High throughput sequencing revealed enhanced cell cycle signaling in SLE patients

Abstract

The multi-system involvement and high heterogeneity of systemic lupus erythematosus (SLE) pose great challenges to its diagnosis and treatment. The purpose of the current study is to identify genes and pathways involved in the pathogenesis of SLE. High throughput sequencing was performed on the PBMCs from SLE patients. We conducted differential gene analysis, gene ontology (GO) analysis, kyoto encyclopedia of genes and genomes (KEGG) analysis, and quantitative real-time PCR (qRT-PCR) verification. Protein–protein interaction (PPI) analysis, alternative splicing analysis, and disease correlation analysis were conducted on some key pathogenic genes as well. Furthermore, si-CDC6 was used for transfection and cell proliferation was monitored using a cell counting kit-8 (CCK-8) assay. We identified 2495 differential genes (1494 upregulated and 1001 downregulated) in SLE patients compared with healthy controls. The significantly upregulated genes were enriched in the biological process-related GO terms of the cell cycle, response to stress, and chromosome organization. KEGG enrichment analysis revealed 7 significantly upregulated pathways including SLE, alcoholism, viral carcinogenesis, cell cycle, proteasome, malaria, and transcriptional misregulation in cancer. We successfully verified some differential genes on the SLE pathway and the cell cycle pathway. CDC6, a key gene in the cell cycle pathway, had remarkably higher MXE alternative splicing events in SLE patients than that in controls, which may explain its significant upregulation in SLE patients. We found that CDC6 participates in the pathogenesis of many proliferation-related diseases and its levels are positively correlated with the severity of SLE. Knockdown of CDC6 suppressed the proliferation of Hela cells and PBMCs from SLE patients in vitro. We identified SLE-related genes and their alternative splicing events. The cell cycle pathway and the cell cycle-related biological processes are over-activated in SLE patients. We revealed a higher incidence of MXE events of CDC6, which may lead to its high expression in SLE patients. Upregulated cell cycle signaling and CDC6 may be related to the hyperproliferation and pathogenesis of SLE.

Unraveling transcriptomic signatures and dysregulated pathways in systemic lupus erythematosus across disease states

“…Additionally, we identified a downregulation of a core signature associated with cell cycle function in patients under remission compared to active patients. This finding aligns with previous research showing enrichment of disease-activity genes in cell cycle pathways, supporting the notion that dysregulated cell cycle processes contribute to SLE pathogenesis [ 43 , 44 ]. Although the expression levels of the genes in cell cycle module in remission patients were lower than in the active state, they remained higher than in healthy individuals.…”

Uncovering lupus nephritis-specific genes and the potential of TNFRSF17-targeted immunotherapy: a high-throughput sequencing study

“…RNA isolation and sequencing were performed as previously described by Yang et al. ( 17 ). Briefly, after cluster generation, library preparations were sequenced on an Illumina HiSeq X Ten, and 150 bp paired-end reads were generated.…”

“…Sequencing data analysis were performed as previously described by Yang et al. ( 17 ). Briefly, Raw sequencing data in fastq format were initially processed using in-house perl scripts.…”