SOX4 and RELA Function as Transcriptional Partners to Regulate the Expression of TNF- Responsive Genes in Fibroblast-Like Synoviocytes

Abstract

SOX4 belongs to the group C of the SOX transcription factor family. It is a critical mediator of tumor necrosis factor alpha (TNF)-induced transformation of fibroblast-like s-ynoviocytes (FLS) in arthritis. In this study we investigated the genome wide association between the DNA binding and transcriptional activities of SOX4 and the NF-kappaB signaling transcription factor RELA/p65 downstream of TNF signaling. We used ChIP-seq assays in mouse FLS to compare the global DNA binding profiles of SOX4 and RELA. RNA-seq of TNF-induced wildtype and SoxC-knockout FLS was used to identify the SOX4-dependent and independent aspects of the TNF-regulated transcriptome. We found that SOX4 and RELA physically interact with each other on the chromatin. Interestingly, ChIP-seq assays revealed that 70.4% of SOX4 peak summits were within 50bp of the RELA peak summits suggesting that both proteins bind in close-proximity on regulatory sequences, enabling them to co-operatively regulate gene expression. By integrating the ChIP-seq results with RNA-seq from SoxC-knockout FLS we identified a set of TNF-responsive genes that are targets of the RELA-SOX4 transcriptional complex. These TNF-responsive and RELA-SOX4-depenedent genes included inflammation mediators, histone remodeling enzymes and components of the AP-1 signaling pathway. We also identified an autoregulatory mode of SoxC gene expression that involves a TNF-mediated switch from RELA binding to SOX4 binding in the 3’ UTR of Sox4 and Sox11 genes. In conclusion, our results show that SOX4 and RELA together orchestrate a multimodal regulation of gene expression downstream of TNF signaling. Their interdependent activities play a pivotal role in the transformation of FLS in arthritis and in the inflammatory pathology of diverse tissues where RELA and SOX4 are co-expressed.

SOXC Transcription Factors as Diagnostic Biomarkers and Therapeutic Targets for Arthritis

“…Among the signaling pathways that regulate FLS transformation, the NF-κB signaling transcription factor RELA/p65, the downstream of TNF-α, was shown to play a crucial role in joint degeneration, synovial hyperplasia, and bone loss [ 26 ]. Related to that, in a genome-wide association study investigating the transcriptional activities and DNA binding of SOX4 and RELA/p65, SOX4 and RELA were found to physically interact with each other on the chromatin and orchestrate several processes to regulate the expression of the downstream genes of TNF and then enhance the transformation of FLSs in arthritis [ 10 ]. Together these data reflect the pivotal role of SOXC TFs, especially SOX4, in regulating FLS and ELS actions under the in vivo inflammatory conditions associated with arthritis.…”

“…As indicated above, RA is basically chronic inflammatory disease, in which a high level of SOX4 seems to be required for the progression of inflammatory conditions at a local site. This has been evidenced by the fact that SOX4 is upregulated in both RA patients and RA mouse models [ 10 , 11 , 17 , 27 , 28 ]. The mechanistic actions associated with SOX4 upregulation and regulatory function during RA are discussed in detail below.…”

“…Mechanistically, SOX4 promoting arthritis has been documented to occur through regulating several signaling pathways. (1) As a critical mediator of the TNF-induced transformation of FLS, SOX4 interacts with RELA (NF-κB signaling molecule) to regulate the expression of TNF downstream genes and thus maintains the transformation of FLS and inflammatory pathology in arthritis [ 10 , 23 ]. (2) SOX4 is regulated by the ROS/TGF-β signal to enhance OA pathogenesis and FLS senescence [ 5 ].…”

“…Through direct and indirect binding to SOX4 TF, several upstream factors and signaling molecules have been recently reported to target SOX4 during arthritis, such as ROS)/TGF, TNF, SMOC2, AGEs, Lnc PART1, and the miRNA, miR-31 ( Figure 1 ). The proinflammatory cytokines can target SOX4 and stabilize it to enhance the transformation of FLS in arthritic disease [ 10 , 23 ]. The transformed FLS promote joint degeneration in the autoimmune forms of arthritis through the production of more inflammatory cytokines and catabolic enzymes [ 25 , 35 ].…”

“…SOXC is a superfamily of TFs that have been recently shown by several studies to be involved in the onset and pathogenesis of arthritis. Interestingly, the great majority of these studies have been conducted during the last 5 years [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]. The SOXC gene family encodes SOX4, SOX11, and SOX12 TFs that contain a conserved high mobility group (HMG)-box domain by which SOXC proteins are able to bind to minor grooves in the DNA.…”