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Ribeiro IP, Esteves L, Santos A, Barroso L, Marques F, Caramelo F, Melo JB, Carreira IM. A seven-gene signature to predict the prognosis of oral squamous cell carcinoma. Oncogene 2021; 40:3859-3869. [PMID: 33972685 DOI: 10.1038/s41388-021-01806-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 11/09/2022]
Abstract
The prognosis of oral squamous cell carcinoma (OSCC) patients remains poor without implemented biomarkers in the clinical routine practice to help in the patient's management. With this study we aimed to identify specific prognostic biomarkers for OSCC using a whole genome technology as well as to verify the clinical utility of a head and neck cancer-specific multiplex ligation-dependent probe amplification (MLPA) panel. A genomic characterization of tumor samples from 62 OSCC patients was performed using array comparative genomic hybridization (aCGH) and a more straightforward and cost-effective molecular technology, MLPA. The identification of a genomic signature and prognosis biomarkers was carried out by applying several statistical methods. With aCGH we observed that the chromosomes most commonly altered were 3p, 3q, 5q, 6p, 7q, 8p, 8q, 11q, 15q, 17q, and 18q. The MLPA results showed that the chromosomes with a higher frequency of alterations were 3p, 3q, 8p, 8q, and 11q. We identified a genomic signature with seven genes OCLN (3p21.31), CLDN16 (3q29), SCRIB (3q29), IKBKB (3q22.3), PAK2 (8q22.3), PIK3CB (3q28), and YWHAZ (8q24.3) that together allow to differentiate the patients that developed metastases or relapses after primary tumor treatment, with an overall accuracy of 79%. Amplification of PIK3CB as a predictor of metastases or relapses development was validated using TCGA data. This amplified gene showed a reduction in more than 5 years in the median survival of the patients. The identified biomarkers might have a significant impact in the patients' management and could leverage the OSCC precision medicine.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- University of Coimbra, Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Luísa Esteves
- University of Coimbra, Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, Coimbra, Portugal
| | - Ana Santos
- University of Coimbra, Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre (CHUC), EPE, Coimbra, Portugal
| | - Francisco Marques
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre (CHUC), EPE, Coimbra, Portugal
| | - Francisco Caramelo
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Laboratory of Biostatistics and Medical Informatics, iCBR-Faculty of Medicine, Coimbra, Portugal
| | - Joana Barbosa Melo
- University of Coimbra, Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Isabel Marques Carreira
- University of Coimbra, Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, Coimbra, Portugal. .,University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, Coimbra, Portugal. .,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal. .,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.
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2
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Haykal MM, Rodrigues-Ferreira S, Nahmias C. Microtubule-Associated Protein ATIP3, an Emerging Target for Personalized Medicine in Breast Cancer. Cells 2021; 10:cells10051080. [PMID: 34062782 PMCID: PMC8147298 DOI: 10.3390/cells10051080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Breast cancer is the leading cause of death by malignancy among women worldwide. Clinical data and molecular characteristics of breast tumors are essential to guide clinician’s therapeutic decisions. In the new era of precision medicine, that aims at personalizing the treatment for each patient, there is urgent need to identify robust companion biomarkers for new targeted therapies. This review focuses on ATIP3, a potent anti-cancer protein encoded by candidate tumor suppressor gene MTUS1, whose expression levels are markedly down-regulated in breast cancer. ATIP3 is a microtubule-associated protein identified both as a prognostic biomarker of patient survival and a predictive biomarker of breast tumors response to taxane-based chemotherapy. We present here recent studies pointing out ATIP3 as an emerging anti-cancer protein and a potential companion biomarker to be combined with future personalized therapy against ATIP3-deficient breast cancer.
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Affiliation(s)
- Maria M. Haykal
- Institut Gustave Roussy, Université Paris-Saclay, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, 94800 Villejuif, France; (M.M.H.); (S.R.-F.)
- LERMIT Laboratory, 92296 Chatenay-Malabry, France
| | - Sylvie Rodrigues-Ferreira
- Institut Gustave Roussy, Université Paris-Saclay, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, 94800 Villejuif, France; (M.M.H.); (S.R.-F.)
- LERMIT Laboratory, 92296 Chatenay-Malabry, France
- Inovarion, 75005 Paris, France
| | - Clara Nahmias
- Institut Gustave Roussy, Université Paris-Saclay, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, 94800 Villejuif, France; (M.M.H.); (S.R.-F.)
- LERMIT Laboratory, 92296 Chatenay-Malabry, France
- Correspondence:
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Dwivedi R, Pandey R, Chandra S, Mehrotra D. Apoptosis and genes involved in oral cancer - a comprehensive review. Oncol Rev 2020; 14:472. [PMID: 32685111 PMCID: PMC7365992 DOI: 10.4081/oncol.2020.472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
Oral cancers needs relentless research due to high mortality and morbidity associated with it. Despite of the comparable ease in accessibility to these sites, more than 2/3rd cases are diagnosed in advanced stages. Molecular/genetic studies augment clinical assessment, classification and prediction of malignant potential of oral lesions, thereby reducing its incidence and increasing the scope for early diagnosis and treatment of oral cancers. Herein we aim to review the role of apoptosis and genes associated with it in oral cancer development in order to aid in early diagnosis, prediction of malignant potential and evaluation of possible treatment targets in oral cancer. An internet-based search was done with key words apoptosis, genes, mutations, targets and analysis to extract 72 articles after considering inclusion and exclusion criteria. The knowledge of genetics and genomics of oral cancer is of utmost need in order to stop the rising prevalence of oral cancer. Translational approach and interventions at the early stage of oral cancer, targeted destruction of cancerous cells by silencing or promoting involved genes should be the ideal intervention.
