Identification of differentially expressed genes and pathways crosstalk analysis in Rheumatoid and Osteoarthritis using next-generation sequencing and protein-protein networks

Abstract

Osteoarthritis occurs when protective cartilage of bones worn out. Similarlty, cartilage damage occurs mainly in the pannus cartilage in rheumatoid arthritis. It is a potentially debilitating condition, affecting women two to three times more often than men. The cause and prognosis of rheumatoid and osteoarthritis are still poorly known. However, advances in the study of disease pathogenesis have encouraged the creation of new therapeutics with improved outcomes. The purpose of this study is to investigate the differentially expressed genes potentially involved in dysregulated rheumatoid arthritis (RA) and their association to other types of arthritis, including osteoarthritis (OA). Complete RNAs were isolated for RNA expression profiling using next-generation sequencing from human primary cultured normal and RA chondrocytes. From RNA sequencing results 250 differentially expressed genes were identified using bioinformatics analysis, of which 32 were found to be significantly playing role in RA pathogenesis and its associated diseases. Molecular ontologies of the identified genes showed they are connected to Innate immune response, Protein phosphorylation, Transcription initiation from RNA polymerase II promoter, Immune response, Neoplasms of bones, as well as osteorthritis, and Rheumatoid arthritis. Among the identified genes, TRAF1, TRAF2, BAMP, STX11, MEOX2, AES, REL, FHL3, PNMA1, SGTA, LZTS2, SIAH2, PNMA1, and TFCP2 were found to be highly enriched in the protein-protein interaction network. The significant cross talks were found in Hypertrophic cardiomyopathy, Small cell lung cancer, Proteasome, p53 signaling pathway, Arrhythmogenic right ventricular cardiomyopathy, Small cell lung cancer, SNARE interactions in vesicular transport, RIG-I-like receptor signaling pathway, and Hypertrophic cardiomyopathy pathways. The results offer new opportunities for target gene control in RA and OA cartilage destruction.

Keywords: Cartilage; Chondrocytes; Cross talk; DEGs; NGS data.

Fig. 1

Heat map of RA DEGs. The relative levels of expression of a single gene for all samples are expressed in each row; each column represents the expression levels for a single sample. The black color reflects favorably reported corresponding gene-term association, green color displays corresponding gene-term association not yet reported.

Fig. 2

The Interaction network of DEGs obtained through Gene Clip 2.0 server, the weight of the edges is written in numbers, the circles represent gene, triangles are displaying the enzymes, whereas transcription factors are shown by squares. The arrowheads represent interactions, whereas green circles are showing the gene regulations, and horizontal lines in front of arrows represent inhibitions.

Fig. 3

The disease gene interaction network of DEGs, blue squares represent associated diseases of DEGs and Red nodes show DEGs, DEGs for which no disease association was observed are shown by light pink color.

Fig. 4

Sub-networks functional modules obtained from the PPI shown in Fig. 3.

Fig. 5

Crosstalk network of Rheumatoid Arthritis related DEGs and their associated pathways.