Supplementary files of a manuscript entiled "Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck Disease identified by RNA-sequencing"

These part of the content are some supplementary files of a manuscript entitled " Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck Disease identified by RNA-sequencing "

Abstract:

Kashin-Beck disease (KBD) is a chronic, endemic and deforming osteochondropathy, whose basic pathological alterations include apoptosis and necrosis of chondrocytes in articular cartilage and growth plate and imbalanced extracellular matrix metabolism. Numerous studies have reported that long noncoding RNAs (lncRNAs) and microRNA (miRNAs) were aberrantly expressed in KBD. In our research, we comprised 5 KBD patients and 5 healthy individuals to compare the expression profiles of mRNAs, lncRNAs and miRNAs through RNA-sequencing (RNA-seq). Bioinformatic analysis of GO and KEGG was employed to conduct functional annotation and pathway enriched analysis. Totally, 3,194 mRNAs, 4,103 lncRNAs and 1,550 miRNAs were detected differentially expressed by RNA-seq (P <0.05; |log2FC |≥ 1). Lysosome pathway, Wnt signaling pathway, TNF signaling pathway, endocytosis and mTOR signaling pathway were identified involved in KBD development according to the result of KEGG analysis. In addition, a ceRNA network based on lncRNA-miRNA-mRNA was constructed to probe into the intricate regulatory mechanism and interaction between transcripts and visualized with Cytoscape software. Four aberrantly expressed genes, FOSB, EGR3, BCAM and SOX6, were determined their ce-lncRNAs through the network. Among the identified DElncRNAs, we selected 8 differentially expressed lncRNAs to confirm the reliability of RNA-seq data by qRT-PCR in 11 KBD patients and 11 healthy individuals. We aimed to provide a comprehensive understanding of mRNA, lncRNAs and miRNAs alterations between KBD patients and healthy individuals, meanwhile, to reveal several potential causative molecular and signaling pathways of KBD involved.