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Affiliation(s)
- Ruby Dwivedi
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rahul Pandey
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Shaleen Chandra
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Divya Mehrotra
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
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4
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Ribeiro IP, Caramelo F, Ribeiro M, Machado A, Miguéis J, Marques F, Carreira IM, Melo JB. Upper aerodigestive tract carcinoma: Development of a (epi)genomic predictive model for recurrence and metastasis. Oncol Lett 2020; 19:3459-3468. [PMID: 32269619 PMCID: PMC7115117 DOI: 10.3892/ol.2020.11459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/31/2019] [Indexed: 12/02/2022] Open
Abstract
Despite the increased molecular knowledge and the diagnostic and therapeutic improvements, the survival of patients with upper aerodigestive tract carcinoma remains poor. The identification of early diagnostic and prognostic biomarkers and the development of molecular models to distinguish patients that will recur and/or develop metastasis after treatment as well as to benefit with target therapies can be important to decrease mortality, improve survival rates and improve the quality of life of these patients. The current study analyzed 21 upper aerodigestive tract carcinomas through array comparative genomic hybridization and methylation-specific multiplex ligation-dependent probe amplification techniques. A number of chromosomal regions and genes were observed with copy number alterations and methylation. A predictive (epi)genomic model that comprises the 3p chromosomal region and WT1, VHL and THBS1 genes was built, highlighting a molecular signature with possible clinical use. The current study may aid in the development of a more individualized patient management and targeted drug design. The power of this genomic and epigenetic model to predict the recurrence and metastasis development should be evaluated and validated in future larger cohort study.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| | - Francisco Caramelo
- iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal.,Laboratory of Biostatistics and Medical Informatics, IBILI-Institute for Biomedical Imaging and Life Sciences, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Margarida Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Ana Machado
- Department of Otorhinolaryngology-Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Jorge Miguéis
- Department of Otorhinolaryngology-Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Francisco Marques
- iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
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5
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Cytogenetics and Cytogenomics Evaluation in Cancer. Int J Mol Sci 2019; 20:ijms20194711. [PMID: 31547595 PMCID: PMC6801775 DOI: 10.3390/ijms20194711] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype-phenotype.
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(Cyto)genomic and epigenetic characterization of BICR 10 cell line and three new established primary human head and neck squamous cell carcinoma cultures. Genes Genomics 2019; 41:1207-1221. [PMID: 31321735 DOI: 10.1007/s13258-019-00850-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/04/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Head and neck squamous cell carcinoma cell lines are useful preclinical models to understand the molecular processes underlying the development of such tumors, and to establish targeted therapies. OBJECTIVE We performed a comprehensive (cyto)genomic and epigenetic characterization of three new established primary human head and neck squamous cell carcinoma cultures and an established, yet undercharacterized cell line: BICR 10. METHODS Karyotyping, multiplex fluorescence in situ hybridization, array comparative genomic hybridization and methylation-specific multiplex ligation-dependent probe amplification were applied. RESULTS The three primary cultures turned out to be a near-triploid and BICR 10 near-diploid. Banding and molecular cytogenetic analysis revealed non-random numerical and structural aberrations. The most common rearrangements identified in BICR 10 cell line were non-complex derivatives of reciprocal translocations, in which the breakpoints often appeared in centromeric/near-centromeric regions. In the 3 primary cell cultures the most common rearrangements observed were iso- and derivatives chromosomes derived from translocations. Overall, gains of 7p, 8q and losses at 3p, 8p, 9p, 18q and Xp were present in all four studied samples. Among the analyzed genes, BICR 10 cell line exhibited enhanced methylation of gene promoter; however, in all studied samples PAX5, WT1 and GATA5 were methylated. CONCLUSION The here reported comprehensive characterization of BICR 10 cell line and the new established cultures enriches the resources available for head and neck cancer research, especially for testing therapeutic agents.
