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de Mey S, Dufait I, De Ridder M. Radioresistance of Human Cancers: Clinical Implications of Genetic Expression Signatures. Front Oncol 2021; 11:761901. [PMID: 34778082 PMCID: PMC8579106 DOI: 10.3389/fonc.2021.761901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Although radiotherapy is given to more than 50% of cancer patients, little progress has been made in identifying optimal radiotherapy - drug combinations to improve treatment efficacy. Using molecular data from The Cancer Genome Atlas (TCGA), we extracted a total of 1016 cancer patients that received radiotherapy. The patients were diagnosed with head-and-neck (HNSC - 294 patients), cervical (CESC - 166 patients) and breast (BRCA - 549 patients) cancer. We analyzed mRNA expression patterns of 50 hallmark gene sets of the MSigDB collection, which we divided in eight categories based on a shared biological or functional process. Tumor samples were split into upregulated, neutral or downregulated mRNA expression for all gene sets using a gene set analysis (GSEA) pre-ranked analysis and assessed for their clinical relevance. We found a prognostic association between three of the eight gene set categories (Radiobiological, Metabolism and Proliferation) and overall survival in all three cancer types. Furthermore, multiple single associations were revealed in the other categories considered. To the best of our knowledge, our study is the first report suggesting clinical relevance of molecular characterization based on hallmark gene sets to refine radiation strategies.
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Affiliation(s)
- Sven de Mey
- Department of Radiotherapy, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Inès Dufait
- Department of Radiotherapy, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mark De Ridder
- Department of Radiotherapy, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
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Yahya N, Chua XJ, Manan HA, Ismail F. Inclusion of dosimetric data as covariates in toxicity-related radiogenomic studies. Strahlenther Onkol 2018; 194:780-786. [DOI: 10.1007/s00066-018-1303-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/06/2018] [Indexed: 12/25/2022]
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Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma. Front Oncol 2018; 8:95. [PMID: 29670856 PMCID: PMC5893829 DOI: 10.3389/fonc.2018.00095] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/19/2018] [Indexed: 01/30/2023] Open
Abstract
Background HPV infection is associated with high p16 expression and good prognosis in head and neck squamous cell carcinomas (HNSCCs). Analysis of CDKN2A, the gene encoding p16, may further elucidate the association between p16 expression and prognosis. We sought to determine whether CDKN2A copy number loss was associated with poor survival in HPV-negative HNSCCs. Methods The Cancer Genome Atlas HNSCC clinical and genomic data were obtained and integrated. Patients <80 years old with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included. Stratifying by copy number loss status, CDKN2A mRNA and p16 protein expression levels were examined and overall survival (OS) and disease-free survival (DFS) were evaluated. Results 401 patients with HPV-negative HNSCC were identified. 146 patients demonstrated CDKN2A copy number loss. The CDKN2A copy number loss group expressed significantly lower levels of CDKN2A mRNA and p16 protein than did the non-copy number loss group. Median OS for patients with and without CDKN2A copy number loss was 16.5 and 46.6 months, respectively (p = 0.007). Median DFS for both groups was 11.6 and 19.2 months, respectively (p = 0.03). In both univariate and multivariable analyses, stage IV designation, receipt of chemotherapy and CDKN2A copy number loss were predictive of OS. Conclusion CDKN2A copy number loss predicted poor survival independently of other patient and treatment factors and may be a clinically useful prognostic factor.
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Affiliation(s)
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, United States.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Allen Mo
- University of Connecticut School of Medicine, Farmington, CT, United States
| | - Thomas Hayman
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, United States
| | - Zain Husain
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, United States.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Joseph N Contessa
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, United States.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Stephen G Gaffney
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - James B Yu
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, United States.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States.,Cancer Outcomes, Public Policy, and Effectiveness Research (COPPER) Center at Yale, Yale School of Medicine, New Haven, CT, United States
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