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

The emerging epitranscriptome plays an essential role in autoimmune disease. As a novel mRNA modification, N4-acetylcytidine (ac 4 C) could promote mRNA stability and translational efficiency. However, whether epigenetic mechanisms of RNA ac 4 C modification are involved in systemic lupus erythematosus (SLE) remains unclear. Herein, we detected eleven modifications in CD4 + T cells of SLE patients using mass spectrometry (LC-MS/MS). Furthermore, using samples from four CD4 + T cell pools, we identified lower modification of ac 4 C mRNA in SLE patients as compared to that in healthy controls (HCs). Meanwhile, significantly lower mRNA acetyltransferase NAT10 expression was detected in lupus CD4 + T cells by RT-qPCR. We then illustrated the transcriptome-wide ac 4 C profile in CD4 + T cells of SLE patients by ac 4 C-RIP-Seq and found ac 4 C distribution in mRNA transcripts to be highly conserved and enriched in mRNA coding sequence regions. Using bioinformatics analysis, the 3879 and 4073 ac 4 C hyper-acetylated and hypoacetylated peaks found in SLE samples, respectively, were found to be significantly involved in SLE-related function enrichments, including multiple metabolic and transcription-related processes, ROS-induced cellular signaling, apoptosis signaling, and NF-κB signaling. Moreover, we demonstrated the ac 4 C-modified regulatory network of gene biological functions in lupus CD4 + T cells. Notably, we determined that the 26 upregulated genes with hyperacetylation played essential roles in autoimmune diseases and disease-related processes. Additionally, the unique ac 4 C-related transcripts, including USP18 , GPX1 , and RGL1 , regulate mRNA catabolic processes and translational initiation. Our study identified novel dysregulated ac 4 C mRNAs associated with critical immune and inflammatory responses, that have translational potential in lupus CD4 + T cells. Hence, our findings reveal transcriptional significance and potential therapeutic targets of mRNA ac 4 C modifications in SLE pathogenesis.