Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis
Colorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-12-01
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| Series: | Molecular & Cellular Oncology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/23723556.2024.2326699 |
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| author | Mansour K. Gatasheh Sathan Raj Natarajan Rajapandiyan Krishnamoorthy Tawfiq S Alsulami Ponnulakshmi Rajagopal Chella Perumal Palanisamy Vishnu Priya Veeraraghavan Selvaraj Jayaraman |
| author_facet | Mansour K. Gatasheh Sathan Raj Natarajan Rajapandiyan Krishnamoorthy Tawfiq S Alsulami Ponnulakshmi Rajagopal Chella Perumal Palanisamy Vishnu Priya Veeraraghavan Selvaraj Jayaraman |
| author_sort | Mansour K. Gatasheh |
| collection | DOAJ |
| description | Colorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through Venn diagrams. From a total of 114 enhanced DEGs, potential hub genes were further filtered based on their nodal strength and edges using STRING database. To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. Additionally, the cBioPortal and HPA databases also revealed genetic alterations and expression levels in these hub genes in CRC patients, further supporting their involvement in colorectal cancer. Gene expression by RT-PCR shows upregulation of hub genes in HT-29 cells. Finally, our integrated bioinformatic analysis revealed that ABCE1, AURKA, HSPD1, PHKA1, CDK4, and YWHAE as hub genes with potential oncogenic roles in CRC. These genes hold promise as diagnostic and prognostic markers for colorectal tumorigenesis, providing insights into targeted therapies for improved patient outcomes. |
| format | Article |
| id | doaj-art-309e8a84a60242bb8f02e836d4fd92a0 |
| institution | Kabale University |
| issn | 2372-3556 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Molecular & Cellular Oncology |
| spelling | doaj-art-309e8a84a60242bb8f02e836d4fd92a02024-12-13T07:00:18ZengTaylor & Francis GroupMolecular & Cellular Oncology2372-35562024-12-0111110.1080/23723556.2024.2326699Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysisMansour K. Gatasheh0Sathan Raj Natarajan1Rajapandiyan Krishnamoorthy2Tawfiq S Alsulami3Ponnulakshmi Rajagopal4Chella Perumal Palanisamy5Vishnu Priya Veeraraghavan6Selvaraj Jayaraman7Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi ArabiaCentre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, IndiaDepartment of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi ArabiaDepartment of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi ArabiaDepartment of Central Research Laboratory, Meenakshi Ammal Dental College and Hospital, Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, IndiaMini-invasive Neurosurgery and Translational Medical Center, Xi’an Central Hospital, Xi’an Jiaotong University, Xi’an, PR ChinaCentre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, IndiaCentre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, IndiaColorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through Venn diagrams. From a total of 114 enhanced DEGs, potential hub genes were further filtered based on their nodal strength and edges using STRING database. To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. Additionally, the cBioPortal and HPA databases also revealed genetic alterations and expression levels in these hub genes in CRC patients, further supporting their involvement in colorectal cancer. Gene expression by RT-PCR shows upregulation of hub genes in HT-29 cells. Finally, our integrated bioinformatic analysis revealed that ABCE1, AURKA, HSPD1, PHKA1, CDK4, and YWHAE as hub genes with potential oncogenic roles in CRC. These genes hold promise as diagnostic and prognostic markers for colorectal tumorigenesis, providing insights into targeted therapies for improved patient outcomes.https://www.tandfonline.com/doi/10.1080/23723556.2024.2326699Colorectal cancerbioinformatics analysistherapeutic targetsdifferential gene expressionhub genes |
| spellingShingle | Mansour K. Gatasheh Sathan Raj Natarajan Rajapandiyan Krishnamoorthy Tawfiq S Alsulami Ponnulakshmi Rajagopal Chella Perumal Palanisamy Vishnu Priya Veeraraghavan Selvaraj Jayaraman Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis Molecular & Cellular Oncology Colorectal cancer bioinformatics analysis therapeutic targets differential gene expression hub genes |
| title | Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis |
| title_full | Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis |
| title_fullStr | Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis |
| title_full_unstemmed | Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis |
| title_short | Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis |
| title_sort | molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy an integrated bioinformatics analysis |
| topic | Colorectal cancer bioinformatics analysis therapeutic targets differential gene expression hub genes |
| url | https://www.tandfonline.com/doi/10.1080/23723556.2024.2326699 |
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