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Agaimy A, Brcic L, Briski LM, Hung YP, Michal M, Michal M, Nielsen GP, Stoehr R, Rosenberg AE. NR4A3 fusions characterize a distinctive peritoneal mesothelial neoplasm of uncertain biological potential with pure adenomatoid/microcystic morphology. Genes Chromosomes Cancer 2023; 62:256-266. [PMID: 36524687 DOI: 10.1002/gcc.23118] [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: 10/28/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
A focal adenomatoid-microcystic pattern is not uncommon in peritoneal mesothelioma, but tumors composed almost exclusively of this pattern are distinctly rare and have not been well characterized. A small subset of mesotheliomas (mostly in children and young adults) are characterized by gene fusions including EWSR1/FUS::ATF1, EWSR1::YY1, and NTRK and ALK rearrangements, and often have epithelioid morphology. Herein, we describe five peritoneal mesothelial neoplasms (identified via molecular screening of seven histologically similar tumors) that are pure adenomatoid/microcystic in morphology and unified by the presence of an NR4A3 fusion. Patients were three males and two females aged 31-70 years (median, 40 years). Three presented with multifocal/diffuse and two with a localized disease. The size of the individual lesions ranged from 1.5 to 8 cm (median, 4.7). The unifocal lesions originated in the small bowel mesentery and the mesosigmoid. Treatment included surgery, either alone (three) or combined with hyperthermic intraperitoneal chemotherapy (two), and neoadjuvant or adjuvant chemotherapy (one case each). At the last follow-up (6-13 months), all five patients were alive and disease-free. All tumors were morphologically similar, characterized by extensive sieve-like microcystic growth with bland-looking flattened cells lining variably sized microcystic spaces and lacked a conventional epithelioid or sarcomatoid component. Immunohistochemistry confirmed mesothelial differentiation, but most cases showed limited expression of D2-40 and calretinin. Targeted RNA sequencing revealed an NR4A3 fusion (fusion partners were EWSR1 in three cases and CITED2 and NIPBL in one case each). The nosology and behavior of this morphomolecularly defined novel peritoneal mesothelial neoplasm of uncertain biological potential and its distinction from adenomatoid variants of conventional mesothelioma merit further delineation as more cases become recognized.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich Alexander University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Laurence M Briski
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael Michal
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Pilsen, Czech Republic
| | - Michal Michal
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Pilsen, Czech Republic
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert Stoehr
- Institute of Pathology, Friedrich Alexander University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Andrew E Rosenberg
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
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Paajanen J, Bueno R, De Rienzo A. The Rocky Road from Preclinical Findings to Successful Targeted Therapy in Pleural Mesothelioma. Int J Mol Sci 2022; 23:13422. [PMID: 36362209 PMCID: PMC9658134 DOI: 10.3390/ijms232113422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2023] Open
Abstract
Pleural mesothelioma (PM) is a rare and aggressive disease that arises from the mesothelial cells lining the pleural cavity. Approximately 80% of PM patients have a history of asbestos exposure. The long latency period of 20-40 years from the time of asbestos exposure to diagnosis, suggests that multiple somatic genetic alterations are required for the tumorigenesis of PM. The genomic landscape of PM has been characterized by inter- and intratumor heterogeneity associated with the impairment of tumor suppressor genes such as CDKN2A, NF2, and BAP1. Current systemic therapies have shown only limited efficacy, and none is approved for patients with relapsed PM. Advances in understanding of the molecular landscape of PM has facilitated several biomarker-driven clinical trials but so far, no predictive biomarkers for targeted therapies are in clinical use. Recent advances in the PM genetics have provided optimism for successful molecular strategies in the future. Here, we summarize the molecular mechanism underlying PM pathogenesis and review potential therapeutic targets.
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Affiliation(s)
| | - Raphael Bueno
- The Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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3
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Peng Q, Wan D, Zhou R, Luo H, Wang J, Ren L, Zeng Y, Yu C, Zhang S, Huang X, Peng Y. The biological function of metazoan-specific subunit nuclear factor related to kappaB binding protein of INO80 complex. Int J Biol Macromol 2022; 203:176-183. [PMID: 35093437 DOI: 10.1016/j.ijbiomac.2022.01.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 12/24/2022]
Abstract
The INO80 chromatin remodeling complex plays an essential role in the regulation of gene transcription, which participate in a variety of important biological processes in cells including DNA repair and DNA replication. Difference from the yeast INO80 complex, metazoan INO80 complex have the specific subunit G, which is known as nuclear factor related to kappaB binding protein (NFRKB). Recently, NFRKB has been received much attention in many aspects, such as DNA repair, cell pluripotency, telomere protection, and protein activity regulation. To dig the new function of metazoan INO80 complex, a better understanding of the role of NFRKB is required. In this review, we provide an overview of the structure and function of NFRKB and discuss its potential role in cancer treatment and telomere regulation. Overall, this review provides an important reference for further research of the INO80 complex and NFRKB.
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Affiliation(s)
- Qiyao Peng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Dan Wan
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Rongrong Zhou
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Hongyu Luo
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 410016, China
| | - Junyi Wang
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Lingyan Ren
- School of Safety Engineering, Chongqing University of Science & Technology, Chongqing 401331, China
| | - Yajun Zeng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Chao Yu
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Shuihan Zhang
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xuekuan Huang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 410016, China.
| | - Yongbo Peng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China.
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4
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Hajj GNM, Cavarson CH, Pinto CAL, Venturi G, Navarro JR, Lima VCCD. Malignant pleural mesothelioma: an update. J Bras Pneumol 2021; 47:e20210129. [PMID: 34909922 PMCID: PMC8836658 DOI: 10.36416/1806-3756/e20210129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/11/2021] [Indexed: 12/14/2022] Open
Abstract
Malignant mesotheliomas are rare types of cancers that affect the mesothelial surfaces, usually the pleura and peritoneum. They are associated with asbestos exposure, but due to a latency period of more than 30 years and difficult diagnosis, most cases are not detected until they reach advanced stages. Treatment options for this tumor type are very limited and survival ranges from 12 to 36 months. This review discusses the molecular physiopathology, current diagnosis, and latest therapeutic options for this disease.
