The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research
Abstract This study explores the role of LINC00839 and its potential interaction with the miR-195-5p/cyclin E1 (CCNE1) axis in oral squamous cell carcinoma (OSCC). Using The Cancer Genome Atlas, we analyzed lncRNA, miRNA, and mRNA sequencing data for OSCC. Different online tools were applied to dete...
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Nature Portfolio
2024-12-01
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| Online Access: | https://doi.org/10.1038/s41598-024-82922-6 |
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| author | Ashkan Kalantary-Charvadeh Saman Morovat Somayeh Aslani Nasrin Ziamajidi Amirnader Emami Razavi Roghayeh Abbasalipourkabir |
| author_facet | Ashkan Kalantary-Charvadeh Saman Morovat Somayeh Aslani Nasrin Ziamajidi Amirnader Emami Razavi Roghayeh Abbasalipourkabir |
| author_sort | Ashkan Kalantary-Charvadeh |
| collection | DOAJ |
| description | Abstract This study explores the role of LINC00839 and its potential interaction with the miR-195-5p/cyclin E1 (CCNE1) axis in oral squamous cell carcinoma (OSCC). Using The Cancer Genome Atlas, we analyzed lncRNA, miRNA, and mRNA sequencing data for OSCC. Different online tools were applied to detect lncRNA-related miRNAs and their target mRNAs, forming a lncRNA/miRNA/mRNA axis. Co-expression analysis determined the correlation between lncRNA and mRNA expression. Afterward, protein-protein interaction network and functional enrichment analyses disclosed the biological activity of target genes. The expression and correlations of LINC00839, miR-195-5p, and CCNE1 were examined in 30 pairs of OSCC and noncancerous tissues. A Chi-square test was used to determine clinicopathological associations, and ROC analysis estimated diagnostic value. A total of 66 differentially expressed lncRNAs, 80 miRNAs, and 1149 mRNAs were identified in OSCC versus non-tumor samples. After filtering lncRNAs based on novelty, and predicting lncRNA-miRNA, and miRNA-mRNA interactions, the LINC00839/miR-195-5p/CCNE1 axis was discovered. RT-qPCR showed upregulation of LINC00839 and CCNE1 was accompanied by the downregulation of miR-195-5p. A significant positive correlation was observed between LINC00839 and CCNE1 mRNA expression, along with a significant negative correlation between LINC00839 and miR-195-5p expression. Moreover, increased LINC00839 was associated with tumor grade and lymph node status, while decreased miR-195-5p was correlated with lymph, depth, and vascular invasion (p < 0.05). The combined ROC curve demonstrated a significant area under the curve of 0.93. This discovery reveals a novel regulatory mechanism underlying OSCC tumorigenesis and may provide effective diagnosis and potential therapeutic targets to cure this devastating cancer. |
| format | Article |
| id | doaj-art-45fa5069fe2c4c9c957f1c6b50397f6b |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-45fa5069fe2c4c9c957f1c6b50397f6b2025-01-05T12:25:38ZengNature PortfolioScientific Reports2045-23222024-12-0114111610.1038/s41598-024-82922-6The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental researchAshkan Kalantary-Charvadeh0Saman Morovat1Somayeh Aslani2Nasrin Ziamajidi3Amirnader Emami Razavi4Roghayeh Abbasalipourkabir5Department of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical SciencesDepartment of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical SciencesDepartment of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical SciencesDepartment of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical SciencesIran National Tumor Bank, Cancer Institute of Iran, Tehran University of Medical SciencesDepartment of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical SciencesAbstract This study explores the role of LINC00839 and its potential interaction with the miR-195-5p/cyclin E1 (CCNE1) axis in oral squamous cell carcinoma (OSCC). Using The Cancer Genome Atlas, we analyzed lncRNA, miRNA, and mRNA sequencing data for OSCC. Different online tools were applied to detect lncRNA-related miRNAs and their target mRNAs, forming a lncRNA/miRNA/mRNA axis. Co-expression analysis determined the correlation between lncRNA and mRNA expression. Afterward, protein-protein interaction network and functional enrichment analyses disclosed the biological activity of target genes. The expression and correlations of LINC00839, miR-195-5p, and CCNE1 were examined in 30 pairs of OSCC and noncancerous tissues. A Chi-square test was used to determine clinicopathological associations, and ROC analysis estimated diagnostic value. A total of 66 differentially expressed lncRNAs, 80 miRNAs, and 1149 mRNAs were identified in OSCC versus non-tumor samples. After filtering lncRNAs based on novelty, and predicting lncRNA-miRNA, and miRNA-mRNA interactions, the LINC00839/miR-195-5p/CCNE1 axis was discovered. RT-qPCR showed upregulation of LINC00839 and CCNE1 was accompanied by the downregulation of miR-195-5p. A significant positive correlation was observed between LINC00839 and CCNE1 mRNA expression, along with a significant negative correlation between LINC00839 and miR-195-5p expression. Moreover, increased LINC00839 was associated with tumor grade and lymph node status, while decreased miR-195-5p was correlated with lymph, depth, and vascular invasion (p < 0.05). The combined ROC curve demonstrated a significant area under the curve of 0.93. This discovery reveals a novel regulatory mechanism underlying OSCC tumorigenesis and may provide effective diagnosis and potential therapeutic targets to cure this devastating cancer.https://doi.org/10.1038/s41598-024-82922-6Oral squamous cell carcinomaLINC00839miR-195-5pCyclin E1DiagnosisPrognosis |
| spellingShingle | Ashkan Kalantary-Charvadeh Saman Morovat Somayeh Aslani Nasrin Ziamajidi Amirnader Emami Razavi Roghayeh Abbasalipourkabir The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research Scientific Reports Oral squamous cell carcinoma LINC00839 miR-195-5p Cyclin E1 Diagnosis Prognosis |
| title | The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research |
| title_full | The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research |
| title_fullStr | The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research |
| title_full_unstemmed | The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research |
| title_short | The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research |
| title_sort | role of long non coding rna linc00839 in oral squamous cell carcinoma based on bioinformatics and experimental research |
| topic | Oral squamous cell carcinoma LINC00839 miR-195-5p Cyclin E1 Diagnosis Prognosis |
| url | https://doi.org/10.1038/s41598-024-82922-6 |
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