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Updated: Oct 17, 2025
RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
Published on: May 19, 2019
RNA-Seq based transcriptome analysis in oral lichen planus
Haoyu Wang1, Yiwen Deng2, Siqi Peng3
1Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Objectives:
Oral lichen planus (OLP) is a T cell-mediated autoimmune disease recognized as an oral potential malignant disorder (OPMD) with the precise mechanism unknown. This study focused on the transcriptional profiles of OLP to elucidate its potential pathogenesis.
Methods:
We conducted RNA sequencing on matched 6 OLP tissues and 6 normal oral mucosal tissues. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and weighted gene co-expression network analysis (WGCNA) were performed on differentially expressed genes (DEGs). We utilized qRT-PCR to validated the top dysregulated genes and hub genes in another 10 pairs of specimens.
Results:
A total of 153 DEGs (p-values< 0.05) were detected from RNA-Seq. According to GO and KEGG analysis, the dysregulated genes were mainly related to T cell related pathway and Wnt signaling. Based on the WGCNA analysis, 5 modules with high intramodular connectivity and hub genes in each module were gained.
Conclusions:
RNA-Seq and bioinformatic methods offered a valuable understanding of the biological pathways and key genes in the regulation of OLP. The identified DEGs and hub genes categorized into 2 groups including T cell regulation and inflammation and Wnt signaling pathway may serve as potential novel molecular targets for therapy.
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