Disease Activity-Associated Alteration of mRNA m5 C Methylation in CD4+ T Cells of Systemic Lupus Erythematosus

Abstract

Epigenetic processes including RNA methylation, post-translational modifications, and non-coding RNA expression have been associated with the heritable risks of systemic lupus erythematosus (SLE). In this study, we aimed to explore the dysregulated expression of 5-methylcytosine (m 5 C) in CD4 + T cells from patients with SLE and the potential function of affected mRNAs in SLE pathogenesis. mRNA methylation profiles were ascertained through chromatography-coupled triple quadrupole mass spectrometry in CD4 + T cells from two pools of patients with SLE exhibiting stable activity, two pools with moderate-to-major activity, and two pools of healthy controls (HCs). Simultaneously, mRNA methylation profiles and expression profiling were performed using RNA-Bis-Seq and RNA-Seq, respectively. Integrated mRNA methylation and mRNA expression bioinformatics analysis was comprehensively performed. mRNA methyltransferase NSUN2 expression was validated in CD4 + T cells from 27 patients with SLE and 28 HCs using real-time polymerase chain reaction and western blot analyses. Hypomethylated-mRNA profiles of NSUN2-knockdown HeLa cells and of CD4 + T cells of patients with SLE were jointly analyzed using bioinformatics. Eleven methylation modifications (including elevated Am, 3 OMeA, m 1 A, and m 6 A and decreased , m 3 C, m 1 G, m 5 U, and t 6 A levels) were detected in CD4 + T cells of patients with SLE. Additionally, decreased m 5 C levels, albeit increased number of m 5 C-containing mRNAs, were observed in CD4 + T cells of patients with SLE compared with that in CD4 + T cells of HCs. m 5 C site distribution in mRNA transcripts was highly conserved and enriched in mRNA translation initiation sites. In particular, hypermethylated m 5 C or/and significantly up-regulated genes in SLE were significantly involved in immune-related and inflammatory pathways, including immune system,

Epitranscriptomic N4-Acetylcytidine Profiling in CD4+ T Cells of Systemic Lupus Erythematosus

“…In contrast with the lower NAT10 expression in SLE patients, hyperacetylated peaks were observed in SLE patients. Similar to the methyltransferases of mRNA m 5 C modification in SLE, downregulated methyltransferase expressions along with aberrant mRNA m 5 C modification (hyper-and hypo-) were also found in SLE patients (Guo et al, 2020). Similar results have been obtained in bladder cancer, zebrafish, and PM2.5induced pulmonary fibrosis mouse models Yang et al, 2019;Han et al, 2020).…”

“…A total of 51 age- and sex-matched HCs without renal failure, heart failure, or arthralgia, and free from any inflammatory conditions, were recruited from the same hospital. For mRNA liquid chromatography-coupled triple quadrupole tandem mass spectrometry (LC-MS/MS) and RNA ac 4 C-RIP-Seq, 10 SLE patients and 18 HCs were divided into four groups as our previous report ( Guo et al, 2020 ). For each SLE group, five SLE samples were mixed and sequenced; similarly, each control group comprised nine mixed and sequenced.…”

“…Moreover, several studies have found that epigenetic changes, such as DNA and mRNA modifications are dysregulated and can alter gene expression in SLE CD4 + T cells ( Zhang et al, 2013 ; Zhao et al, 2014 , 2016 ). Recently, we also identified novel aberrant mRNA modification, 5-methylcytidine (m 5 C), linked to critical immune pathways in lupus CD4 + T cells ( Guo et al, 2020 ).…”

Alteration of mRNA 5-Methylcytosine Modification in Neurons After OGD/R and Potential Roles in Cell Stress Response and Apoptosis

“…Finally, the GSEA results indicated that gene sets of apoptotic processes and response to stress were significantly up-regulated ( Figure 6C ). Moreover, our analysis revealed that the level of methylation increased significantly after OGD/R ( Figure 6D ), while the four-quadrant diagram indicated that a strong correlation did not exist between the mRNA m 5 C modification level and the expression level ( Figure 6E ), and similar results were previously reported in systemic lupus erythematosus (SLE; Guo et al, 2020 ). We further investigated the biological process enrichment of mRNAs that were both upregulated and hypermethylated using GO functional analysis.…”

“…To further explore the role of mRNA m 5 C modification in neurons, we performed bioinformatics analysis of 406 differentially expressed m 5 C-methylated transcripts, including 282 hypermethylated and 124 hypomethylated transcripts ( p < 0.05). Our analyses did not reveal a strong relationship between the m 5 C methylation level and the corresponding mRNA expression level, which is similar to the results of previous reports on bladder cancer and SLE ( Chen et al, 2019b ; Guo et al, 2020 ), and previous studies have shown that m 5 C methylation plays an important role in promoting the process of nuclear export ( Yang et al, 2017 ). Therefore, the specific regulatory mechanism of m 5 C on mRNA deserves further exploration.…”