EXPLORING THE ROLE OF ADENOMATOUS POLYPOSIS COLI IN HEAD AND NECK SQUAMOUS CELL CARCINOMA VIA MULTI-LEVEL IN SILICO METHODOLOGY
Main Article Content
Keywords
UALCAN, TCGMA, KM plotter, cBioPortal, APC, HNSC, GEPIA2, mu Target
Abstract
In this study we focused on the expression, promoter methylation, mutation analysis and overall survival of APC gene in Head and Neck Squamous cell Carcinoma (HNSC) patients. First of all, the expression pattern of APC gene was analyzed in HNSC patient sample as compared to control group by using UALCAN. Results of the analysis found remarkable down-regulation of APC gene expression in HNSC patients. When promoter methylation of APC gene was analyzed in HNSC patients versus normal group, a remarkable hypomethylation was found. Subsequently, KM plotter and GEPIA2 tools were used to analyze the overall survival (OS) of HNSC patient with respect to APC expression. Results showed that HNSC patients having higher expression of APC had shorter OS. Mutation analysis of APC gene in HNSC sample by cBioPortal discloses that minor genetic variations in APC gene. The correlation APC gene expression with other mutated genes in HNSC was evaluated using the mu-Target database. Results showed that mutations in GCNT$, AFG3L2, CCDC112, PRAGD and ADTRP genes may be associated by expression alteration in APC genes across HNSC patients. Finally, this study concluded that APC may be regarded as a unique prognostic biomarker for HNSC treatment.
References
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46. Chaturvedi, A.K., et al., Human papillomavirus and rising oropharyngeal cancer incidence in the United States. Journal of clinical oncology, 2011. 29(32): p. 4294-4301.
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2. Pavlopoulou, A., D.A. Spandidos, and I. Michalopoulos, Human cancer databases (review). Oncol Rep, 2015. 33(1): p. 3-18.
3. Dwivedi, M., A perspective review on cancer–the deadliest disease. International Journal of Cancer. 1(1).
4. Heymach, J., et al., Clinical cancer advances 2018: annual report on progress against cancer from the American Society of Clinical Oncology. Journal of Clinical Oncology, 2018. 36(10): p. 1020-1044.
5. Debela, D.T., et al., New approaches and procedures for cancer treatment: Current perspectives. SAGE open medicine, 2021. 9: p. 20503121211034366.
6. Yasir, M., et al., Anti-bacterial activity of essential oils against multidrug-resistant foodborne pathogens isolated from raw milk. Brazilian Journal of Biology, 2022. 84: p. e259449.
7. Hameed, Y. and S. Ejaz, TP53 lacks tetramerization and N-terminal domains due to novel inactivating mutations detected in leukemia patients. Journal of Cancer Research and Therapeutics, 2021. 17(4): p. 931-937.
8. Usman, M., Y. Hameed, and M. Ahmad, Does human papillomavirus cause human colorectal cancer? Applying Bradford Hill criteria postulates. ecancermedicalscience, 2020. 14.
9. Bray, F., et al., Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a cancer journal for clinicians, 2024. 74(3): p. 229-263.
10. Nicholson, B.D., et al., The Suspected CANcer (SCAN) pathway: protocol for evaluating a new standard of care for patients with non-specific symptoms of cancer. BMJ open, 2018. 8(1): p. e018168.
11. Reya, T., et al., Stem cells, cancer, and cancer stem cells. nature, 2001. 414(6859): p. 105-111.
12. Aupérin, A., Epidemiology of head and neck cancers: an update. Current opinion in oncology, 2020. 32(3): p. 178-186.
13. Mathew, A., et al. Symptom clusters in head and neck cancer: a systematic review and conceptual model. in Seminars in oncology nursing. 2021. Elsevier.
14. Johnson, D.E., et al., Head and neck squamous cell carcinoma. Nature Reviews Disease Primers, 2020. 6(1): p. 92.
15. Barsouk, A., et al., Epidemiology, Risk Factors, and Prevention of Head and Neck Squamous Cell Carcinoma. Med Sci (Basel), 2023. 11(2).
