilage.

Methods: We performed RNA sequencing in 130 samples (n=35 and n=30 pairs for messenger RNA (mRNA) and miRNA, respectively) on macroscopically preserved and lesioned OA cartilage from the same patient and performed differential expression (DE) analysis of miRNA and mRNAs. To build an OA-specific miRNA interactome, a prioritisation scheme was applied based on inverse Pearson's correlations and inverse DE of miRNAs and mRNAs. Subsequently, these were filtered by those present in predicted (TargetScan/microT-CDS) and/or experimentally validated (miRTarBase/TarBase) public databases. Pathway enrichment analysis was applied to elucidate OA-related pathways likely mediated by miRNA regulatory mechanisms.

Results: We found 142 miRNAs and 2387 mRNAs to be differentially expressed between lesioned and preserved OA articular cartilage. After applying prioritisation towards likely miRNA-mRNA targets, a regulatory network of 62 miRNAs targeting 238 mRNAs was created. Subsequent pathway enrichment analysis of these mRNAs (or genes) elucidated that genes within the 'nervous system development' are likely mediated by miRNA regulatory mechanisms (familywise error=8.4×10^-5). Herein NTF3 encodes neurotrophin-3, which controls survival and differentiation of neurons and which is closely related to the nerve growth factor.

Conclusions: By an integrated approach of miRNA and mRNA sequencing data of OA cartilage, an OA miRNA interactome and related pathways were elucidated. Our functional data demonstrated interacting levels at which miRNA affects expression of genes in the cartilage and exemplified the complexity of functionally validating a network of genes that may be targeted by multiple miRNAs.

Keywords: data integration; mRNA; microRNAs; osteoarthritis; regulatory networks.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cartilage, Articular / chemistry*
Computational Biology / methods*
Humans
MicroRNAs / analysis*
Osteoarthritis / genetics*
RNA, Messenger / analysis*
Sequence Analysis, RNA

Substances

MicroRNAs
RNA, Messenger