Identification of long non-coding RNA involved in osteogenic differentiation from mesenchymal stem cells using RNA-Seq data

Abstract

ABSTRACT. The aim of this study was to identify long non-coding RNA (lncRNA) associated with osteogenic differentiation from mesenchymal stem cells (MSCs) using high-throughput RNA sequencing (RNA-Seq) data. RNA-Seq dataset was obtained from the European Bioinformatics Institute (accession No. PRJEB4496), including two replicates each for immortalized mesenchymal stem cells iMSC#3 cultured in growth medium (GM) and differentiation medium (DM) for 28 days. The clean reads were aligned to a hg19 reference genome by Tophat and assembled by Cufflinks to identify the known and novel transcripts. RPKM values were calculated to screen for differentially expressed RNA. Novel lncRNA were screened based on various filter criteria. Subsequently, the underlying function of novel lncRNAs were predicted by functional annotation by ERPIN, a coexpression network was constructed by WGCNA and the KEGG pathway enriched by KOBAS. A total of 3171 RNA differentially expressed between the DM and GM groups (2597 mRNA and 574 lncRNA) were identified. Among the 574 differentially expressed lncRNA, 357 were known and 217 were novel lncRNA. Furthermore, 32 novel lncRNA were found to be miRNA precursors (including miR-689, miR-640, miR-601, and miR-544). A total of 18269 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 18268-18279 (2015) Identifying lncRNA affecting osteogenic differentiation 14,275 co-expression relationships and 217 co-expression networks were obtained between novel lncRNA and mRNA. The differentially expressed lncRNA and mRNA were enriched into 6 significant pathways, including those for cancer, ECM-receptor interaction, and focal adhesion. Therefore, novel lncRNAwere identified and their underlying function predicted, which may provide the basis for future analyses of the role of lncRNA in osteoblastic differentiation.

Silencing of Long Non-Coding RNA NONHSAT009968 Ameliorates the Staphylococcal Protein A-Inhibited Osteogenic Differentiation in Human Bone Mesenchymal Stem Cells

“…Song et al identified 574 lncRNAs that were differentially expressed during osteogenic differentiation [23], and the function of some of these lncRNAs on osteogenic differentiation has been confirmed. For example, down-regulation of lncRNA-ANCR promotes osteogenic differentiation of periodontal ligament stem cells [11] and upregulation of lncRNA MEG3 promotes osteogenic differentiation of MSCs [23]. These studies indicate that lncRNAs play an important role in regulating osteogenic differentiation of MSCs.…”

“…In a recent study, Song et al identified lncRNAs associated with osteogenic differentiation from mesenchymal stem cells (MSCs) using high-throughput RNA sequencing (RNA-Seq) data [23]. Song et al identified 574 lncRNAs that were differentially expressed during osteogenic differentiation [23], and the function of some of these lncRNAs on osteogenic differentiation has been confirmed.…”

“…In a recent study, Song et al identified lncRNAs associated with osteogenic differentiation from mesenchymal stem cells (MSCs) using high-throughput RNA sequencing (RNA-Seq) data [23]. Song et al identified 574 lncRNAs that were differentially expressed during osteogenic differentiation [23], and the function of some of these lncRNAs on osteogenic differentiation has been confirmed. For example, down-regulation of lncRNA-ANCR promotes osteogenic differentiation of periodontal ligament stem cells [11] and upregulation of lncRNA MEG3 promotes osteogenic differentiation of MSCs [23].…”

“…The network regulating the osteogenic differentiation process of BMSCs has been studied comprehensively. The osteogenic differentiation ability of BMSCs may be affected by many regulatory factors, such as proteins, microRNAs, and lncRNAs [23][24][25][26][27]. Osteomyelitis, which commonly occurs during bone healing, is known to inhibit osteogenic differentiation and bone formation [28].…”

Detailed analysis of public RNAseq data and long non-coding RNA: a proposed enhancement to mesenchymal stem cell characterisation

“…Considering their different therapeutic properties (chondro and osteo differentiation potential, immunomodulation and production of trophic factors) [14] and given the increasing usage of these cells for academic and preclinical research [15], a detailed molecular characterisation of MSCs and predictive marker of functionality will constitute an important tool in regenerative medicine. lncRNAs have emerged as a class of transcripts with tissue-specific expression and important functions, such as the regulation of MSCs function [16,17,18], and remain largely unexplored in these cells.…”