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Affiliation(s)
- Glaucia N M Hajj
- Instituto International de Pesquisa, A.C. Camargo Cancer Center, São Paulo (SP), Brasil.,Instituto Nacional de Oncogenômica e Inovação Terapêutica, São Paulo (SP), Brasil
| | - Carolina H Cavarson
- Instituto International de Pesquisa, A.C. Camargo Cancer Center, São Paulo (SP), Brasil.,Instituto Nacional de Oncogenômica e Inovação Terapêutica, São Paulo (SP), Brasil
| | | | - Gabriela Venturi
- Instituto International de Pesquisa, A.C. Camargo Cancer Center, São Paulo (SP), Brasil.,BP Mirante, São Paulo (SP), Brasil
| | | | - Vladmir C Cordeiro de Lima
- Instituto Nacional de Oncogenômica e Inovação Terapêutica, São Paulo (SP), Brasil.,Rede D'Or, São Paulo (SP), Brasil
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5
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Johnson BW, Takahashi K, Cheng YY. Preclinical Models and Resources to Facilitate Basic Science Research on Malignant Mesothelioma - A Review. Front Oncol 2021; 11:748444. [PMID: 34900693 PMCID: PMC8660093 DOI: 10.3389/fonc.2021.748444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma is an aggressive cancer with poor prognosis, predominantly caused by human occupational exposure to asbestos. The global incidence of mesothelioma is predicted to increase as a consequence of continued exposure to asbestos from a variety of sources, including construction material produced in the past in developed countries, as well as those currently being produced in developing countries. Mesothelioma typically develops after a long latency period and consequently it is often diagnosed in the clinic at an advanced stage, at which point standard care of treatment, such as chemo- and radio-therapy, are largely ineffective. Much of our current understanding of mesothelioma biology, particularly in relation to disease pathogenesis, diagnosis and treatment, can be attributed to decades of preclinical basic science research. Given the postulated rising incidence in mesothelioma cases and the limitations of current diagnostic and treatment options, continued preclinical research into mesothelioma is urgently needed. The ever-evolving landscape of preclinical models and laboratory technology available to researchers have made it possible to study human disease with greater precision and at an accelerated rate. In this review article we provide an overview of the various resources that can be exploited to facilitate an enhanced understanding of mesothelioma biology and their applications to research aimed to improve the diagnosis and treatment of mesothelioma. These resources include cell lines, animal models, mesothelioma-specific biobanks and modern laboratory techniques/technologies. Given that different preclinical models and laboratory technologies have varying limitations and applications, they must be selected carefully with respect to the intended objectives of the experiments. This review therefore aims to provide a comprehensive overview of the various preclinical models and technologies with respect to their advantages and limitations. Finally, we will detail about a highly valuable preclinical laboratory resource to curate high quality mesothelioma biospecimens for research; the biobank. Collectively, these resources are essential to the continued advancement of precision medicine to curtail the increasing health burden caused by malignant mesothelioma.
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Affiliation(s)
| | - Ken Takahashi
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
| | - Yuen Yee Cheng
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
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Guo Z, Shen L, Li N, Wu X, Wang C, Gu Z, Chen Z, Liu J, Mao W, Han Y. Aurora Kinase A as a Diagnostic and Prognostic Marker of Malignant Mesothelioma. Front Oncol 2021; 11:789244. [PMID: 34956905 PMCID: PMC8692759 DOI: 10.3389/fonc.2021.789244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background Malignant mesothelioma (MM) is a highly aggressive cancer with a poor prognosis. Despite the use of several well-known markers, the diagnosis of MM is still challenging in some cases. we applied bioinformatics to identify key genes and screen for diagnostic and prognostic markers of MM. Methods The expression profiles of GSE2549 and GSE112154 microarray datasets from the Gene Expression Omnibus database contained 87 cases of MM tissue and 8 cases of normal mesothelial tissue in total. The GEO2R tool was used to detect differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were performed using DAVID Bioinformatics Resources. The DEGs protein-protein interaction networks were constructed from the STRING database. Cytoscape was used to identify significant modules and hub genes. The GEPIA database was used to explore relationships between hub genes and prognosis of MM. Immunohistochemistry was used to analyze protein expression in tissue microarrays with 47 Chinese MM tissues. Statistical analyses diagnostic and prognostic values. Results 346 DEGs were identified: 111 genes upregulated, and 235 downregulated. GO analysis showed that the primary biological processes of these DEGs were cell adhesion, leukocyte migration, and angiogenesis. The main cellular components included the extracellular space, extracellular exosome, and extracellular region. The molecular functions were integrin binding, heparin binding, and calcium ion binding. KEGG pathway analysis showed that DEGs are primarily involved in PPAR signaling pathway, extracellular matrix–receptor interactions, and regulation of lipolysis in adipocytes. Survival analysis showed that seven genes—AURKA, GAPDH, TOP2A, PPARG, SCD, FABP4, and CEBPA—may be potential prognostic markers for MM. Immunohistochemical studies showed that Aurora kinase A (AURKA gene encode, Aurora-A) and GAPDH were highly expressed in MM tissue in comparison with normal mesothelial tissue. Kaplan-Meier analysis confirmed a correlation between Aurora-A protein expression and overall survival but did not confirm a correlation with GAPDH. The receiver operating characteristic curves of Aurora-A protein expression suggested acceptable accuracy (AUC = 0.827; 95% CI [0.6686 to 0.9535]; p = 0.04). The sensitivity and specificity of Aurora-A were 83.33% and 77.78%, respectively. Conclusion Aurora-A could be an optimal diagnostic biomarker and a potential prognostic marker for MM.