16. Cancer, N.C.C.f., Cancer of the upper aerodigestive tract: assessment and management in people aged 16 and over. 2016.
17. Wang, Y.-x., D. Hu, and X. Yan, Diagnostic accuracy of Cyfra 21-1 for head and neck squamous cell carcinoma: a meta-analysis. European Review for Medical & Pharmacological Sciences, 2013. 17(17).
18. Lesko, A.C., et al., The APC tumor suppressor is required for epithelial cell polarization and three-dimensional morphogenesis. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 2015. 1853(3): p. 711-723.
19. Prosperi, J.R., H.H. Luu, and K.H. Goss, Dysregulation of the Wnt pathway in solid tumors. Targeting the Wnt pathway in Cancer, 2011: p. 81-128.
20. Prosperi, J.R., et al., Apc mutation enhances PyMT-induced mammary tumorigenesis. PloS one, 2011. 6(12): p. e29339.
21. Enyakoit, G.O., Cytogenetic analysis of DNA copy number aberrations in high malignancy grade astrocytomas. 2008: University of London, University College London (United Kingdom).
22. Minde, D.P., et al., Messing up disorder: how do missense mutations in the tumor suppressor protein APC lead to cancer? Molecular cancer, 2011. 10: p. 1-9.
23. Pérez-Sayáns, M., et al., The role of the adenomatous polyposis coli (APC) in oral squamous cell carcinoma. Oral oncology, 2011. 48: p. 56-60.
24. Markowitz, S.D. and M.M. Bertagnolli, Molecular basis of colorectal cancermolecular origins of cancer. The New England Journal of Medicine, 2009. 361(25): p. 2449.
25. Worsham, M.J., et al., Epigenetic events of disease progression in head and neck squamous cell carcinoma. Archives of Otolaryngology–Head & Neck Surgery, 2006. 132(6): p. 668-677.
26. Maciejczyk, A., et al., Elevated BUBR1 expression is associated with poor survival in early breast cancer patients: 15-year follow-up analysis. J Histochem Cytochem, 2013. 61(5): p. 330-9.
27. Dong, Y., et al., Prognostic model development and molecular subtypes identification in bladder urothelial cancer by oxidative stress signatures. Aging, 2024. 16(3): p. 2591-2616.
28. Chandrashekar, D.S., et al., UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia, 2017. 19(8): p. 649-658.
29. Maciejczyk, A., et al., Elevated BUBR1 expression is associated with poor survival in early breast cancer patients: 15-year follow-up analysis. Journal of Histochemistry & Cytochemistry, 2013. 61(5): p. 330-339.
30. Tang, Z., et al., GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Research, 2019. 47(W1): p. W556-W560.
31. Cerami, E., et al., The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer discovery, 2012. 2(5): p. 401-404.
32. Dong, Y., et al., Prognostic model development and molecular subtypes identification in bladder urothelial cancer by oxidative stress signatures. Aging (Albany NY), 2024. 16(3): p. 2591.
33. Futreal, P.A., et al., A census of human cancer genes. Nature reviews cancer, 2004. 4(3): p. 177-183.
34. Jia, B., et al., Prognostic roles of MAGE family members in breast cancer based on KM-Plotter Data. Oncol Lett, 2019. 18(4): p. 3501-3516.
35. Hu, H., et al., CDCA8, a mitosis-related gene, as a prospective pan-cancer biomarker: implications for survival prognosis and oncogenic immunology. American Journal of Translational Research, 2024. 16(2): p. 432.
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39. Society, A.C., Cancer and the poor: a report to the nation, 1989, American Cancer Society Atlanta, GA.
40. McQueen, A., et al., Risk perceptions and worry about cancer: does gender make a difference? Journal of health communication, 2008. 13(1): p. 56-79.
41. WHO, G., International statistical classification of diseases and related health problems. 1992.
42. Group, U.C.S.W., United States cancer statistics: 1999–2010 incidence and mortality web-based report. Atlanta: US Department of Health and Human Services, Centers for Disease Control and Prevention and National Cancer Institute, 2013. 201.
