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Papenberg BW, Ingles J, Gao S, Feng J, Allen JL, Markwell SM, Interval ET, Montague PA, Wen S, Weed SA. Copy number alterations identify a smoking-associated expression signature predictive of poor outcome in head and neck squamous cell carcinoma. Cancer Genet 2021; 256-257:136-148. [PMID: 34130230 PMCID: PMC8273756 DOI: 10.1016/j.cancergen.2021.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/23/2021] [Accepted: 05/23/2021] [Indexed: 11/17/2022]
Abstract
Cigarette smoking is a risk factor for the development of head and neck squamous cell carcinoma (HNSCC), partially due to tobacco-induced large-scale chromosomal copy-number alterations (CNAs). Identifying CNAs caused by smoking is essential in determining how gene expression from such regions impact tumor progression and patient outcome. We utilized The Cancer Genome Atlas (TCGA) whole genome sequencing data for HNSCC to directly identify amplified or deleted genes correlating with smoking pack-year based on linear modeling. Internal cross-validation identified 35 CNAs that significantly correlated with patient smoking, independent of human papillomavirus (HPV) status. The most abundant CNAs were chromosome 11q13.3-q14.4 amplification and 9p23.1/9p24.1 deletion. Evaluation of patient amplicons reveals four different patterns of 11q13 gene amplification in HNSCC resulting from breakage-fusion-bridge (BFB) events. . Predictive modeling identified 16 genes from these regions that denote poorer overall and disease-free survival with increased pack-year use, constituting a smoking-associated expression signature (SAES). Patients with altered expression of signature genes have increased risk of death and enhanced cervical lymph node involvement. The identified SAES can be utilized as a novel predictor of increased disease aggressiveness and poor outcome in smoking-associated HNSCC.
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Affiliation(s)
| | | | - Si Gao
- Department of Biostatistics USA
| | | | - Jessica L Allen
- Department of Biochemistry, Program in Cancer Cell Biology USA
| | | | - Erik T Interval
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University, Morgantown, West Virginia, 26506 USA
| | - Phillip A Montague
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University, Morgantown, West Virginia, 26506 USA
| | | | - Scott A Weed
- Department of Biochemistry, Program in Cancer Cell Biology USA.
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2
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Hermida-Prado F, Menéndez ST, Albornoz-Afanasiev P, Granda-Diaz R, Álvarez-Teijeiro S, Villaronga MÁ, Allonca E, Alonso-Durán L, León X, Alemany L, Mena M, Del-Rio-Ibisate N, Astudillo A, Rodríguez R, Rodrigo JP, García-Pedrero JM. Distinctive Expression and Amplification of Genes at 11q13 in Relation to HPV Status with Impact on Survival in Head and Neck Cancer Patients. J Clin Med 2018; 7:E501. [PMID: 30513772 DOI: 10.3390/jcm7120501] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
Clear differences have been established between head and neck squamous cell carcinomas (HNSCC) depending on human papillomavirus (HPV) infection status. This study specifically investigated the status of the CTTN, CCND1 and ANO1 genes mapping at the 11q13 amplicon in relation to the HPV status in HNSCC patients. CTTN, CCND1 and ANO1 protein expression and gene amplification were respectively analyzed by immunohistochemistry and real-time PCR in a homogeneous cohort of 392 surgically treated HNSCC patients. The results were further confirmed using an independent cohort of 279 HNSCC patients from The Cancer Genome Atlas (TCGA). The impact on patient survival was also evaluated. CTTN, CCND1 and ANO1 gene amplification and protein expression were frequent in HPV-negative tumors, while absent or rare in HPV-positive tumors. Using an independent validation cohort of 279 HNSCC patients, we consistently found that these three genes were frequently co-amplified (28%) and overexpressed (39–46%) in HPV-negative tumors, whereas almost absent in HPV-positive tumors. Remarkably, these alterations (in particular CTTN and ANO1 overexpression) were associated with poor prognosis. Taken together, the distinctive expression and amplification of these genes could cooperatively contribute to the differences in prognosis and clinical outcome between HPV-positive and HPV-negative tumors. These findings could serve as the basis to design more personalized therapeutic strategies for HNSCC patients.
