RNA-Seq based transcriptome analysis in oral lichen planus
Abstract 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 R...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | Hereditas |
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| Online Access: | https://doi.org/10.1186/s41065-021-00202-z |
| _version_ | 1818908724143587328 |
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| author | Haoyu Wang Yiwen Deng Siqi Peng Li Yan Hui Xu Qingzhong Wang Zhengyu Shen |
| author_facet | Haoyu Wang Yiwen Deng Siqi Peng Li Yan Hui Xu Qingzhong Wang Zhengyu Shen |
| author_sort | Haoyu Wang |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-19T22:15:34Z |
| format | Article |
| id | doaj.art-1e2baee23746482d9448b799480196aa |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-12-19T22:15:34Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-1e2baee23746482d9448b799480196aa2022-12-21T20:03:46ZengBMCHereditas1601-52232021-10-01158111110.1186/s41065-021-00202-zRNA-Seq based transcriptome analysis in oral lichen planusHaoyu Wang0Yiwen Deng1Siqi Peng2Li Yan3Hui Xu4Qingzhong Wang5Zhengyu Shen6Department of Dermatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral Mucosal Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of StomatologyShanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineDepartment of Dermatology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Dermatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineShanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineDepartment of Dermatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineAbstract 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.https://doi.org/10.1186/s41065-021-00202-zOral lichen planusRNA sequencingWeighted gene co-expression network analysisPathogenesis |
| spellingShingle | Haoyu Wang Yiwen Deng Siqi Peng Li Yan Hui Xu Qingzhong Wang Zhengyu Shen RNA-Seq based transcriptome analysis in oral lichen planus Hereditas Oral lichen planus RNA sequencing Weighted gene co-expression network analysis Pathogenesis |
| title | RNA-Seq based transcriptome analysis in oral lichen planus |
| title_full | RNA-Seq based transcriptome analysis in oral lichen planus |
| title_fullStr | RNA-Seq based transcriptome analysis in oral lichen planus |
| title_full_unstemmed | RNA-Seq based transcriptome analysis in oral lichen planus |
| title_short | RNA-Seq based transcriptome analysis in oral lichen planus |
| title_sort | rna seq based transcriptome analysis in oral lichen planus |
| topic | Oral lichen planus RNA sequencing Weighted gene co-expression network analysis Pathogenesis |
| url | https://doi.org/10.1186/s41065-021-00202-z |
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