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7
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Ribeiro IP, de Melo JB, Carreira IM. Head and neck cancer: searching for genomic and epigenetic biomarkers in body fluids - the state of art. Mol Cytogenet 2019; 12:33. [PMID: 31333762 PMCID: PMC6621978 DOI: 10.1186/s13039-019-0447-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) affects multiple sites of the upper aerodigestive tract and exhibited high incidence and mortality worldwide, being frequently diagnosed at advanced stage. Early detection of HNSCC plays a crucial role in a successful therapy. In the last years, the survival rates of these tumors have not improved significantly due to the late diagnosis and the lack of precise disease biomarkers and targeted therapies. The introduction in the clinical practice of body fluids to detect and analyze circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) and exosomes provides a minimally or non-invasive method also called as liquid biopsy for diagnostic and prognostic biomarkers detection, representing a shift of paradigm in precision medicine through the revolution in the way to perform HNSCC diagnosis and to screen high risk population. Despite the use of body fluids being an emergent and up-to date issue to early diagnosis HNSCC and their recurrences, no strategy has yet proven to be consistently effective and able to be translated to clinical application in the routine clinical management of these patients. In this review we will discuss the recent discoveries using blood and saliva to identify biomarkers for the early detection and prognosis of HNSCC.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- 1Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Pólo Ciências da Saúde, Coimbra, Portugal.,2iCBR-CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- 1Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Pólo Ciências da Saúde, Coimbra, Portugal.,2iCBR-CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel Marques Carreira
- 1Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Pólo Ciências da Saúde, Coimbra, Portugal.,2iCBR-CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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8
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Jiang Y, Mei W, Gu Y, Lin X, He L, Zeng H, Wei F, Wan X, Yang H, Major P, Tang D. Construction of a set of novel and robust gene expression signatures predicting prostate cancer recurrence. Mol Oncol 2018; 12:1559-1578. [PMID: 30024105 PMCID: PMC6120243 DOI: 10.1002/1878-0261.12359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 07/06/2018] [Accepted: 07/06/2018] [Indexed: 01/06/2023] Open
Abstract
We report here numerous novel genes and multiple new signatures which robustly predict prostate cancer (PC) recurrence. We extracted 696 differentially expressed genes relative to a reported PC signature from the TCGA dataset (n = 492) and built a 15‐gene signature (SigMuc1NW) using Elastic‐net with 10‐fold cross‐validation through analyzing their expressions at 1.5 standard deviation/SD below and 2 SD above a population mean. SigMuc1NW predicts biochemical recurrence (BCR) following surgery with 56.4% sensitivity, 72.6% specificity, and 63.24 median months disease free (MMDF) (P = 1.12e‐12). The prediction accuracy is improved with the use of SigMuc1NW's cutpoint (P = 3e‐15) and is further enhanced (sensitivity 67%, specificity 75.7%, MMDF 45.2, P = 0) when all 15 genes were analyzed through their cutpoints instead of their SDs. These genes individually associate with BCR using either SD or cutpoint as the cutoff points. Eight of 15 genes are individual risk factors after adjusting for age at diagnosis, Gleason score, surgical margin, and tumor stage. Eleven of 15 genes are novel to PC. SigMuc1NW discriminates BCR with time‐dependent AUC (tAUC) values of 76.6% at 11.5 months (76.6%–11.5 m), 73.8%‐22.3 m, 78.5%‐32.1 m, and 76.4%–48.4 m. SigMuc1NW is correlated with adverse features of PC, high Gleason scores (odds ratio/OR 1.48, P < 2e‐16), and advanced tumor stages (OR 1.33, P = 4.37e‐13). SigMuc1NW remains an independent risk factor of BCR (HR 2.44, 95% CI 1.53–3.87, P = 1.62e‐4) after adjusting for age at diagnosis, Gleason score, surgical margin, and tumor stage. In an independent PC (MSKCC) cohort (n = 140), these 15 genes were altered in PC vs normal tissue, metastatic PCs vs primary PCs, and recurrent PCs vs nonrecurrent PCs. Importantly, a 10‐gene subsignature SigMuc1NW1 predicts BCR in MSKCC (P = 3.11e‐15) and TCGA (P = 3.13e‐12); SigMuc1NW1 discriminates BCR at 18.4 m with tAUC as 82.5%. Collectively, our analyses support SigMuc1NW as a novel and robust signature in predicting BCR of PC.
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Affiliation(s)
- Yanzhi Jiang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsa, Hunan, China.,Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Canada
| | - Wenjuan Mei
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Canada.,Department of Nephrology, The First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Yan Gu
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Canada
| | - Xiaozeng Lin
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Canada
| | - Lizhi He
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Hui Zeng
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Canada.,Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang City, China
| | - Fengxiang Wei
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Xinhong Wan
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Huixiang Yang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsa, Hunan, China
| | - Pierre Major
- Division of Medical Oncology, Department of Oncology, McMaster University, Hamilton, Ontario, Canada
| | - Damu Tang
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Canada
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Ribeiro IP, Caramelo F, Esteves L, Oliveira C, Marques F, Barroso L, Melo JB, Carreira IM. Genomic and epigenetic signatures associated with survival rate in oral squamous cell carcinoma patients. J Cancer 2018; 9:1885-1895. [PMID: 29896272 PMCID: PMC5995936 DOI: 10.7150/jca.23239] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/17/2018] [Indexed: 11/05/2022] Open