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Ramos-García P, González-Moles MÁ, González-Ruiz L, Ayén Á, Ruiz-Ávila I, Navarro-Triviño FJ, Gil-Montoya JA. An update of knowledge on cortactin as a metastatic driver and potential therapeutic target in oral squamous cell carcinoma. Oral Dis 2018; 25:949-971. [PMID: 29878474 DOI: 10.1111/odi.12913] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/15/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
Cortactin is a protein encoded by the CTTN gene, localized on chromosome band 11q13. As a result of the amplification of this band, an important event in oral carcinogenesis, CTTN is also usually amplified, promoting the frequent overexpression of cortactin. Cortactin enhances cell migration in oral cancer, playing a key role in the regulation of filamentous actin and of protrusive structures (invadopodia and lamellipodia) on the cell membrane that are necessary for the acquisition of a migratory phenotype. We also analyze a series of emerging functions that cortactin may exert in oral cancer (cell proliferation, angiogenesis, regulation of exosomes, and interactions with the tumor microenvironment). We review its molecular structure, its most important interactions (with Src, Arp2/3 complex, and SH3-binding partners), the regulation of its functions, and its specific oncogenic role in oral cancer. We explore the mechanisms of its overexpression in cancer, mainly related to genetic amplification. We analyze the prognostic implications of the oncogenic activation of cortactin in potentially malignant disorders and in head and neck cancer, where it appears to be relevant in the development of lymph node metastasis. Finally, we discuss its usefulness as a therapeutic target and suggest future research lines.
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Affiliation(s)
| | - Miguel Ángel González-Moles
- School of Dentistry, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria, Granada, Spain
| | - Lucía González-Ruiz
- Servicio de Dermatología, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | - Ángela Ayén
- School of Medicine, University of Granada, Granada, Spain
| | - Isabel Ruiz-Ávila
- Instituto de Investigación Biosanitaria, Granada, Spain.,Servicio de Anatomía Patológica, Complejo Hospitalario Universitario de Granada, Granada, Spain
| | | | - José Antonio Gil-Montoya
- School of Dentistry, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria, Granada, Spain
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4
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Betts JA, Moradi Marjaneh M, Al-Ejeh F, Lim YC, Shi W, Sivakumaran H, Tropée R, Patch AM, Clark MB, Bartonicek N, Wiegmans AP, Hillman KM, Kaufmann S, Bain AL, Gloss BS, Crawford J, Kazakoff S, Wani S, Wen SW, Day B, Möller A, Cloonan N, Pearson J, Brown MA, Mercer TR, Waddell N, Khanna KK, Dray E, Dinger ME, Edwards SL, French JD. Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage. Am J Hum Genet 2017; 101:255-266. [PMID: 28777932 PMCID: PMC5544418 DOI: 10.1016/j.ajhg.2017.07.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-associated SNPs fall within a distal enhancer that regulates CCND1. Here, we report that, in addition to regulating CCND1, this enhancer regulates two estrogen-regulated long noncoding RNAs, CUPID1 and CUPID2. We provide evidence that the risk-associated SNPs are associated with reduced chromatin looping between the enhancer and the CUPID1 and CUPID2 bidirectional promoter. We further show that CUPID1 and CUPID2 are predominantly expressed in hormone-receptor-positive breast tumors and play a role in modulating pathway choice for the repair of double-strand breaks. These data reveal a mechanism for the involvement of this region in breast cancer.
