Identification of Prognosis Associated microRNAs in HNSCC Subtypes Based on TCGA Dataset
Abstract
:1. Introduction
2. Materials and Methods
2.1. MiRNAs Differential Expression Analysis (DEA)
2.2. Survival Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Alsahafi, E.; Begg, K.; Amelio, I.; Raulf, N.; Lucarelli, P.; Sauter, T.; Tavassoli, M. Clinical update on head and neck cancer: Molecular biology and ongoing challenges. Cell Death Dis. 2019, 10, 540. [Google Scholar] [PubMed] [Green Version]
- Bray, F.; Me, J.F.; Soerjomataram, I.; Siegel, R.; Torre, L.A.; Jemal, A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA A Cancer J. Clin. 2018, 68, 394–424. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Taghavi, N.; Yazdi, I. Prognostic factors of survival rate in oral squamous cell carcinoma: Clinical, histologic, genetic and molecular concepts. Arch. Iran. Med. 2015, 18, 314–319. [Google Scholar] [PubMed]
- Tuna, M.; Amos, C.I.; Mills, G.B. Genome-Wide Analysis of Head and Neck Squamous Cell Carcinomas Reveals HPV, TP53, Smoking and Alcohol-Related Allele-Based Acquired Uniparental Disomy Genomic Alterations. Neoplasia 2019, 21, 197–205. [Google Scholar] [CrossRef] [PubMed]
- Leemans, C.R.; Snijders, P.J.F.; Brakenhoff, R.H. The molecular landscape of head and neck cancer. Nat. Rev. Cancer 2018, 18, 269–282. [Google Scholar]
- Mohr, A.M.; Mott, J.L. Overview of MicroRNA Biology. Semin. Liver Dis. 2015, 35, 3–11. [Google Scholar] [CrossRef] [Green Version]
- Sayáns, M.P.; Pilar, G.-D.; Barros-Angueira, F.; Suárez-Peñaranda, J.M.; Fernández, A.C.; Gándara-Rey, J.M.; García, A.G. Current trends in miRNAs and their relationship with oral squamous cell carcinoma. J. Oral Pathol. Med. 2011, 41, 433–443. [Google Scholar] [CrossRef]
- Guo, W.; Chen, X.; Zhu, L.; Wang, Q. A six-mRNA signature model for the prognosis of head and neck squamous cell carcinoma. Oncotarget 2017, 8, 94528–94538. [Google Scholar]
- Zeljic, K.; Jovanovic, I.; Jovanovic, J.; Magic, Z.; Stankovic, A.; Supic, G. MicroRNA meta-signature of oral cancer: Evidence from a meta-analysis. Upsala J. Med Sci. 2018, 123, 43–49. [Google Scholar] [CrossRef]
- Janiszewska, J.; Szaumkessel, M.; Szyfter, K. microRNAs are important players in head and neck carcinoma: A review. Crit. Rev. Oncol. 2013, 88, 716–728. [Google Scholar] [CrossRef]
- Min, A.; Zhu, C.; Peng, S.; Rajthala, S.; Costea, D.E.; Sapkota, D. MicroRNAs as Important Players and Biomarkers in Oral Carcinogenesis. BioMed Res. Int. 2015, 2015, 1–10. [Google Scholar] [CrossRef] [Green Version]
- Van Der Ree, M.H.; Van Der Meer, A.J.; Van Nuenen, A.C.; De Bruijne, J.; Ottosen, S.; Janssen, H.L.; Kootstra, N.A.; Reesink, H.W. Miravirsen dosing in chronic hepatitis C patients results in decreased microRNA-122 levels without affecting other microRNAs in plasma. Aliment. Pharmacol. Ther. 2015, 43, 102–113. [Google Scholar] [CrossRef] [Green Version]
- Beg, M.S.; Brenner, A.J.; Sachdev, J.; Borad, M.; Kang, Y.-K.; Stoudemire, J.; Smith, S.; Bader, A.G.; Kim, S.; Hong, D.S. Phase I study of MRX34, a liposomal miR-34a mimic, administered twice weekly in patients with advanced solid tumors. Investig. New Drugs 2016, 35, 180–188. [Google Scholar]
- Pérez-Sayáns, M.; Chamorro-Petronacci, C.M.; Lorenzo-Pouso, A.I.; Iruegas, E.P.; Carrión, A.B.; Peñaranda, J.M.S.; García-García, A. Comprehensive Genomic Review of TCGA Head and Neck Squamous Cell Carcinomas (HNSCC). J. Clin. Med. 2019, 8, 1896. [Google Scholar] [CrossRef] [Green Version]
- Von Elm, E.; Altman, D.G.; Initiative, F.T.S.; Pocock, S.J.; Gøtzsche, P.C.; Vandenbroucke, J.P. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: Guidelines for reporting observational studies. J. Clin. Epidemiol. 2008, 61, 344–349. [Google Scholar] [CrossRef] [Green Version]