Abstract
Purpose: Although oral squamous cell carcinoma (OSCC) presents great mortality and morbidity worldwide, the mechanisms behind its clinical behavior remain unclear. Biomarkers are needed to forecast patients' survival and, among those patients undergoing curative therapy, which are more likely to develop tumor recurrence/metastasis. Demonstrating clinical relevance of these biomarkers could be crucial both for surveillance and in helping to establish adjuvant therapy strategies. We aimed to identify genomic and epigenetic biomarkers of OSCC prognosis as well as to explore a noninvasive strategy to perform its detection. Methods: OSCC tumor and non-tumor tissue samples and cells scrapped from the tumor surface were genomic and epigenetically evaluated by Methylation-Specific Multiplex Ligation-dependent Probe Amplification technique. Results: Copy number alterations in ATM, CASR, TP73, CADM1, RARB, CDH13, PAX5, RB1 genes and GATA5, PAX6, CADM1 and CHFR promoter methylation were shown to be associated with worse OSCC patients' survival. Copy number alterations in BRCA1, CDKN2A, CHFR, GATA5, PYCARD, STK11, TP53, VHL genes and GATA5, CADM1, KLLN, MSH6, PAX5, WT1 promoter methylation were shown to be associated with development of metastasis/relapses during or after OSCC patients' treatment. We also found a good agreement in the status of CDKN2A promoter methylation evaluated noninvasively or in the tumor tissue. Conclusions: Genomic and epigenetic signatures were validated in a larger and geographically separate cohort, from TCGA database, which reinforce their clinical applicability. Noninvasive methodologies for detection of these signatures require further studies before translation in to clinical practice.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Luísa Esteves
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Camila Oliveira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Francisco Marques
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC, EPE, 3000-075 Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre, CHUC, EPE, 3000-075 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
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10
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Ribeiro IP, Rodrigues JM, Mascarenhas A, Kosyakova N, Caramelo F, Liehr T, Melo JB, Carreira IM. Cytogenetic, genomic, and epigenetic characterization of the HSC-3 tongue cell line with lymph node metastasis. J Oral Sci 2018; 60:70-81. [PMID: 29479029 DOI: 10.2334/josnusd.16-0811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Oral carcinoma develops from squamous epithelial cells by the acquisition of multiple (epi) genetic alterations that target different genes and molecular pathways. Herein, we performed a comprehensive genomic and epigenetic characterization of the HSC-3 cell line through karyotyping, multicolor fluorescence in situ hybridization, array comparative genomic hybridization, and methylation-specific multiplex ligation-dependent probe amplification. HSC-3 turned out to be a near-triploid cell line with a modal number of 61 chromosomes. Banding and molecular cytogenetic analyses revealed that nonrandom gains of chromosomal segments occurred more frequently than losses. Overall, gains of chromosome 1, 3q, 5p, 7p, 8q, 9q, 10, 11p, 11q13, 12, 13, 14, 17, 18p, 20, Yp, and Xq were observed. The largest region affected by copy number loss was observed at chromosome 18q. Several of the observed genomic imbalances and their mapped genes were already associated with oral carcinoma and/or adverse prognosis, invasion, and metastasis in cancer. The most common rearrangements observed were translocations in the centromeric/near-centromeric regions. RARB, ESR1, and CADM1 genes were methylated and showed copy number losses, whereas TP73 and GATA5 presented with methylation and copy number gains. Thus, the current study presents a comprehensive characterization of the HSC-3 cell line; the use of this cell line may contribute to enriching the resources available for oral cancer research, especially for the testing of therapeutic agents.
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Affiliation(s)
- Ilda P Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra.,Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra
| | - Joana M Rodrigues
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra
| | | | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra.,Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra.,Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra
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11
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Genomic predictive model for recurrence and metastasis development in head and neck squamous cell carcinoma patients. Sci Rep 2017; 7:13897. [PMID: 29066758 PMCID: PMC5654944 DOI: 10.1038/s41598-017-14377-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022] Open
Abstract
The head and neck squamous cell carcinoma (HNSCC) population consists mainly of high-risk for recurrence and locally advanced stage patients. Increased knowledge of the HNSCC genomic profile can improve early diagnosis and treatment outcomes. The development of models to identify consistent genomic patterns that distinguish HNSCC patients that will recur and/or develop metastasis after treatment is of utmost importance to decrease mortality and improve survival rates. In this study, we used array comparative genomic hybridization data from HNSCC patients to implement a robust model to predict HNSCC recurrence/metastasis. This predictive model showed a good accuracy (>80%) and was validated in an independent population from TCGA data portal. This predictive genomic model comprises chromosomal regions from 5p, 6p, 8p, 9p, 11q, 12q, 15q and 17p, where several upstream and downstream members of signaling pathways that lead to an increase in cell proliferation and invasion are mapped. The introduction of genomic predictive models in clinical practice might contribute to a more individualized clinical management of the HNSCC patients, reducing recurrences and improving patients’ quality of life. The power of this genomic model to predict the recurrence and metastases development should be evaluated in other HNSCC populations.