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MESH Headings
- Breast Neoplasms/genetics
- Cell Line, Tumor
- Chromatin/metabolism
- Chromosomes, Human, Pair 11/genetics
- Cyclin D1/genetics
- DNA Breaks, Double-Stranded
- DNA Damage/genetics
- DNA Repair/genetics
- Enhancer Elements, Genetic/genetics
- Estrogens/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease/genetics
- Humans
- MCF-7 Cells
- Polymorphism, Single Nucleotide/genetics
- Promoter Regions, Genetic/genetics
- RNA Interference
- RNA, Long Noncoding/genetics
- RNA, Small Interfering/genetics
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Joshua A Betts
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mahdi Moradi Marjaneh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Fares Al-Ejeh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Yi Chieh Lim
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Wei Shi
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Haran Sivakumaran
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Romain Tropée
- Queensland University of Technology at the Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Ann-Marie Patch
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michael B Clark
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX1 2JD, UK; Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Adrian P Wiegmans
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristine M Hillman
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Susanne Kaufmann
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda L Bain
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Brian S Gloss
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen Kazakoff
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Shivangi Wani
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Shu W Wen
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Bryan Day
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Andreas Möller
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Nicole Cloonan
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - John Pearson
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy R Mercer
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicola Waddell
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kum Kum Khanna
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Eloise Dray
- Queensland University of Technology at the Translational Research Institute, Brisbane, QLD 4102, Australia; Queensland University of Technology, Institute of Health and Biomedical Innovation, Brisbane, QLD 4059, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Stacey L Edwards
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
| | - Juliet D French
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
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van Kempen PMW, Noorlag R, Braunius WW, Moelans CB, Rifi W, Savola S, Koole R, Grolman W, van Es RJJ, Willems SM. Clinical relevance of copy number profiling in oral and oropharyngeal squamous cell carcinoma. Cancer Med 2015. [PMID: 26194878 PMCID: PMC4618623 DOI: 10.1002/cam4.499] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Current conventional treatment modalities in head and neck squamous cell carcinoma (HNSCC) are nonselective and have shown to cause serious side effects. Unraveling the molecular profiles of head and neck cancer may enable promising clinical applications that pave the road for personalized cancer treatment. We examined copy number status in 36 common oncogenes and tumor suppressor genes in a cohort of 191 oropharyngeal squamous cell carcinomas (OPSCC) and 164 oral cavity squamous cell carcinomas (OSCC) using multiplex ligation probe amplification. Copy number status was correlated with human papillomavirus (HPV) status in OPSCC, with occult lymph node status in OSCC and with patient survival. The 11q13 region showed gain or amplifications in 59% of HPV-negative OPSCC, whereas this amplification was almost absent in HPV-positive OPSCC. Additionally, in clinically lymph node-negative OSCC (Stage I–II), gain of the 11q13 region was significantly correlated with occult lymph node metastases with a negative predictive value of 81%. Multivariate survival analysis revealed a significantly decreased disease-free survival in both HPV-negative and HPV-positive OPSCC with a gain of Wnt-induced secreted protein-1. Gain of CCND1 showed to be an independent predictor for worse survival in OSCC. These results show that copy number aberrations, mainly of the 11q13 region, may be important predictors and prognosticators which allow for stratifying patients for personalized treatment of HNSCC.
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Affiliation(s)
- Pauline M W van Kempen
- Department of Otorhinolaryngology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob Noorlag
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Weibel W Braunius
- Department of Otorhinolaryngology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Widad Rifi
- Tumor diagnostics, MRC-Holland, Amsterdam, The Netherlands
| | - Suvi Savola
- Tumor diagnostics, MRC-Holland, Amsterdam, The Netherlands
| | - Ronald Koole
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilko Grolman
- Department of Otorhinolaryngology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert J J van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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6
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Chung CC, Boland J, Yeager M, Jacobs KB, Zhang X, Deng Z, Matthews C, Berndt SI, Chanock SJ. Comprehensive resequence analysis of a 123-kb region of chromosome 11q13 associated with prostate cancer. Prostate 2012; 72:476-86. [PMID: 22468268 PMCID: PMC3325513 DOI: 10.1002/pros.21450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13.3 in men of European decent. A fine-mapping analysis with tag SNPs in the cancer genetic markers of susceptibility study identified three independent loci, marked by rs10896438, rs12793759, and rs10896449. This study further annotates common and uncommon variation across this region. METHODS A next generation resequence analysis of a 122.9-kb region of 11q13.3(68,642,755-68,765,690) was conducted in 78 unrelated individuals of European background,1 CEPH trio, and 1 YRI trio. RESULTS In total, 644 polymorphic loci were identified by our sequence analysis. Of these,166 variants—118 SNPs and 48 insertion-deletion polymorphisms (indels)—were novel,namely not present in the 1000 Genomes or International HapMap Projects. We identified 22,25, 6, and 4 variants strongly correlated (r2 ≥ 0.8) with rs10896438, rs10896449, rs12793759,and rs11228565, respectively. HapMap SNPs were in linkage disequilibrium (r2 ≥ 0.8) with 48%, 69%, 14%, and 60% of SNPs marking bins by rs10896438, rs10896449, rs12793759, and rs11228565, respectively. CONCLUSIONS Our next generation resequence analysis compliments publicly available datasets of European descent (HapMap, build 28 and 1000 Genome, Pilot 1, October 2010),underscoring the value of targeted resequence analysis prior to initiating functional studies based on public databases alone. Increasing the number of common variants enables investigators to better prioritize variants for functional studies designed to uncover the biological basis of the direct association(s) in the region.
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Affiliation(s)
- Charles C Chung
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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