- Colaprico, A.; Silva, T.C.; Olsen, C.; Garofano, L.; Cava, C.; Garolini, D.; Sabedot, T.S.; Malta, T.M.; Pagnotta, S.M.; Castiglioni, I.; et al. TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 2015, 44, e71. [Google Scholar] [CrossRef] [PubMed]
- Vlachos, I.S.; Zagganas, K.; Paraskevopoulou, M.D.; Georgakilas, G.; Karagkouni, D.; Vergoulis, T.; Dalamagas, T.; Hatzigeorgiou, A.G. DIANA-miRPath v3.0: Deciphering microRNA function with experimental support. Nucleic Acids Res. 2015, 43, W460–W466. [Google Scholar] [CrossRef] [PubMed]
- Jamali, Z.; Aminabadi, N.A.; Attaran, R.; Pournagiazar, F.; Oskouei, S.G.; Ahmadpour, F. MicroRNAs as prognostic molecular signatures in human head and neck squamous cell carcinoma: A systematic review and meta-analysis. Oral Oncol. 2015, 51, 321–331. [Google Scholar] [CrossRef] [PubMed]
- Nathan, C.A.; Stern, W. 2016 Oral, Head and Neck Cancer Awareness Week: April 10–16. Ear Nose Throat J. 2016, 95, 52–55. [Google Scholar]
- Petronacci, C.M.C.; Pérez-Sayáns, M.; Iruegas, M.E.P.; Peñaranda, J.M.S.; Pouso, A.I.L.; Carrión, A.B.; García, A.G. miRNAs expression of oral squamous cell carcinoma patients. Medicine 2019, 98, e14922. [Google Scholar] [CrossRef]
- Amiri-Dashatan, N.; Koushki, M.; Jalilian, A.; Ahmadi, N.A.; Tavirani, M.R. Integrated Bioinformatics Analysis of mRNAs and miRNAs Identified Potential Biomarkers of Oral Squamous Cell Carcinoma. Asian Pac. J. Cancer Prev. 2020, 21, 1841–1848. [Google Scholar] [CrossRef] [PubMed]
- Wong, N.; Khwaja, S.S.; Baker, C.M.; Gay, H.A.; Thorstad, W.L.; Daly, M.D.; Lewis, J.S.; Wang, X. Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas. Cancer Med. 2016, 5, 1619–1628. [Google Scholar] [CrossRef] [PubMed]
- Santos-De-Frutos, K.; Segrelles, C.; Lorz, C. Hippo Pathway and YAP Signaling Alterations in Squamous Cancer of the Head and Neck. J. Clin. Med. 2019, 8, 2131. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- White, R.A.; Malkoski, S.P.; Wang, X.-J. TGFβ signaling in head and neck squamous cell carcinoma. Oncogene 2010, 29, 5437–5446. [Google Scholar] [PubMed] [Green Version]
- Flowers, S.A.; Zhou, X.; Wu, J.; Wang, Y.; Makambi, K.; Kallakury, B.V.; Singer, M.S.; Rosen, S.D.; Davidson, B.; Goldman, R. Expression of the extracellular sulfatase SULF2 is associated with squamous cell carcinoma of the head and neck. Oncotarget 2016, 7, 43177–43187. [Google Scholar]
- Solomon, M.C.; Radhakrishnan, R.A. MicroRNA’s—The vibrant performers in the oral cancer scenario. Jpn. Dent. Sci. Rev. 2020, 56, 85–89. [Google Scholar] [CrossRef]
- Sarode, S.; Sarode, S.; Maniyar, N.; Anand, R.; Patil, S. Oral cancer databases: A comprehensive review. J. Oral Pathol. Med. 2017, 47, 547–556. [Google Scholar]
- Caponigro, F.; Ionna, F.; Scarpati, G.D.V.; Longo, F.; Addeo, R.; Manzo, R.; Muto, P.; Pisconti, S.; Leopaldi, L.; Perri, F. Translational Research: A Future Strategy for Managing Squamous Cell Carcinoma of the Head and Neck? Anti-Cancer Agents Med. Chem. 2019, 18, 1220–1227. [Google Scholar] [CrossRef]
- Lin, N.; Lin, Y.; Fu, X.; Wu, C.; Xu, J.; Cui, Z.; Lin, D. MicroRNAs as a Novel Class of Diagnostic Biomarkers in Detection of Oral Carcinoma: A Meta-Analysis Study. Clin Lab. 2016, 62, 451–461. [Google Scholar]
- Danielsson, K.; Wahlin, Y.B.; Gu, X.; Boldrup, L.; Nylander, K. Altered expression of miR-21, miR-125b, and miR-203 indicates a role for these microRNAs in oral lichen planus. J. Oral Pathol. Med. 2011, 41, 90–95. [Google Scholar] [CrossRef]
- Manikandan, M.; Rao, A.K.D.M.; Rajkumar, K.S.; Rajaraman, R.; Munirajan, A.K. Altered levels of miR-21, miR-125b-2*, miR-138, miR-155, miR-184, and miR-205 in oral squamous cell carcinoma and association with clinicopathological characteristics. J. Oral Pathol. Med. 2014, 44, 792–800. [Google Scholar] [CrossRef] [PubMed]