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Affiliation(s)
- Zhenying Guo
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Li Shen
- Office of Education, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ningning Li
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaoxiao Wu
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Canming Wang
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Zheng Gu
- Department of Clinical Medicine Engineering, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Zhongjian Chen
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Junping Liu
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Weimin Mao
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou, China
- Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Yuchen Han,
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7
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Goričar K, Holcar M, Mavec N, Kovač V, Lenassi M, Dolžan V. Extracellular Vesicle Enriched miR-625-3p Is Associated with Survival of Malignant Mesothelioma Patients. J Pers Med 2021; 11:jpm11101014. [PMID: 34683154 PMCID: PMC8538530 DOI: 10.3390/jpm11101014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma (MM) is characterized by poor prognosis and short survival. Extracellular vesicles (EVs) are membrane-bound particles released from cells into various body fluids, and their molecular composition reflects the characteristics of the origin cell. Blood EVs or their miRNA cargo might serve as new minimally invasive biomarkers that would enable earlier detection of MM or treatment outcome prediction. Our aim was to evaluate miRNAs enriched in serum EVs as potential prognostic biomarkers in MM patients in a pilot longitudinal study. EVs were isolated from serum samples obtained before and after treatment using ultracentrifugation on 20% sucrose cushion. Serum EV-enriched miR-103-3p, miR-126-3p and miR-625-3p were quantified using qPCR. After treatment, expression of miR-625-3p and miR-126-3p significantly increased in MM patients with poor treatment outcome (p = 0.012 and p = 0.036, respectively). A relative increase in miR-625-3p expression after treatment for more than 3.2% was associated with shorter progression-free survival (7.5 vs. 19.4 months, HR = 3.92, 95% CI = 1.20-12.80, p = 0.024) and overall survival (12.5 vs. 49.1 months, HR = 5.45, 95% CI = 1.06-28.11, p = 0.043) of MM patients. Bioinformatic analysis showed enrichment of 33 miR-625-3p targets in eight biological pathways. Serum EV-enriched miR-625-3p could therefore serve as a prognostic biomarker in MM and could contribute to a more personalized treatment.
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Affiliation(s)
- Katja Goričar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Marija Holcar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Nina Mavec
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Viljem Kovač
- Institute of Oncology Ljubljana, Zaloška 2, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Vita Dolžan
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
- Correspondence: ; Tel.: +386-1-543-76
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Tholen LE, Bos C, Jansen PWTC, Venselaar H, Vermeulen M, Hoenderop JGJ, de Baaij JHF. Bifunctional protein PCBD2 operates as a co-factor for hepatocyte nuclear factor 1β and modulates gene transcription. FASEB J 2021; 35:e21366. [PMID: 33749890 DOI: 10.1096/fj.202002022r] [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: 08/28/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 11/11/2022]
Abstract
Hepatocyte nuclear factor 1β (HNF1β) is an essential transcription factor in development of the kidney, liver, and pancreas. HNF1β-mediated transcription of target genes is dependent on the cell type and the development stage. Nevertheless, the regulation of HNF1β function by enhancers and co-factors that allow this cell-specific transcription is largely unknown. To map the HNF1β interactome we performed mass spectrometry in a mouse kidney inner medullary collecting duct cell line. Pterin-4a-carbinolamine dehydratase 2 (PCBD2) was identified as a novel interaction partner of HNF1β. PCBD2 and its close homolog PCBD1 shuttle between the cytoplasm and nucleus to exert their enzymatic and transcriptional activities. Although both PCBD proteins share high sequence identity (48% and 88% in HNF1 recognition helix), their tissue expression patterns are unique. PCBD1 is most abundant in kidney and liver while PCBD2 is also abundant in lung, spleen, and adipose tissue. Using immunolocalization studies and biochemical analysis we show that in presence of HNF1β the nuclear localization of PCBD1 and PCBD2 increases significantly. Promoter luciferase assays demonstrate that co-factors PCBD1 and PCBD2 differentially regulate the ability of HNF1β to activate the promoters of transcriptional targets important in renal electrolyte homeostasis. Deleting the N-terminal sequence of PCBD2, not found in PCBD1, diminished the differential effects of the co-factors on HNF1β activity. All together these results indicate that PCBD1 and PCBD2 can exert different effects on HNF1β-mediated transcription. Future studies should confirm whether these unique co-factor activities also apply to HNF1β-target genes involved in additional processes besides ion transport in the kidney.
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Affiliation(s)
- Lotte E Tholen
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caro Bos
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Torricelli F, Saxena A, Nuamah R, Neat M, Harling L, Ng W, Spicer J, Ciarrocchi A, Bille A. Genomic analysis in short- and long-term patients with malignant pleura mesothelioma treated with palliative chemotherapy. Eur J Cancer 2020; 132:104-111. [PMID: 32339978 DOI: 10.1016/j.ejca.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 03/18/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) is an aggressive tumour with poor prognosis. The aim of this study was to identify genetic mutations associated with poor or extended survival in patients who received palliative chemotherapy. METHODS A total of 720 patients diagnosed with MPM between 2005 and 2015 were identified. Overall survival (OS) was longer than 30 months from diagnosis for 27 patients. Twelve of 27 (44%) of the pleural biopsies from long-term survivors were retrieved and matched with 12 biopsies from patients who survived less than 12 months; one biopsy was then excluded for poor DNA quality. RESULTS A total of 11 patients had a mean OS of 5.5 months, whereas 12 patients lived more than 30 months (mean OS: 55.8 ± 25). Mutational analysis identified 428 alterations; of which, 148, classified as somatic and functional, were considered further. Among these, 85% were missense variants, 8% were variants causing a stop gain and 6% were splice variants. Loss-of-function mutations in UQCRC1 were significantly associated with reduced survival in patients with MPM (p = 0.027), while a higher frequency of mutations in MXRA5 and RAPGEF6 was registered in long-term survivors. CONCLUSION This is the first study evaluating the relationship between the mutational profile and outcome in patients with MPM after palliative chemotherapy. UQCRC1 codes for cytochrome b-c1 complex subunit 1 which plays a fundamental role in normal mitochondrial functions and in cell metabolism. Recent studies described UQCRC1 deregulation in other cancers. Our results suggest a possible role for mitochondrial metabolism in the biology of mesothelioma.
