Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis
The claudin multigene family is associated with various aberrant physiological and cellular signaling pathways. However, the association of claudins with survival prognosis, signaling pathways, and diagnostic efficacy in colon cancer remains poorly understood.Methods: Through the effective utilizati...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1221815/full |
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| author | Rana A. Alghamdi Rana A. Alghamdi Maryam H. Al-Zahrani |
| author_facet | Rana A. Alghamdi Rana A. Alghamdi Maryam H. Al-Zahrani |
| author_sort | Rana A. Alghamdi |
| collection | DOAJ |
| description | The claudin multigene family is associated with various aberrant physiological and cellular signaling pathways. However, the association of claudins with survival prognosis, signaling pathways, and diagnostic efficacy in colon cancer remains poorly understood.Methods: Through the effective utilization of various bioinformatics methods, including differential gene expression analysis, gene set enrichment analysis protein-protein interaction (PPI) network analysis, survival analysis, single sample gene set enrichment analysis (ssGSEA), mutational variance analysis, and identifying receiver operating characteristic curve of claudins in The Cancer Genome Atlas colon adenocarcinoma (COAD).Results: We found that: CLDN2, CLDN1, CLDN14, CLDN16, CLDN18, CLDN9, CLDN12, and CLDN6 are elevated in COAD. In contrast, the CLDN8, CLDN23, CLDN5, CLDN11, CLDN7, and CLDN15 are downregulated in COAD. By analyzing the public datasets GSE15781 and GSE50760 from NCBI-GEO (https://www.ncbi.nlm.nih.gov/geo/), we have confirmed that CLDN1, CLDN2, and CLDN14 are significantly upregulated and CLDN8 and CLDN23 are significantly downregulated in normal colon, colon adenocarcinoma tumor, and liver metastasis of colon adenocarcinoma tissues from human samples. Various claudins are mutated and found to be associated with diagnostic efficacy in COAD.Conclusion: The claudin gene family is associated with prognosis, immune regulation, signaling pathway regulations, and diagnosis of COAD. These findings may provide new molecular insight into claudins in the treatment of colon cancer. |
| first_indexed | 2024-03-11T23:34:32Z |
| format | Article |
| id | doaj.art-241ab88df13e4d77a4fc1b2d66afd297 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-11T23:34:32Z |
| publishDate | 2023-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-241ab88df13e4d77a4fc1b2d66afd2972023-09-20T04:43:46ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-09-011410.3389/fgene.2023.12218151221815Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysisRana A. Alghamdi0Rana A. Alghamdi1Maryam H. Al-Zahrani2Department of Chemistry, Science and Arts College, King Abdulaziz University, Rabigh, Saudi ArabiaRegenerative Medicine Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi ArabiaBiochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi ArabiaThe claudin multigene family is associated with various aberrant physiological and cellular signaling pathways. However, the association of claudins with survival prognosis, signaling pathways, and diagnostic efficacy in colon cancer remains poorly understood.Methods: Through the effective utilization of various bioinformatics methods, including differential gene expression analysis, gene set enrichment analysis protein-protein interaction (PPI) network analysis, survival analysis, single sample gene set enrichment analysis (ssGSEA), mutational variance analysis, and identifying receiver operating characteristic curve of claudins in The Cancer Genome Atlas colon adenocarcinoma (COAD).Results: We found that: CLDN2, CLDN1, CLDN14, CLDN16, CLDN18, CLDN9, CLDN12, and CLDN6 are elevated in COAD. In contrast, the CLDN8, CLDN23, CLDN5, CLDN11, CLDN7, and CLDN15 are downregulated in COAD. By analyzing the public datasets GSE15781 and GSE50760 from NCBI-GEO (https://www.ncbi.nlm.nih.gov/geo/), we have confirmed that CLDN1, CLDN2, and CLDN14 are significantly upregulated and CLDN8 and CLDN23 are significantly downregulated in normal colon, colon adenocarcinoma tumor, and liver metastasis of colon adenocarcinoma tissues from human samples. Various claudins are mutated and found to be associated with diagnostic efficacy in COAD.Conclusion: The claudin gene family is associated with prognosis, immune regulation, signaling pathway regulations, and diagnosis of COAD. These findings may provide new molecular insight into claudins in the treatment of colon cancer.https://www.frontiersin.org/articles/10.3389/fgene.2023.1221815/fullclaudinbioinformatics methodssurvival prognosisintegrated bioinformatic analysisCLDN2immune infiltrations |
| spellingShingle | Rana A. Alghamdi Rana A. Alghamdi Maryam H. Al-Zahrani Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis Frontiers in Genetics claudin bioinformatics methods survival prognosis integrated bioinformatic analysis CLDN2 immune infiltrations |
| title | Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis |
| title_full | Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis |
| title_fullStr | Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis |
| title_full_unstemmed | Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis |
| title_short | Identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis |
| title_sort | identification of key claudin genes associated with survival prognosis and diagnosis in colon cancer through integrated bioinformatic analysis |
| topic | claudin bioinformatics methods survival prognosis integrated bioinformatic analysis CLDN2 immune infiltrations |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1221815/full |
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