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12
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Ribeiro IP, Marques F, Barroso L, Rodrigues J, Caramelo F, Melo JB, Carreira IM. Genomic profile of oral squamous cell carcinomas with an adjacent leukoplakia or with an erythroleukoplakia that evolved after the treatment of primary tumor: A report of two cases. Mol Med Rep 2017; 16:6780-6786. [PMID: 28901451 PMCID: PMC5865835 DOI: 10.3892/mmr.2017.7428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022] Open
Abstract
Oral leukoplakia and erythroleukoplakia are common oral potentially malignant disorders diagnosed in the oral cavity. The specific outcome of these lesions remains to be elucidated, as their malignant transformation rate exhibits great variation. The ability to predict which of those potentially malignant lesions are likely to progress to cancer would be vital to guide their future clinical management. The present study reported two patients with tongue squamous cell carcinoma: Case study 1 was diagnosed with a simultaneous leukoplakia and case study 2 developed an erythroleukoplakia following the primary tumor treatment. Whole genome copy number alterations were analyzed using array comparative genomic hybridization. The present study determined more genomic imbalances in the tissues from leukoplakia and erythroleukoplakia compared with their respective tumors. The present study also identified in tumor and potentially malignant lesions common alterations of chromosomal regions and genes, including FBXL5, UGT2B15, UGT2B28, KANSL1, GSTT1 and DUSP22, being some of these typical aberrations described in oral cancer and others are linked to chemoradioresistance. Several putative genes associated with hallmarks of malignancy that may have an important role in predicting the progression of leukoplakia and erythroleukoplakia to squamous cell carcinoma, namely gains in BNIPL, MCL1, STAG2, CSPP1 and ZNRF3 genes were also identified.
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Affiliation(s)
- Ilda P Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000‑354 Coimbra, Portugal
| | - Francisco Marques
- Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, 3000‑354 Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre, EPE, 3000‑075 Coimbra, Portugal
| | - Joana Rodrigues
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000‑354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra, 3000‑354 Coimbra, Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000‑354 Coimbra, Portugal
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000‑354 Coimbra, Portugal
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13
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Ribeiro IP, Marques F, Barroso L, Miguéis J, Caramelo F, Santos A, Julião MJ, Melo JB, Carreira IM. Genetic and epigenetic characterization of the tumors in a patient with a tongue primary tumor, a recurrence and a pharyngoesophageal second primary tumor. Mol Cytogenet 2017; 10:13. [PMID: 28413448 PMCID: PMC5387319 DOI: 10.1186/s13039-017-0310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/14/2017] [Indexed: 11/13/2022] Open
Abstract
Background The choice of therapeutic modality for oral carcinoma in recurrent or second primary tumors remains controversial, as the treatment modalities available might be reduced by the treatment of the first tumor, and the overall survival is lower when compared with patients with a single or first tumor. Identifying biomarkers that predict the risk of relapse and the response to treatment is an emerging clinical issue. Case presentation A Caucasian 49-years-old man was treated with chemotherapy followed by chemoradiotherapy for a primary left side tongue tumor, achieving a complete response. After 49-months of follow-up, a local recurrence was diagnosed. After 3 months, a second primary tumor at the pharyngoesophageal region was detected. Genomic and epigenetic characterization of these three tumors was performed using array Comparative Genomic Hybridization, Multiplex Ligation-dependent Probe Amplification (MLPA) and Methylation Specific MLPA. Results The three tumors of this patient shared several imbalances in all chromosomes excluding chromosomes 9, 20 and 22, where genes related to important functional mechanisms of tumorigenesis are mapped. The shared genomic imbalances, such as losses at 1p, 2p, 3p, 4q, 5q, 6q, 7q, 8p, 10p, 11q, 12p, 12q, 13q, 15q, 16p, 16q, 17p, 17q, 18q, 19p, 19q, 21q and Xp and gains at 3q, 7q, 14q and 15q showed a common clonal origin for the diagnosed relapses. We identified some chromosomal imbalances and genes mapped in the chromosomes 2, 3, 4, 6, 7, 11, 14, 17, 18 and 22 as putative linked to chemoradioresistance and chemoradiosensitivity. We also observed that gains in short arm of chromosomes 6, 7, 8 and 18 were acquired after treatment of the primary tumor. We identified losses of VHL gene and promoter methylation of WT1 and GATA5 genes, as predictors of relapses. Conclusions A common clonal origin for the diagnosed relapses was observed and we identified some putative candidate biomarkers of prognosis, relapse risk and treatment response that could guide the development of management strategies for these patients.