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Affiliation(s)
- Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alka Saxena
- UK NIHR GSTFT/KCL Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Rosamond Nuamah
- UK NIHR GSTFT/KCL Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Michael Neat
- Cancer Genetics, Viapath, Guy's Hospital, London, UK
| | - Leanne Harling
- Department of Surgery and Cancer, Imperial College London, UK
| | - Wen Ng
- Department of Pathology, Guy's Hospital, London, UK
| | - James Spicer
- Division of Cancer Studies, King's College London, Guy's Hospital, London, UK
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Andrea Bille
- Division of Cancer Studies, King's College London, Guy's Hospital, London, UK; Department of Thoracic Surgery, Guy's Hospital, London, UK.
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10
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Brich S, Bozzi F, Perrone F, Tamborini E, Cabras AD, Deraco M, Stacchiotti S, Dagrada GP, Pilotti S. Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma. Mod Pathol 2020; 33:217-227. [PMID: 31570769 DOI: 10.1038/s41379-019-0371-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 01/07/2023]
Abstract
The aim of this study was to assess the performance of fluorescence in situ hybridization (FISH) in identifying the copy number profiles of the three key peritoneal mesothelioma tumor suppressor genes BAP1, CDKN2A, and NF2, with particular emphasis on minute homozygous deletions, a copy number abnormality recently unveiled at the 3p21 (BAP1) chromosomal region using high-throughput methods. FISH was performed on 75 formalin-fixed-paraffin-embedded peritoneal mesotheliomas and recognized two types of monoallelic loss (monosomy, and hemizygous deletion) and two types of biallelic loss (canonical homozygous deletion with a complete loss of FISH signal and homozygous deletion with diminished signal). Diminished FISH signals revealed deletions occurring within the genomic region covered by the gene-specific probe and affected all three tumor suppressors. BAP1 homozygous deletions with diminished signal outnumbered canonical homozygous deletions (13 vs 3): conversely, canonical homozygous deletions were prevalent for CDKN2A (2 vs 14). Diminished signal homozygous deletion was the only pattern of biallelic loss observed for NF2 (2 cases). Hemizygous deletion mainly affected BAP1 (21 vs 6), while monosomy was prevalent for CDKN2A (14 vs 7) and particularly for NF2 where it accounts for all monoallelic losses. FISH/immunohistochemistry (BAP1, CDKN2A, and MTAP) correlation showed that all homozygous deletions, including those with diminished signals, resulted in a null BAP1 and CDKN2A immunophenotype but only canonical CDKN2A homozygous deletions resulted in MTAP loss of expression. BAP1 hemizygous deletion, but not monosomy, was also invariably associated with loss of protein expression whereas neither type of CDKN2A monoallelic loss correlated with p16 or MTAP immunohistochemistry. Array comparative genomic hybridization performed on a spontaneously emerging peritoneal mesothelioma cell line provided support for the interpretation of the FISH patterns and allowed us to extend the number of chromatin remodeling factors involved in mesothelioma to SETD7 and PCGF5, two previously unreported genes.
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Affiliation(s)
- Silvia Brich
- Department of Pathology, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Fabio Bozzi
- Department of Pathology, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Pathology, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Pathology, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Marcello Deraco
- Peritoneal Surface Malignancies Unit, Colon and Rectal Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvia Stacchiotti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Gian Paolo Dagrada
- Department of Pathology, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Silvana Pilotti
- Department of Pathology, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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11
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Sage AP, Martinez VD, Minatel BC, Pewarchuk ME, Marshall EA, MacAulay GM, Hubaux R, Pearson DD, Goodarzi AA, Dellaire G, Lam WL. Genomics and Epigenetics of Malignant Mesothelioma. High Throughput 2018; 7:E20. [PMID: 30060501 PMCID: PMC6163664 DOI: 10.3390/ht7030020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
Malignant mesothelioma is an aggressive and lethal asbestos-related disease. Diagnosis of malignant mesothelioma is particularly challenging and is further complicated by the lack of disease subtype-specific markers. As a result, it is especially difficult to distinguish malignant mesothelioma from benign reactive mesothelial proliferations or reactive fibrosis. Additionally, mesothelioma diagnoses can be confounded by other anatomically related tumors that can invade the pleural or peritoneal cavities, collectively resulting in delayed diagnoses and greatly affecting patient management. High-throughput analyses have uncovered key genomic and epigenomic alterations driving malignant mesothelioma. These molecular features have the potential to better our understanding of malignant mesothelioma biology as well as to improve disease diagnosis and patient prognosis. Genomic approaches have been instrumental in identifying molecular events frequently occurring in mesothelioma. As such, we review the discoveries made using high-throughput technologies, including novel insights obtained from the analysis of the non-coding transcriptome, and the clinical potential of these genetic and epigenetic findings in mesothelioma. Furthermore, we aim to highlight the potential of these technologies in the future clinical applications of the novel molecular features in malignant mesothelioma.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Michelle E Pewarchuk
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Gavin M MacAulay
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Roland Hubaux
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Dustin D Pearson
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Aaron A Goodarzi
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Graham Dellaire
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
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12
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Johnson TG, Schelch K, Cheng YY, Williams M, Sarun KH, Kirschner MB, Kao S, Linton A, Klebe S, McCaughan BC, Lin RCY, Pirker C, Berger W, Lasham A, van Zandwijk N, Reid G. Dysregulated Expression of the MicroRNA miR-137 and Its Target YBX1 Contribute to the Invasive Characteristics of Malignant Pleural Mesothelioma. J Thorac Oncol 2018; 13:258-272. [PMID: 29113949 DOI: 10.1016/j.jtho.2017.10.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/10/2017] [Accepted: 10/21/2017] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Malignant pleural mesothelioma (MPM) is an aggressive malignancy linked to asbestos exposure. On a genomic level, MPM is characterized by frequent chromosomal deletions of tumor suppressors, including microRNAs. MiR-137 plays a tumor suppressor role in other cancers, so the aim of this study was to characterize it and its target Y-box binding protein 1 (YBX1) in MPM. METHODS Expression, methylation, and copy number status of miR-137 and its host gene MIR137HG were assessed by polymerase chain reaction. Luciferase reporter assays confirmed a direct interaction between miR-137 and Y-box binding protein 1 gene (YBX1). Cells were transfected with a miR-137 inhibitor, miR-137 mimic, and/or YBX1 small interfering RNA, and growth, colony formation, migration and invasion assays were conducted. RESULTS MiR-137 expression varied among MPM cell lines and tissue specimens, which was associated with copy number variation and promoter hypermethylation. High miR-137 expression was linked to poor patient survival. The miR-137 inhibitor did not affect target levels or growth, but interestingly, it increased miR-137 levels by means of mimic transfection suppressed growth, migration, and invasion, which was linked to direct YBX1 downregulation. YBX1 was overexpressed in MPM cell lines and inversely correlated with miR-137. RNA interference-mediated YBX1 knockdown significantly reduced cell growth, migration, and invasion. CONCLUSIONS MiR-137 can exhibit a tumor-suppressive function in MPM by targeting YBX1. YBX1 knockdown significantly reduces tumor growth, migration, and invasion of MPM cells. Therefore, YBX1 represents a potential target for novel MPM treatment strategies.
