The dissection of gene patterns altered in knee cartilage in a rat model of osteoarthritis

Purpose: Osteoarthritis (OA) is a joint disease that mostly affects cartilage. It is the most common cause of musculoskeletal pain and disability in the knee joint. Gene regulations are implicated in driving an imbalance between the expression of catabolic and anabolic factors, leading eventually to osteoarthritic cartilage degeneration. Functional genomics is a challenging new way to address a complex disease like osteoarthritis on a molecular level. A functional genomic approach to OA focuses on measuring changes in gene expression, allowing to discover new factors involved in the disease as well as factors involved in joint tissue development or maintenance. A deeper understanding of molecular events within the tissue cells (i.e., the chondrocytes) will provide new cellular targets for therapeutic intervention. Methods: We applied transcriptomics study in order to compare data between healthy and various OA states to better understand the mechanisms underlying a disease. In our model, knee OA was induced in male Wistar rats by intra-articular sodium monoiodoacetate (MIA) injection. Whole-genome microarrays were used to analyze gene expression alterations in a time-course of OA development (2, 14 and 28 days) in rat knee joint. We used bioinformatics tools to recognize and characterize patterns of co-expressed transcripts. Results: The identified groups of genes were analyzed for enrichment of regulatory mechanisms, functional classes and cell-type specific expression. The analysis of transcriptional alterations revealed 272 regulated transcripts (ANOVA FDR<0.1% and fold>2). Bioinformatics approaches led to the identification of five main gene expression patterns (A-E) and indicated biological pathways that mediate the alterations in transcription. Functional links that connect the identified expression patterns to the PPAR signaling, adipogenesis (A); Wnt signaling (B); endochondral ossification (C); matrix metalloproteinases, ACE/RAGE pathway (D); Toll-like receptor and IL1 signaling (E) pathways were found. The dynamic profiles of transcriptional changes were assigned to cellular compartments of the knee joint. Conclusions: Our study provides evidences that the progression of cartilage damage is driven by complex but precise regulation of gene patterns that are induced or suppressed during a various stages of cartilage damage. We see a sharp temporary loss of the transcripts involved in WNT pathway as well as constant downregulation of genes related to endochondral ossification. While, the decrease of transcript abundance of genes connected to PPARG-signaling was more gradual. Transcripts related to immunological response show early, while connected to matrix metalloproteinases delayed increase in the abundance levels. We conclude that the expression of PPARG-signaling genes correlates negatively with the different stages of OA, and matrix metalloproteinases genes correlate positively with OA development. Moreover, our results indicate that the observed transcriptional alterations are located in the diverse cellular compartments of the knee cartilage. We can speculate that during OA pathogenesis synoviocytes, osteoblasts, fibroblasts epithelial and immunological cells process specific molecular complementary (disease-relevant intracellular signaling cascades) or contrary physiological programs. The presented classification of transcriptional alterations associated with the development of cartilage degeneration provides novel insight into the OA disease process. Integration across multiple tissues holds the promise of identifying new areas of so far unrecognized molecular networks and of characterising OA processes in depth, thus leading to the development of new therapeutic interventions. Supported by National Science Centre, Poland grants: OPUS UMO-2014/13/B/NZ7/02311, ETIUDA UMO-2015/16/T/NZ7/00052 and statutory funds.