- Odar, K.; Boštjančič, E.; Gale, N.; Glavač, D.; Zidar, N. Differential expression of microRNAs miR-21, miR-31, miR-203, miR-125a-5p and miR-125b and proteins PTEN and p63 in verrucous carcinoma of the head and neck. Histopathology 2012, 61, 257–265. [Google Scholar] [CrossRef] [PubMed]
- He, Q.; Chen, Z.; Cabay, R.J.; Zhang, L.; Luan, X.; Chen, D.; Yu, T.; Wang, A.; Zhou, X. microRNA-21 and microRNA-375 from oral cytology as biomarkers for oral tongue cancer detection. Oral Oncol. 2016, 57, 15–20. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zheng, J.; Xue, H.; Wang, T.; Jiang, Y.; Liu, B.; Li, J.; Liu, Y.; Wang, W.; Zhang, B.; Sun, M. miR-21 downregulates the tumor suppressor P12CDK2AP1 and Stimulates Cell Proliferation and Invasion. J. Cell. Biochem. 2011, 112, 872–880. [Google Scholar] [CrossRef] [PubMed]
- Cen, W.-N.; Pang, J.-S.; Huang, J.-C.; Hou, J.; Bao, W.-G.; He, R.; Ma, J.; Peng, Z.-G.; Hu, X.-H.; Ma, F.-C. The expression and biological information analysis of miR-375-3p in head and neck squamous cell carcinoma based on 1825 samples from GEO, TCGA, and peer-reviewed publications. Pathol. Res. Pr. 2018, 214, 1835–1847. [Google Scholar] [CrossRef]
- Wang, J.; Huang, H.; Wang, C.; Liu, X.; Hu, F.; Liu, M. MicroRNA-375 sensitizes tumour necrosis factor-alpha (TNF-α)-induced apoptosis in head and neck squamous cell carcinoma in vitro. Int. J. Oral Maxillofac. Surg. 2013, 42, 949–955. [Google Scholar] [CrossRef]
- Hu, A.; Huang, J.J.; Xu, W.H.; Jin, X.J.; Li, J.P.; Tang, Y.J.; Huang, X.-F.; Cui, H.-C.; Sun, G.-B.; Li, R.-L.; et al. MiR-21/miR-375 ratio is an independent prognostic factor in patients with laryngeal squamous cell carcinoma. Am. J. Cancer Res. 2015, 5, 1775–1785. [Google Scholar]
- Sannigrahi, M.; Sharma, R.; Singh, V.; Panda, N.K.; Rattan, V.; Khullar, M. DNA methylation regulated microRNAs in HPV-16-induced head and neck squamous cell carcinoma (HNSCC). Mol. Cell. Biochem. 2018, 448, 321–333. [Google Scholar] [CrossRef]
- Affinito, O.; Pane, K.; Smaldone, G.; Orlandella, F.M.; Mirabelli, P.; Beneduce, G.; Parasole, R.; Ripaldi, M.; Salvatore, M.; Franzese, M. lncRNAs–mRNAs Co–Expression Network Underlying Childhood B–Cell Acute Lymphoblastic Leukaemia: A Pilot Study. Cancers 2020, 12, 2489. [Google Scholar] [CrossRef]
- Petronacci, C.M.C.; Sayáns, M.P.; Padín-Iruegas, M.E.; Marichalar-Mendia, X.; Torreira, M.G.; García, A.G. Differential expression of snoRNAs in oral squamous cell carcinomas: New potential diagnostic markers. J. Enzym. Inhib. Med. Chem. 2018, 33, 424–427. [Google Scholar] [CrossRef] [Green Version]
- Wagner, E. Tumor-targeted Delivery of Anti-microRNA for Cancer Therapy: pHLIP is Key. Angew. Chem. Int. Ed. 2015, 54, 5824–5826. [Google Scholar] [CrossRef]
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Chamorro Petronacci, C.M.; García García, A.; Padín Iruegas, E.; Rivas Mundiña, B.; Lorenzo Pouso, A.I.; Pérez Sayáns, M. Identification of Prognosis Associated microRNAs in HNSCC Subtypes Based on TCGA Dataset. Medicina 2020, 56, 535. https://doi.org/10.3390/medicina56100535
Chamorro Petronacci CM, García García A, Padín Iruegas E, Rivas Mundiña B, Lorenzo Pouso AI, Pérez Sayáns M. Identification of Prognosis Associated microRNAs in HNSCC Subtypes Based on TCGA Dataset. Medicina. 2020; 56(10):535. https://doi.org/10.3390/medicina56100535
Chicago/Turabian StyleChamorro Petronacci, Cintia M., Abel García García, Elena Padín Iruegas, Berta Rivas Mundiña, Alejandro I. Lorenzo Pouso, and Mario Pérez Sayáns. 2020. "Identification of Prognosis Associated microRNAs in HNSCC Subtypes Based on TCGA Dataset" Medicina 56, no. 10: 535. https://doi.org/10.3390/medicina56100535