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Affiliation(s)
| | - Karin Schelch
- Asbestos Diseases Research Institute, Sydney, Australia
| | - Yuen Y Cheng
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medicine, University of Sydney, Sydney, Australia
| | - Marissa Williams
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medicine, University of Sydney, Sydney, Australia
| | - Kadir H Sarun
- Asbestos Diseases Research Institute, Sydney, Australia
| | | | - Steven Kao
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medicine, University of Sydney, Sydney, Australia; Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, Australia
| | - Anthony Linton
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medicine, University of Sydney, Sydney, Australia; Concord Cancer Centre, Concord Repatriation General Hospital, Sydney, Australia
| | - Sonja Klebe
- Department of Anatomical Pathology, Flinders University; Department of Anatomical Pathology, SA Pathology at Flinders Medical Centre, Adelaide, Australia
| | - Brian C McCaughan
- Department of Anatomical Pathology, SA Pathology at Flinders Medical Centre, Adelaide, Australia; Sydney Cardiothoracic Surgeons, RPAH Medical Centre, Sydney, Australia
| | - Ruby C Y Lin
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Christine Pirker
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Annette Lasham
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Nico van Zandwijk
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medicine, University of Sydney, Sydney, Australia
| | - Glen Reid
- Asbestos Diseases Research Institute, Sydney, Australia; School of Medicine, University of Sydney, Sydney, Australia.
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13
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Hu B, Shi C, Jiang HX, Qin SY. Identification of novel therapeutic target genes and pathway in pancreatic cancer by integrative analysis. Medicine (Baltimore) 2017; 96:e8261. [PMID: 29049217 PMCID: PMC5662383 DOI: 10.1097/md.0000000000008261] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Gene alterations are crucial to the molecular pathogenesis of pancreatic cancer. The present study was designed to identify the potential candidate genes in the pancreatic carcinogenesis. METHODS Gene Expression Omnibus database (GEO) datasets of pancreatic cancer tissue were retrieval and the differentially expressed genes (DEGs) from individual microarray data were merged. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) networks, and gene coexpression analysis were performed. RESULTS Three GEO datasets, including 74 pancreatic cancer samples and 55 controls samples were selected. A total of 2325 DEGs were identified, including 1383 upregulated and 942 downregulated genes. The GO terms for molecular functions, biological processes, and cellular component were protein binding, small molecule metabolic process, and integral to membrane, respectively. The most significant pathway in KEGG analysis was metabolic pathways. PPI network analysis indicated that the significant hub genes including cytochrome P450, family 2, subfamily E, polypeptide 1 (CYP2E1), mitogen-activated protein kinase 3 (MAPK3), and phospholipase C, gamma 1 (PLCG1). Gene coexpression network analysis identified 4 major modules, and the potassium channel tetramerization domain containing 10 (KCTD10), kin of IRRE like (KIRREL), dipeptidyl-peptidase 10 (DPP10), and unc-80 homolog (UNC80) were the hub gene of each modules, respectively. CONCLUSION Our integrative analysis provides a comprehensive view of gene expression patterns associated with the pancreatic carcinogenesis.
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14
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Meißner T, Mark A, Williams C, Berdel WE, Wiebe S, Kerkhoff A, Wardelmann E, Gaiser T, Müller-Tidow C, Rosenstiel P, Arnold N, Leyland-Jones B, Franke A, Stanulla M, Forster M. Metastatic triple-negative breast cancer patient with TP53 tumor mutation experienced 11 months progression-free survival on bortezomib monotherapy without adverse events after ending standard treatments with grade 3 adverse events. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001677. [PMID: 28679691 PMCID: PMC5495034 DOI: 10.1101/mcs.a001677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 04/24/2017] [Indexed: 01/02/2023] Open
Abstract
A triple-negative breast cancer patient had no hereditary BRCA1, BRCA2, or TP53 risk variants. After exhaustion of standard treatments, she underwent experimental treatments and whole-exome sequencing of tumor, blood, and a metastasis. Well-tolerated experimental bortezomib monotherapy was administered for a progression-free period of 11 mo. After progression, treatments were changed and the exome data were evaluated, expanded with RNA and exome sequencing of a late-stage metastasis. In the final stage, eribulin alone and in combination with anthracyclines were administered. While suffering from grade 3 adverse events, skin metastases progressed. She lived 51 mo after initial diagnosis.Toxicity from anthracyclines and cisplatin may have been due to associated germline variants CBR3 C4Y and V224M and GSTP1 I105V, respectively. Somatic mutations predicted or reported as pathogenic were detected in 38 genes in tumor tissues. All tumor samples harbored the heterozygous TP53 Y220C variant, known to destabilize p53 and down-regulate p53-mediated apoptosis. The success of bortezomib may be explained by the previously reported up-regulation of caspase-mediated apoptosis, which is p53-independent. Phylogenetic analysis of blood, primary tumor, and two metastases inferred an ancestral tumor cell with 12 expressed tumor mutations from which all three tumors may have evolved.Although our first urgent analysis could only include 40 genes, postmortem analysis uncovered the aggressiveness and suggested experimental therapies including 16 actionable targets, partly validated by immunohistochemistry. Exome and transcriptome analyses yielded comprehensive therapy-relevant information and should be considered for patients at first diagnosis.
