New Developments in Transcriptomic Analysis of Synovial Tissue

Abstract

Transcriptomic technologies are constantly changing and improving, resulting in an ever increasing understanding of gene expression in health and disease. These technologies have been used to investigate the pathological changes occurring in the joints of rheumatoid arthritis patients, leading to discoveries of disease mechanisms, and novel potential therapeutic targets. Microarrays were initially used on both whole tissue and cell subsets to investigate research questions, with bulk RNA sequencing allowing for further elaboration of these findings. A key example is the classification of pathotypes in rheumatoid arthritis using RNA sequencing that had previously been discovered using microarray and histology. Single-cell sequencing has now delivered a step change in understanding of the diversity and function of subpopulations of cells, in particular synovial fibroblasts. Future technologies, such as high resolution spatial transcriptomics, will enable step changes integrating single cell transcriptomic and geographic data to provide an integrated understanding of synovial pathology.

Three hematologic/immune system-specific expressed genes are considered as the potential biomarkers for the diagnosis of early rheumatoid arthritis through bioinformatics analysis

“…Currently, transcriptomic and microarray analyses have been widely used in a variety of diseases, including a variety of tumours and RA, to identify new biomarkers to improve diagnosis and treatment [8][9][10][11][12]. In addition, competitive endogenous RNA (ceRNA) networks can elucidate a new mechanism for promoting the development of the disease in a transcriptional regulatory network [13].…”

Identification of Potential Key Genes in the Pathogenesis of Chronic Obstructive Pulmonary Disease Through Bioinformatics Analysis

“…Transcriptomic and high-throughput microarray/RNA-seq analyses have been widely applied to many diseases, including COPD, to explore the mechanisms and advance diagnosis/treatment ( Kaczkowski et al, 2016 ; Macias-Segura et al, 2018 ; Demircioglu et al, 2019 ; Li et al, 2019 ; Morrow et al, 2019 ; Carr et al, 2020 ; Cheng et al, 2021 ). In addition, the competitive endogenous RNA (ceRNA) networks can also provide new insights into the mechanisms of disease development in a transcriptional regulatory network ( Salmena et al, 2011 ).…”

Novel NFκB Inhibitor SC75741 Mitigates Chondrocyte Degradation and Prevents Activated Fibroblast Transformation by Modulating miR-21/GDF-5/SOX5 Signaling

“…These inflammatory mediators are produced by several types of cells in the joints, including synovial fibroblasts (SFs) [ 14 , 15 ], the dominant cells in the synovium [ 16 ]. Activated synovial fibroblasts (AFs) in the synovium regulate the influx and efflux of leukocytes and are involved in cartilage alteration [ 17 ], which in turn creates a vicious cycle that amplifies synovial inflammation through the induction of certain signaling molecules, damaging the cartilage and eventually the bone [ 11 ]. Studies have indicated that mechanical stress and elevated levels of proinflammatory cytokines in OA-affected joints disrupt osteoclast differentiation [ 18 ] and play a causative role in upsetting the critical balance between anabolic and catabolic signals in cartilage homeostasis [ 19 , 20 ].…”