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Affiliation(s)
- Ilda P Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
| | - Francisco Marques
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, Coimbra, 3000-075 Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC, Coimbra, 3000-075 EPE Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre, CHUC, Coimbra, 3000-075 EPE Portugal
| | - Jorge Miguéis
- Department of Otorhinolaryngology - Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC, Coimbra, EPE Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
| | - André Santos
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal
| | - Maria J Julião
- Department of Pathology, Coimbra Hospital and University Centre, CHUC, Coimbra, 3000-075 EPE Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
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14
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Ribeiro IP, Barroso L, Marques F, Melo JB, Carreira IM. Early detection and personalized treatment in oral cancer: the impact of omics approaches. Mol Cytogenet 2016; 9:85. [PMID: 27895714 PMCID: PMC5120562 DOI: 10.1186/s13039-016-0293-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/09/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Oral cancer is one of the most common malignant lesions of the head and neck. This cancer is an aggressive and lethal disease with no significant improvements in the overall survival in the last decades. Moreover, the incidence of oral HPV-positive tumors is rising, especially in young people. This oral neoplasm develops through numerous molecular imbalances that affect key genes and signaling pathways; however, the molecular mechanisms involved in the pathogenesis and progression of oral tumors are still to be fully determined. In order to improve the quality of life and long-term survival rate of these patients, it is vital to establish accurate biomarkers that help in the early diagnosis, prognosis and development of target treatments. Such biomarkers may possibly allow for selection of patients that will benefit from each therapy modality, helping in the optimization of intensity and sequence of the treatments in order to decrease side effects and improve survival. CONCLUSION In this review we discuss the current knowledge of oral cancer and the potential role of omics approaches to identify molecular biomarkers in the improvement of early diagnosis, treatment and prognosis. The pursuit to improve the quality of life and decrease mortality rates of the oral patients needs to be centralized on the identification of critical genes in oral carcinogenesis. Understanding the molecular biology of oral cancer is vital for search new therapies, being the molecular-targeted therapies the most promising treatment for these patients.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Unit, Coimbra Hospital and University Centre, CHUC, EPE, Coimbra, 3000-075 Portugal
| | - Francisco Marques
- Department of Dentistry, Faculty of Medicine, University of Coimbra, Coimbra, 3000-075 Portugal
- Stomatology Unit, Coimbra Hospital and University Centre, CHUC, EPE, Coimbra, 3000-075 Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra, 3000-354 Portugal
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, 3000-354 Portugal
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15
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Ribeiro IP, Caramelo F, Marques F, Domingues A, Mesquita M, Barroso L, Prazeres H, Julião MJ, Baptista IP, Ferreira A, Melo JB, Carreira IM. WT1, MSH6, GATA5 and PAX5 as epigenetic oral squamous cell carcinoma biomarkers - a short report. Cell Oncol (Dordr) 2016; 39:573-582. [PMID: 27491556 DOI: 10.1007/s13402-016-0293-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Oral squamous cell carcinoma (OSCC) is a frequently occurring aggressive malignancy with a heterogeneous clinical behavior. Based on the paucity of specific early diagnostic and prognostic biomarkers, which hampers the appropriate treatment and, ultimately the development of novel targeted therapies, we aimed at identifying such biomarkers through a genetic and epigenetic analysis of these tumors. METHODS 93 primary OSCCs were subjected to DNA copy number alteration (CNA) and methylation status analyses using methylation-specific multiplex ligation-dependent probe amplification (MS-MPLA). The genetic and epigenetic OSCC profiles obtained were associated with the patients' clinic-pathological features. RESULTS We found that WT1 gene promoter methylation is a predictor of a better prognosis and that MSH6 and GATA5 gene promoter methylation serve as predictors of a worse prognosis. GATA5 gene promoter methylation was found to be significantly associated with a shorter survival rate. In addition, we found that PAX5 gene promoter methylation was significantly associated with tongue tumors. To the best of our knowledge, this is the first study that highlights this specific set of genes as epigenetic diagnostic and prognostic biomarkers in OSCC. CONCLUSIONS Our data highlight the importance of epigenetically assessing OSCCs to identify key genes that may serve as diagnostic and prognostic biomarkers and, potentially, as candidate therapeutic targets.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal
| | - Francisco Marques
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075, Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre (CHUC), EPE, 3000-075, Coimbra, Portugal
| | - Ana Domingues
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal
| | - Margarida Mesquita
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre (CHUC), EPE, 3000-075, Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre (CHUC), EPE, 3000-075, Coimbra, Portugal
| | - Hugo Prazeres
- Molecular Pathology Laboratory, Portuguese Institute of Oncology of Coimbra FG, EPE, 3000-075, Coimbra, Portugal
| | - Maria José Julião
- Department of Pathology, Coimbra Hospital and University Centre (CHUC), EPE, 3000-075, Coimbra, Portugal
| | - Isabel Poiares Baptista
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075, Coimbra, Portugal
| | - Artur Ferreira
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre (CHUC), EPE, 3000-075, Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal. .,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal.
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16
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Fang Z, Dai W, Wang X, Chen W, Shen C, Ye G, Li L. Circulating miR-205: a promising biomarker for the detection and prognosis evaluation of bladder cancer. Tumour Biol 2015; 37:8075-82. [PMID: 26715266 DOI: 10.1007/s13277-015-4698-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 07/08/2014] [Indexed: 10/22/2022] Open
Abstract
MicroRNA (miRNA) expression profile analysis indicated that miR-205 was upregulated in bladder cancer tissue compared to healthy tissue. The aim of this study is to analyze value of circulating miR-205 for the detection and prognosis evaluation of bladder cancer (BC). Eighty-nine patients with BC and 56 healthy controls (HC) were enrolled in the study. miR-205 expression was determined using TaqMan quantitative real-time polymerase chain reaction assay and further correlated with patients' clinicopathological parameters and follow-up data. The results indicated that plasma miR-205 was upregulated in BC compared with HC (P < 0.001) and in muscle invasive BC (MIBC) compared to nonmuscle invasive BC (NMIBC) (P = 0.016). miR-205 yielded an area under the receiver-operating characteristic curve of 0.950 with 76.4 % sensitivity and 96.4 % specificity in discriminating BC from HC, and 0.668 with 57.1 % sensitivity and 77.0 % specificity in distinguishing MIBC from NMIBC. Plasma miR-205 expression was significantly associated with tumor stage (P < 0.001) and pathological grade (P = 0.048). The results indicated that BC patients with high miR-205 expression experienced shorter disease-free survival and disease-specific survival (P = 0.022 and P = 0.026; P = 0.027 and P = 0.034; respectively), which was not proven by multivariate Cox regression analysis (multi-Cox) (P = 0.0765 and P = 0.279, respectively). Log-rank test showed that NMIBC patients with high miR-205 expression experienced shorter cancer-free survival (P = 0.044). Log-rank test and univariate and multivariate Cox regression analyses did not indicate that high miR-205 expression in NMIBC patients was associated with cancer-specific survival (P = 0.079, P = 0.089, and P = 0.201, respectively). In conclusion, miR-205 may be a promising biomarker for the detection and prognosis evaluation of BC.