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Affiliation(s)
- Tobias Meißner
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, La Jolla, California 92037, USA
| | - Adam Mark
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, La Jolla, California 92037, USA
| | - Casey Williams
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, South Dakota 57105, USA
| | - Wolfgang E Berdel
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Stephanie Wiebe
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Andrea Kerkhoff
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Timo Gaiser
- Institute of Pathology Mannheim, University Hospital Mannheim, D-68167 Mannheim, Germany
| | - Carsten Müller-Tidow
- Department of Medicine IV, Hematology and Oncology, University Hospital of Halle (Saale), D-06120 Halle, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany.,Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts-University of Kiel, D-24105 Kiel, Germany
| | - Brian Leyland-Jones
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, South Dakota 57105, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Martin Stanulla
- Department of Pediatric Haematology and Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
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15
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Kang HC, Kim HK, Lee S, Mendez P, Kim JW, Woodard G, Yoon JH, Jen KY, Fang LT, Jones K, Jablons DM, Kim IJ. Whole exome and targeted deep sequencing identify genome-wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas. Oncotarget 2016; 7:8321-31. [PMID: 26824986 PMCID: PMC4884995 DOI: 10.18632/oncotarget.7032] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/15/2016] [Indexed: 12/29/2022] Open
Abstract
Malignant pleural mesothelioma (MPM), a rare malignancy with a poor prognosis, is mainly caused by exposure to asbestos or other organic fibers, but the underlying genetic mechanism is not fully understood. Genetic alterations and causes for multiple primary cancer development including MPM are unknown. We used whole exome sequencing to identify somatic mutations in a patient with MPM and two additional primary cancers who had no evidence of venous, arterial, lymphovascular, or perineural invasion indicating dissemination of a primary lung cancer to the pleura. We found that the MPM had R282W, a key TP53 mutation, and genome-wide allelic loss or loss of heterozygosity, a distinct genomic alteration not previously described in MPM. We identified frequent inactivating SETDB1 mutations in this patient and in 68 additional MPM patients (mutation frequency: 10%, 7/69) by targeted deep sequencing. Our observations suggest the possibility of a new genetic mechanism in the development of either MPM or multiple primary cancers. The frequent SETDB1 inactivating mutations suggest there could be new diagnostic or therapeutic options for MPM.
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Affiliation(s)
- Hio Chung Kang
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Hong Kwan Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | | | - Gavitt Woodard
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jun-Hee Yoon
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Kuang-Yu Jen
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Li Tai Fang
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Kirk Jones
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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16
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Nabavi N, Bennewith KL, Churg A, Wang Y, Collins CC, Mutti L. Switching off malignant mesothelioma: exploiting the hypoxic microenvironment. Genes Cancer 2016; 7:340-354. [PMID: 28191281 PMCID: PMC5302036 DOI: 10.18632/genesandcancer.124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/31/2016] [Indexed: 12/21/2022] Open
Abstract
Malignant mesotheliomas are aggressive, asbestos-related cancers with poor patient prognosis, typically arising in the mesothelial surfaces of tissues in pleural and peritoneal cavity. The relative unspecific symptoms of mesotheliomas, misdiagnoses, and lack of precise targeted therapies call for a more critical assessment of this disease. In the present review, we categorize commonly identified genomic aberrations of mesotheliomas into their canonical pathways and discuss targeting these pathways in the context of tumor hypoxia, a hallmark of cancer known to render solid tumors more resistant to radiation and most chemo-therapy. We then explore the concept that the intrinsic hypoxic microenvironment of mesotheliomas can be Achilles' heel for targeted, multimodal therapeutic intervention.
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Affiliation(s)
- Noushin Nabavi
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, BC, Canada
- Department of Urologic Sciences, University of British Columbia, BC, Canada
- Department of Experimental Therapeutics, BC Cancer Agency, BC, Canada
| | - Kevin L. Bennewith
- Department of Integrative Oncology, BC Cancer Agency, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada
| | - Andrew Churg
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada
| | - Yuzhuo Wang
- Department of Urologic Sciences, University of British Columbia, BC, Canada
- Department of Experimental Therapeutics, BC Cancer Agency, BC, Canada
| | - Colin C. Collins
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, BC, Canada
- Department of Urologic Sciences, University of British Columbia, BC, Canada
| | - Luciano Mutti
- Italian Group for Research and Therapy for Mesothelioma (GIMe) & School of Environment and Life Sciences, University of Salford, Manchester, United Kingdom
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17
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Hylebos M, Van Camp G, van Meerbeeck JP, Op de Beeck K. The Genetic Landscape of Malignant Pleural Mesothelioma: Results from Massively Parallel Sequencing. J Thorac Oncol 2016; 11:1615-26. [PMID: 27282309 DOI: 10.1016/j.jtho.2016.05.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/27/2016] [Accepted: 05/22/2016] [Indexed: 12/18/2022]
Abstract
Malignant pleural mesothelioma (MPM) is a rare yet aggressive tumor that is causally associated with-mostly professional-asbestos exposure. Given the long latency between exposure and disease, and because asbestos is still being used, MPM will remain a global health issue for decades to come. Notwithstanding the increasing incidence of MPM and the fact that patients with MPM face a poor prognosis, currently available treatment options are limited. To enable the development of novel targeted therapies, identification of the genetic alterations underlying MPM will be crucial. The first studies reporting on the genomic background of MPM identified recurrent somatic mutations in a number of tumor suppressor genes (i.e., cyclin-dependent kinase inhibitor 2A gene [CDKN2A], neurofibromin 2 (merlin) gene [NF2], and BRCA1 associated protein 1 gene [BAP1]). More recently, massively parallel sequencing strategies have been used and have provided a more genome-wide view on the genetic landscape of MPM. This review summarizes their results, describing alterations that cluster mainly in four pathways: the tumor protein p53/DNA repair, cell cycle, mitogen-activated protein kinase, and phosphoinisitide 3-kinase (PI3K)/AKT pathways. As these pathways are important during tumor development, they provide interesting candidates for targeting with novel drugs.