43. Pavlopoulou, A. and S. Kossida, Cytosine methyltransferases as tumor markers. Current Genomics, 2010. 11(8): p. 568-577.
44. Usman, M., et al., Breast cancer risk and human papillomavirus infection: a Bradford Hill criteria based evaluation. Infectious Disorders-Drug Targets (Formerly Current Drug Targets-Infectious Disorders), 2022. 22(4): p. 41-50.
45. Mao, J., et al., [Retracted] Risk Factors for TERT Promoter Mutations with Papillary Thyroid Carcinoma Patients: A Meta‐Analysis and Systematic Review. Computational and Mathematical Methods in Medicine, 2022. 2022(1): p. 1721526.
46. Chaturvedi, A.K., et al., Human papillomavirus and rising oropharyngeal cancer incidence in the United States. Journal of clinical oncology, 2011. 29(32): p. 4294-4301.
47. Pekarek, L., et al., An Overview of the Role of MicroRNAs on Carcinogenesis: A Focus on Cell Cycle, Angiogenesis and Metastasis. International Journal of Molecular Sciences, 2023. 24(8): p. 7268.
48. KONTOMANOLIS, E.N., et al., Role of Oncogenes and Tumor-suppressor Genes in Carcinogenesis: A Review. Anticancer Research, 2020. 40(11): p. 6009-6015.
49. Dunlop, M.G., et al., Cancer Risk Associated with Germline DNA Mismatch Repair Gene Mutations. Human Molecular Genetics, 1997. 6(1): p. 105-110.
50. Mitelman, F., B. Johansson, and F. Mertens, The impact of translocations and gene fusions on cancer causation. Nature Reviews Cancer, 2007. 7(4): p. 233-245.
51. Gao, J., et al., Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Science Signaling, 2013. 6(269): p. pl1-pl1.
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Sep 30, 2024
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How to Cite
Muhammad Ali, Muhammad Afzal, Reema Bughio, Bismah Ahmad, Mehtab Alam, Samina Imtiaz, Momna Khalid, Laiba Imran, Nimra Arshad, & Saira Jabeen. (2024). EXPLORING THE ROLE OF ADENOMATOUS POLYPOSIS COLI IN HEAD AND NECK SQUAMOUS CELL CARCINOMA VIA MULTI-LEVEL IN SILICO METHODOLOGY. Journal of Population Therapeutics and Clinical Pharmacology, 31(9), 2461-2474. https://doi.org/10.53555/r5q6qr82
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Author Biographies
Muhammad Ali
Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jalan lr. Sutami 36A, Surakarta, 57126, Indonesia
Muhammad Afzal
Department of Biochemistry, Faisalabad Medical University, Faisalabad, Pakistan
Reema Bughio
Department of Animal Breeding and Genetics SBBUVAS Sakrand, Pakistan
Bismah Ahmad
CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan
Mehtab Alam
Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Pakistan
Samina Imtiaz
Department of Genetics University of Karachi, Pakistan
Momna Khalid
Department of Zoology, Kinnaird College for Women University Lahore, Pakistan
Laiba Imran
Department: Institute of Chemistry, University of Sargodha, Pakistan
Nimra Arshad
Department of Biochemistry, Institute of Chemistry, GC University, Faisalabad, Pakistan
Saira Jabeen
Bahawalpur Victoria Hospital (BVH), Bahawalpur, Pakistan
How to Cite
Muhammad Ali, Muhammad Afzal, Reema Bughio, Bismah Ahmad, Mehtab Alam, Samina Imtiaz, Momna Khalid, Laiba Imran, Nimra Arshad, & Saira Jabeen. (2024). EXPLORING THE ROLE OF ADENOMATOUS POLYPOSIS COLI IN HEAD AND NECK SQUAMOUS CELL CARCINOMA VIA MULTI-LEVEL IN SILICO METHODOLOGY. Journal of Population Therapeutics and Clinical Pharmacology, 31(9), 2461-2474. https://doi.org/10.53555/r5q6qr82