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Affiliation(s)
- Zhenqiang Fang
- Department of Urology, Center of Nephrology, The Second Affiliated Hospital of the Third Military Medical University, Chongqing, 400037, China
| | - Wei Dai
- Chongqing Petroleum Hospital, Chongqing, 400037, China
| | - Xiangwei Wang
- Department of Urology, Center of Nephrology, The Second Affiliated Hospital of the Third Military Medical University, Chongqing, 400037, China
| | - Wei Chen
- Department of Urology, Center of Nephrology, The Second Affiliated Hospital of the Third Military Medical University, Chongqing, 400037, China
| | - Chongxin Shen
- Department of Urology, Center of Nephrology, The Second Affiliated Hospital of the Third Military Medical University, Chongqing, 400037, China
| | - Gang Ye
- Department of Urology, Center of Nephrology, The Second Affiliated Hospital of the Third Military Medical University, Chongqing, 400037, China
| | - Longkun Li
- Department of Urology, Center of Nephrology, The Second Affiliated Hospital of the Third Military Medical University, Chongqing, 400037, China.
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17
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Lin HY, Hung SK, Lee MS, Chiou WY, Huang TT, Tseng CE, Shih LY, Lin RI, Lin JMJ, Lai YH, Chang CB, Hsu FC, Chen LC, Tsai SJ, Su YC, Li SC, Lai HC, Hsu WL, Liu DW, Tai CK, Wu SF, Chan MWY. DNA methylome analysis identifies epigenetic silencing of FHIT as a determining factor for radiosensitivity in oral cancer: an outcome-predicting and treatment-implicating study. Oncotarget 2015; 6:915-34. [PMID: 25460508 PMCID: PMC4359265 DOI: 10.18632/oncotarget.2821] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/24/2014] [Indexed: 12/17/2022] Open
Abstract
Radioresistance is still an emerging problem for radiotherapy of oral cancer. Aberrant epigenetic alterations play an important role in cancer development, yet the role of such alterations in radioresistance of oral cancer is not fully explored. Using a methylation microarray, we identified promoter hypermethylation of FHIT (fragile histidine triad) in radioresistant OML1-R cells, established from hypo-fractionated irradiation of parental OML1 radiosensitive oral cancer cells. Further analysis confirmed that transcriptional repression of FHIT was due to promoter hypermethylation, H3K27me3 and overexpression of methyltransferase EZH2 in OML1-R cells. Epigenetic interventions or depletion of EZH2 restored FHIT expression. Ectopic expression of FHIT inhibited tumor growth in both in vitro and in vivo models, while also resensitizing radioresistant cancer cells to irradiation, by restoring Chk2 phosphorylation and G2/M arrest. Clinically, promoter hypermethylation of FHIT inversely correlated with its expression and independently predicted both locoregional control and overall survival in 40 match-paired oral cancer patient samples. Further in vivo therapeutic experiments confirmed that inhibition of DNA methylation significantly resensitized radioresistant oral cancer cell xenograft tumors. These results show that epigenetic silencing of FHIT contributes partially to radioresistance and predicts clinical outcomes in irradiated oral cancer. The radiosensitizing effect of epigenetic interventions warrants further clinical investigation.
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Affiliation(s)
- Hon-Yi Lin
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Shih-Kai Hung
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Moon-Sing Lee
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Wen-Yen Chiou
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Tze-Ta Huang
- Department of Oral and Maxillofacial Surgery, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC.,Institute of Oral Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Chih-En Tseng
- Department of Anatomic Pathology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Liang-Yu Shih
- Department of Anatomic Pathology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Ru-Inn Lin
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Jora M J Lin
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Yi-Hui Lai
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Chia-Bin Chang
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Feng-Chun Hsu
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC
| | - Liang-Cheng Chen
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC
| | - Shiang-Jiun Tsai
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC
| | - Yu-Chieh Su
- Department of Hematology-Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Szu-Chi Li
- Department of Hematology-Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Hung-Chih Lai
- Department of Hematology-Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Wen-Lin Hsu
- Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Dai-Wei Liu
- Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Chien-Kuo Tai
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Shu-Fen Wu
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Michael W Y Chan
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.Human Epigenomics Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
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Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P. Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival. PLoS One 2015; 10:e0135074. [PMID: 26247464 PMCID: PMC4527746 DOI: 10.1371/journal.pone.0135074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
Oral squamous cell cancer of the oral cavity and oropharynx (OSCC) is associated with high case-fatality. For reasons that are largely unknown, patients with the same clinical and pathologic staging have heterogeneous response to treatment and different probability of recurrence and survival, with patients with Human Papillomavirus (HPV)-positive oropharyngeal tumors having the most favorable survival. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we used Affymtrix 6.0 SNP arrays to examine paired DNA from peripheral blood and tumor cell populations isolated by laser capture microdissection to assess genome-wide loss of heterozygosity (LOH) and DNA copy number aberration (CNA) and their associations with risk factors, tumor characteristics, and oral cancer-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p and 11q that seem to play an important role in oral cancer biology and survival from this disease. If confirmed, these findings could assist in designing personalized treatment or in the creation of models to predict survival in patients with HPV-negative OSCC.