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Affiliation(s)
- Marieke Hylebos
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Antwerp, Belgium.
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Jan P van Meerbeeck
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium; Thoracic Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Antwerp, Belgium
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18
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Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet 2016; 48:407-16. [PMID: 26928227 DOI: 10.1038/ng.3520] [Citation(s) in RCA: 613] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/04/2016] [Indexed: 02/06/2023]
Abstract
We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.
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Affiliation(s)
- Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric W Stawiski
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Leonard D Goldstein
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Steffen Durinck
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Assunta De Rienzo
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Florian Gnad
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Lucian R Chirieac
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniele Sciaranghella
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nhien Dao
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Corinne E Gustafson
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kiara J Munir
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason A Hackney
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Amitabha Chaudhuri
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Ravi Gupta
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Karen Toy
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Connie Ha
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Ying-Jiun Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Na Zhang
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thomas D Wu
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - David J Sugarbaker
- Division of Thoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Frederic J de Sauvage
- Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA
| | - William G Richards
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
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De Rienzo A, Archer MA, Yeap BY, Dao N, Sciaranghella D, Sideris AC, Zheng Y, Holman AG, Wang YE, Dal Cin PS, Fletcher JA, Rubio R, Croft L, Quackenbush J, Sugarbaker PE, Munir KJ, Battilana JR, Gustafson CE, Chirieac LR, Ching SM, Wong J, Tay LC, Rudd S, Hercus R, Sugarbaker DJ, Richards WG, Bueno R. Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma. Cancer Res 2015; 76:319-28. [PMID: 26554828 DOI: 10.1158/0008-5472.can-15-0751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/19/2015] [Indexed: 12/29/2022]
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive cancer that occurs more frequently in men, but is associated with longer survival in women. Insight into the survival advantage of female patients may advance the molecular understanding of MPM and identify therapeutic interventions that will improve the prognosis for all MPM patients. In this study, we performed whole-genome sequencing of tumor specimens from 10 MPM patients and matched control samples to identify potential driver mutations underlying MPM. We identified molecular differences associated with gender and histology. Specifically, single-nucleotide variants of BAP1 were observed in 21% of cases, with lower mutation rates observed in sarcomatoid MPM (P < 0.001). Chromosome 22q loss was more frequently associated with the epithelioid than that nonepitheliod histology (P = 0.037), whereas CDKN2A deletions occurred more frequently in nonepithelioid subtypes among men (P = 0.021) and were correlated with shorter overall survival for the entire cohort (P = 0.002) and for men (P = 0.012). Furthermore, women were more likely to harbor TP53 mutations (P = 0.004). Novel mutations were found in genes associated with the integrin-linked kinase pathway, including MYH9 and RHOA. Moreover, expression levels of BAP1, MYH9, and RHOA were significantly higher in nonepithelioid tumors, and were associated with significant reduction in survival of the entire cohort and across gender subgroups. Collectively, our findings indicate that diverse mechanisms highly related to gender and histology appear to drive MPM.
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Affiliation(s)
- Assunta De Rienzo
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts.
| | - Michael A Archer
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Beow Y Yeap
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nhien Dao
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Daniele Sciaranghella
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Antonios C Sideris
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yifan Zheng
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Alexander G Holman
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Harvard School of Public Health, Boston, Massachusetts
| | - Yaoyu E Wang
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Harvard School of Public Health, Boston, Massachusetts
| | - Paola S Dal Cin
- Departments of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Fletcher
- Departments of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Renee Rubio
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Harvard School of Public Health, Boston, Massachusetts
| | - Larry Croft
- Malaysian Genomics Resource Centre, Kuala Lumpur, Malaysia
| | - John Quackenbush
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Harvard School of Public Health, Boston, Massachusetts
| | - Peter E Sugarbaker
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Kiara J Munir
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Jesse R Battilana
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Corinne E Gustafson
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Lucian R Chirieac
- Departments of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Soo Meng Ching
- Malaysian Genomics Resource Centre, Kuala Lumpur, Malaysia
| | - James Wong
- Malaysian Genomics Resource Centre, Kuala Lumpur, Malaysia
| | | | - Stephen Rudd
- Malaysian Genomics Resource Centre, Kuala Lumpur, Malaysia
| | - Robert Hercus
- Malaysian Genomics Resource Centre, Kuala Lumpur, Malaysia
| | - David J Sugarbaker
- Debakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - William G Richards
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Raphael Bueno
- The Thoracic Surgery Oncology laboratory and the International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
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FOROOTAN SHIVASEYED, BUTLER JOEM, GARDENER DEREK, BAIRD ALISONE, DODSON ANDREW, DARBY ALISTAIR, KENNY JOHN, HALL NEIL, COSSINS ANDREWR, FOSTER CHRISTOPHERS, GOSDEN CHRISTINEM. Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications. Int J Oncol 2015; 48:130-44. [DOI: 10.3892/ijo.2015.3222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/31/2015] [Indexed: 11/05/2022] Open
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Temiz NA, Donohue DE, Bacolla A, Vasquez KM, Cooper DN, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT. The somatic autosomal mutation matrix in cancer genomes. Hum Genet 2015; 134:851-64. [PMID: 26001532 PMCID: PMC4495249 DOI: 10.1007/s00439-015-1566-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/12/2015] [Indexed: 01/26/2023]
Abstract
DNA damage in somatic cells originates from both environmental and endogenous sources, giving rise to mutations through multiple mechanisms. When these mutations affect the function of critical genes, cancer may ensue. Although identifying genomic subsets of mutated genes may inform therapeutic options, a systematic survey of tumor mutational spectra is required to improve our understanding of the underlying mechanisms of mutagenesis involved in cancer etiology. Recent studies have presented genome-wide sets of somatic mutations as a 96-element vector, a procedure that only captures the immediate neighbors of the mutated nucleotide. Herein, we present a 32 × 12 mutation matrix that captures the nucleotide pattern two nucleotides upstream and downstream of the mutation. A somatic autosomal mutation matrix (SAMM) was constructed from tumor-specific mutations derived from each of 909 individual cancer genomes harboring a total of 10,681,843 single-base substitutions. In addition, mechanistic template mutation matrices (MTMMs) representing oxidative DNA damage, ultraviolet-induced DNA damage, (5m)CpG deamination, and APOBEC-mediated cytosine mutation, are presented. MTMMs were mapped to the individual tumor SAMMs to determine the maximum contribution of each mutational mechanism to the overall mutation pattern. A Manhattan distance across all SAMM elements between any two tumor genomes was used to determine their relative distance. Employing this metric, 89.5% of all tumor genomes were found to have a nearest neighbor from the same tissue of origin. When a distance-dependent 6-nearest neighbor classifier was used, 10.4% of the SAMMs had an Undetermined tissue of origin, and 92.2% of the remaining SAMMs were assigned to the correct tissue of origin. [corrected]. Thus, although tumors from different tissues may have similar mutation patterns, their SAMMs often display signatures that are characteristic of specific tissues.
