Comprehensive Analysis and Functional Characteristics of Differential Expression of N6-Methyladenosine Methylation Modification in the Whole Transcriptome of Rheumatoid Arthritis

Abstract

N6-methyladenosine (m6A) modification is the most prevalent chemical modification in eukaryotic mRNA and is associated with the development of various immune diseases. However, the role of m6A methylation in rheumatoid arthritis (RA) development is unclear. We preliminarily explored the role of m6A methylation-related mRNAs in RA for its clinical application. The discovery of m6A methylation-modifying genes in this study may provide a fresh perspective on the development of drugs for RA treatment. High-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to assess whole-transcriptome m6A modifications in the synovium of patients with RA. The relationship between m6A-modified target genes and RA inflammation and macrophages was determined. The expression of the m6A-modified significant transcript-enriched inflammatory signaling pathway was assessed through animal experiments. Differentially expressed m6A genes were correlated with macrophage activation involved in immune response, vascular endothelium, MAPK signaling pathway, PI3K − Akt signaling pathway, and other inflammatory processes. Furthermore, combined analysis with m6A-seq and RNA-seq revealed 120 genes with significant changes in both m6A modification and mRNA expression. We selected the top 3 candidate mRNAs that were upregulated and downregulated simultaneously. The expression of phosphatase and tensin homolog deleted on chromosome ten (PTEN) mRNA and protein in RA patients was lower than that in healthy control (HC). SHC-binding protein 1 (SHCBP1) and neurexophilin-3 (NXPH3) mRNA expressions were increased in RA patients. The expression of M1 macrophages was increased in RA patients. RA markers are such as rheumatoid factor (RF) and peptide containing citrulline (CCP). Further animal experiments showed that the expression of synovial MAPK, PI3K, and Akt1 proteins in the RA model was increased, and the PTEN, p-PTEN protein expression was decreased. PI3K, Akt1, PTEN, and p-PTEN were correlated to RA joint inflammation. This study revealed a unique pattern of differential m6A methylation modifications in RA and concluded that m6A modification is related to the occurrence of RA synovial inflammation.

Global research hotspots and frontier trends of epigenetic modifications in autoimmune diseases: A bibliometric analysis from 2012 to 2022

“…[ 66 ] In RA, DNA methylation changes in immune-related genes such as HLA-DRB1 and PTPN22 are closely associated with disease risk and clinical manifestations. [ 67 , 68 ] Moreover, abnormal regulation of gene methylation is also associated with the development and pathological features of autoimmune diseases such as SLE and Sjögren’s syndrome. [ 69 , 70 ] Additionally, the abnormal expression of certain microRNAs is linked to the occurrence and progression of autoimmune diseases.…”

Role of m6A modification and novel circ_0066715/ miR-486-5p/ ETS1 axis in rheumatoid arthritis macrophage polarization progression

“…m6A methylation modification is also crucial in RA development [14,42,43]. m6A methylation is an abundant internal modification on RNA [44][45][46]. The binding protein can recognize the m6A methylation site of mRNA, affecting the abundance and function of mRNAs with m6A modification sites.…”

M6A methylation modification in autoimmune diseases, a promising treatment strategy based on epigenetics

“…The expression of m6A modified significantly transcriptor-rich inflammatory signaling pathway was evaluated through animal experiments, and it was found that the differential expression of m6A gene is closely related to macrophage activation and inflammatory processes such as MAPK, PI3K-Akt and JAK-STAT signaling pathways. Some genes enriched in the PI3K-Akt and MAPK pathways are mostly inhibitors of the corresponding pathways, including PTEN, ASPM and SHCBP1 [ 46 , 47 ]. Through data mining, Liu et al [ 48 ] demonstrated that the m6A-RNA methylation regulators (m6A-RMRs) were more differentially expressed in rheumatoid arthritis (RA) and autoimmune skin diseases than those in other autoimmune diseases.…”