Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma
Abstract This study analyzed oral squamous cell carcinoma (OSCC) genomes and transcriptomes in relation to perineural invasion (PNI) and prognosis using Cancer Genome Atlas data and validated these results with GSE41613 data. Gene set enrichment analysis (GSEA), gene ontology (GO) and Kyoto Encyclop...
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| Format: | Article |
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Nature Portfolio
2024-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-52745-6 |
| _version_ | 1797274775527096320 |
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| author | Su Kyung Kuk Kitae Kim Jae Il Lee KangMi Pang |
| author_facet | Su Kyung Kuk Kitae Kim Jae Il Lee KangMi Pang |
| author_sort | Su Kyung Kuk |
| collection | DOAJ |
| description | Abstract This study analyzed oral squamous cell carcinoma (OSCC) genomes and transcriptomes in relation to perineural invasion (PNI) and prognosis using Cancer Genome Atlas data and validated these results with GSE41613 data. Gene set enrichment analysis (GSEA), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes were conducted. We identified 22 DNA mutations associated with both overall survival (OS) and PNI. Among them, TGFBR1 and RPS6KA4 mRNAs were overexpressed, while TYRO3 and GPR137 mRNAs were underexpressed in PNI patients. Among the 141 mRNA genes associated with both OS and PNI, we found overlap with PNI-related DNA mutations, including ZNF43, TEX10, TPSD1, and PSD3. In GSE41613 data, TGFBR1, RPS6KA4, TYRO3, GPR137, TEX10 and TPSD1 mRNAs were expressed differently according to the prognosis. The 22 DNA-mutated genes clustered into nervous system development, regulation of DNA-templated transcription, and transforming growth factor beta binding. GSEA analysis of mRNAs revealed upregulation of hallmarks epithelial mesenchymal transition (EMT), TNFα signaling via NF-κB, and IL2 STAT5 signaling. EMT upregulation aligned with the TGFBR1 DNA mutation, supporting its significance in PNI. These findings suggest a potential role of PNI genes in the prognosis of OSCC, providing insights for diagnosis and treatment of OSCC. |
| first_indexed | 2024-03-07T15:03:35Z |
| format | Article |
| id | doaj.art-b09eeab52e89491aadc0a3a79330f19c |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T15:03:35Z |
| publishDate | 2024-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-b09eeab52e89491aadc0a3a79330f19c2024-03-05T19:01:05ZengNature PortfolioScientific Reports2045-23222024-01-0114111210.1038/s41598-024-52745-6Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinomaSu Kyung Kuk0Kitae Kim1Jae Il Lee2KangMi Pang3Division of Biomedical Informatics, College of Medicine, Seoul National UniversityDepartment of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National UniversityDepartment of Oral Pathology, School of Dentistry and Dental Research, Seoul National UniversityDepartment of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National UniversityAbstract This study analyzed oral squamous cell carcinoma (OSCC) genomes and transcriptomes in relation to perineural invasion (PNI) and prognosis using Cancer Genome Atlas data and validated these results with GSE41613 data. Gene set enrichment analysis (GSEA), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes were conducted. We identified 22 DNA mutations associated with both overall survival (OS) and PNI. Among them, TGFBR1 and RPS6KA4 mRNAs were overexpressed, while TYRO3 and GPR137 mRNAs were underexpressed in PNI patients. Among the 141 mRNA genes associated with both OS and PNI, we found overlap with PNI-related DNA mutations, including ZNF43, TEX10, TPSD1, and PSD3. In GSE41613 data, TGFBR1, RPS6KA4, TYRO3, GPR137, TEX10 and TPSD1 mRNAs were expressed differently according to the prognosis. The 22 DNA-mutated genes clustered into nervous system development, regulation of DNA-templated transcription, and transforming growth factor beta binding. GSEA analysis of mRNAs revealed upregulation of hallmarks epithelial mesenchymal transition (EMT), TNFα signaling via NF-κB, and IL2 STAT5 signaling. EMT upregulation aligned with the TGFBR1 DNA mutation, supporting its significance in PNI. These findings suggest a potential role of PNI genes in the prognosis of OSCC, providing insights for diagnosis and treatment of OSCC.https://doi.org/10.1038/s41598-024-52745-6 |
| spellingShingle | Su Kyung Kuk Kitae Kim Jae Il Lee KangMi Pang Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma Scientific Reports |
| title | Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma |
| title_full | Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma |
| title_fullStr | Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma |
| title_full_unstemmed | Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma |
| title_short | Prognostic DNA mutation and mRNA expression analysis of perineural invasion in oral squamous cell carcinoma |
| title_sort | prognostic dna mutation and mrna expression analysis of perineural invasion in oral squamous cell carcinoma |
| url | https://doi.org/10.1038/s41598-024-52745-6 |
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