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Open AccessArticle

Comprehensive Genomic Review of TCGA Head and Neck Squamous Cell Carcinomas (HNSCC)

1
Health Research Institute Foundation of Santiago (FIDIS); Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, University of Santiago de Compostela, C.P. 15782 Santiago de Compostela, Spain
2
Area of Human Anatomy and Embryology, Faculty of Physiotherapy, Department of Functional Biology and Health Sciences, University of Vigo, 36310 Vigo, Pontevedra, Spain
3
Pathological Anatomy Service, University Hospital Complex of Santiago (CHUS), C.P. 15782 Santiago de Compostela, Spain
*
Author to whom correspondence should be addressed.
J. Clin. Med. 2019, 8(11), 1896; https://doi.org/10.3390/jcm8111896
Received: 10 October 2019 / Revised: 30 October 2019 / Accepted: 4 November 2019 / Published: 7 November 2019
(This article belongs to the Special Issue Frontiers in Oral Cancer—Basic and Clinical Sciences)
The aim of this present study was to comprehensively describe somatic DNA alterations and transcriptional alterations in the last extension of the HNSCC subsets in TCGA, encompassing a total of 528 tumours. In order to achieve this goal, transcriptional analysis, functional enrichment assays, survival analysis, somatic copy number alteration analysis and somatic alteration analysis were carried out. A total of 3491 deregulated genes were found in HNSCC patients, and the functional analysis carried out determined that tissue development and cell differentiation were the most relevant signalling pathways in upregulated and downregulated genes, respectively. Somatic copy number alteration analysis showed a “top five” altered HNSCC genes: CDKN2A (deleted in 32.03% of patients), CDKN2B (deleted in 28.34% of patients), PPFIA1 (amplified in 26.02% of patients), FADD (amplified in 25.63% of patients) and ANO1 (amplified in 25.44% of patients). Somatic mutations analysis revealed TP53 mutation in 72% of the tumour samples followed by TTN (39%), FAT1 (23%) and MUC16 (19%). Another interesting result is the mutual exclusivity pattern that was discovered between the TP53 and PIK3CA mutations, and the co-occurrence of CDKN2A with the TP53 and FAT1 alterations. On analysis to relate differential expression genes and somatic copy number alterations, some genes were overexpressed and amplified, for example, FOXL2, but other deleted genes also showed overexpression, such as CDKN2A. Survival analysis revealed that overexpression of some oncogenes, such as EGFR, CDK6 or CDK4 were associated with poorer prognosis tumours. These new findings help us to develop new therapies and programs for the prevention of HNSCC. View Full-Text
Keywords: head and neck neoplasms; DNA copy number variation; genomics; oncogenes; differentially expressed genes head and neck neoplasms; DNA copy number variation; genomics; oncogenes; differentially expressed genes
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Pérez Sayáns, M.; Chamorro Petronacci, C.M.; Lorenzo Pouso, A.I.; Padín Iruegas, E.; Blanco Carrión, A.; Suárez Peñaranda, J.M.; García García, A. Comprehensive Genomic Review of TCGA Head and Neck Squamous Cell Carcinomas (HNSCC). J. Clin. Med. 2019, 8, 1896.

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