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Affiliation(s)
- Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Yuzheng Zhang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa M. Loomis
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa P. Upton
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David R. Doody
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eduardo Mendez
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Neal Futran
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
| | - Stephen M. Schwartz
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Pei Wang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genetics and Genomics Sciences, Mt. Sinai School of Medicine, New York, New York, United States of America
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Clinical and Genetic Factors Associated with Cutaneous Squamous Cell Carcinoma in Kidney and Heart Transplant Recipients. Transplant Direct 2015; 1. [PMID: 26146661 DOI: 10.1097/txd.0000000000000521] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cutaneous squamous cell carcinoma (cSCC) occurs with higher frequency and recurrence rates, increased morbidity and mortality, and more aggressive metastasis in kidney and heart transplant recipients compared to the general population but all transplant recipients do not develop cSCC. In addition, the phenotypic expression of cSCC among transplant recipients can vary between mild disease to extensive recurrent metastatic disease. These clinically observed differences in occurrence and severity of cSCC among transplant recipients suggest the possibility that an underlying genetic component might modify risk. METHODS We identified 88 white post-transplant cSCC cases (71 kidney and 17 heart) and 300 white post-transplant controls (265 kidney and 35 heart) using a DNA biobank linked with de-identified electronic medical records. Logistic regression was used to determine adjusted odds ratios (OR) for clinical characteristics and single nucleotide polymorphisms (SNP) associated with cSCC in both a candidate SNP and genome wide analysis. RESULTS Age (OR 1.08 [1.05-1.11], p<0.001) and azathioprine exposure (OR 8.64 [3.92-19.03], p<0.001) were significantly associated while gender, smoking tobacco use, dialysis duration and immunosuppression duration were not. Ten candidate SNPs previously associated with non-melanoma skin cancer in the general population were significantly associated with cSCC in transplant recipients. Genome wide association analysis implicated SNPs in genes previously associated with malignancy, CSMD1 (OR 3.14 [1.90-5.20]) and CACNA1D (OR 2.67 [1.73-4.10]). CONCLUSIONS This study shows an association of increasing age and azathioprine exposure with cSCC and confirms a genetic contribution for cSCC development in kidney and heart transplant recipients.
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Gotoh M, Ichikawa H, Arai E, Chiku S, Sakamoto H, Fujimoto H, Hiramoto M, Nammo T, Yasuda K, Yoshida T, Kanai Y. Comprehensive exploration of novel chimeric transcripts in clear cell renal cell carcinomas using whole transcriptome analysis. Genes Chromosomes Cancer 2014; 53:1018-32. [PMID: 25230976 PMCID: PMC4304365 DOI: 10.1002/gcc.22211] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/07/2014] [Indexed: 01/01/2023] Open
Abstract
The aim of this study was to clarify the participation of expression of chimeric transcripts in renal carcinogenesis. Whole transcriptome analysis (RNA sequencing) and exploration of candidate chimeric transcripts using the deFuse program were performed on 68 specimens of cancerous tissue (T) and 11 specimens of non-cancerous renal cortex tissue (N) obtained from 68 patients with clear cell renal cell carcinomas (RCCs) in an initial cohort. As positive controls, two RCCs associated with Xp11.2 translocation were analyzed. After verification by reverse transcription (RT)-PCR and Sanger sequencing, 26 novel chimeric transcripts were identified in 17 (25%) of the 68 clear cell RCCs. Genomic breakpoints were determined in five of the chimeric transcripts. Quantitative RT-PCR analysis revealed that the mRNA expression levels for the MMACHC, PTER, EPC2, ATXN7, FHIT, KIFAP3, CPEB1, MINPP1, TEX264, FAM107A, UPF3A, CDC16, MCCC1, CPSF3, and ASAP2 genes, being partner genes involved in the chimeric transcripts in the initial cohort, were significantly reduced in 26 T samples relative to the corresponding 26 N samples in the second cohort. Moreover, the mRNA expression levels for the above partner genes in T samples were significantly correlated with tumor aggressiveness and poorer patient outcome, indicating that reduced expression of these genes may participate in malignant progression of RCCs. As is the case when their levels of expression are reduced, these partner genes also may not fully function when involved in chimeric transcripts. These data suggest that generation of chimeric transcripts may participate in renal carcinogenesis by inducing dysfunction of tumor-related genes.
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Affiliation(s)
- Masahiro Gotoh
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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