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Affiliation(s)
- Nuri A. Temiz
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Masonic Cancer Center, University of Minnesota, 2-120 CCRB, 2231 6th St SE, Minneapolis, MN 55455 USA
| | - Duncan E. Donohue
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />US Army Medical Research and Material Command, 568 Doughten Dr., Fort Detrick, Frederick, MD 21702 USA
| | - Albino Bacolla
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, TX 78723 USA
| | - Karen M. Vasquez
- />Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, TX 78723 USA
| | - David N. Cooper
- />Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Uma Mudunuri
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Joseph Ivanic
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Regina Z. Cer
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, Frederick, MD 21702 USA
| | - Ming Yi
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Robert M. Stephens
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Jack R. Collins
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Brian T. Luke
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
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22
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Davidson B. Prognostic factors in malignant pleural mesothelioma. Hum Pathol 2015; 46:789-804. [DOI: 10.1016/j.humpath.2015.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 12/11/2022]
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Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med 2015; 13:122. [PMID: 25889843 PMCID: PMC4422481 DOI: 10.1186/s12967-015-0485-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malignant mesothelioma (MM) arises from mesothelial cells that line the pleural, peritoneal and pericardial surfaces. The majority of MMs are pleural and have been associated with asbestos exposure. Previously, pleural MMs have been genetically characterized by the loss of BAP1 (40-60%) as well as loss of NF2 (75%) and CDKN2A (60%). The rare peritoneal form of MM occurs in ~10% cases. With only ~300 cases diagnosed in the US per year, its link to asbestos exposure is not clear and its mutational landscape unknown. METHODS We analyzed the somatic mutational landscape of 12 peritoneal MM of epitheloid subtype using copy number analysis (N = 9), whole exome sequencing (N = 7) and targeted sequencing (N = 12). RESULTS Peritoneal MM display few copy number alterations, with most samples having less than 10 Mbp total changes, mostly through deletions and no high copy number amplification. Chromosome band 3p21 encoding BAP1 is the most recurrently deleted region (5/9), while, in contrast to pleural MM, NF2 and CDKN2A are not affected. We further identified 87 non-silent mutations across 7 sequenced tumors, with a median of 8 mutated genes per tumor, resulting in a very low mutation rate (median 1.3 10(-6)). BAP1 was the only recurrently mutated gene (N = 3/7). In one additional case, loss of the entire chromosome 3 leaves a non-functional copy of BAP1 carrying a rare nonsense germline variant, thus suggesting a potential genetic predisposition in this patient. Finally, with targeted sequencing of BAP1 in 3 additional cases, we conclude that BAP1 is frequently altered through copy number losses (N = 3/12), mutations (N = 3/12) or both (N = 2/12) sometimes at a sub-clonal level. CONCLUSION Our findings suggest a major role for BAP1 in peritoneal MM susceptibility and oncogenesis and indicate important molecular differences to pleural MM as well as potential strategies for therapy and prevention.
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Affiliation(s)
- Hakan Alakus
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany. .,Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
| | - Shawn E Yost
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA.
| | - Brian Woo
- Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA.
| | - Randall French
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
| | - Grace Y Lin
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Kelly A Frazer
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA. .,Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Andrew M Lowy
- Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
| | - Olivier Harismendy
- Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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24
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Sheffield BS, Tinker AV, Shen Y, Hwang H, Li-Chang HH, Pleasance E, Ch'ng C, Lum A, Lorette J, McConnell YJ, Sun S, Jones SJM, Gown AM, Huntsman DG, Schaeffer DF, Churg A, Yip S, Laskin J, Marra MA. Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing. PLoS One 2015; 10:e0119689. [PMID: 25798586 PMCID: PMC4370594 DOI: 10.1371/journal.pone.0119689] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/15/2015] [Indexed: 12/31/2022] Open
Abstract
Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of the molecular biology of peritoneal mesothelioma. Translation of the emerging data into better treatments and outcome is needed. From two patients with peritoneal mesothelioma, we derived whole genome sequences, RNA expression profiles, and targeted deep sequencing data. Molecular data were made available for translation into a clinical treatment plan. Treatment responses and outcomes were later examined in the context of molecular findings. Molecular studies presented here provide the first reported whole genome sequences of peritoneal mesothelioma. Mutations in known mesothelioma-related genes NF2, CDKN2A, LATS2, amongst others, were identified. Activation of MET-related signaling pathways was demonstrated in both cases. A hypermutated phenotype was observed in one case (434 vs. 18 single nucleotide variants) and was associated with a favourable outcome despite sarcomatoid histology and multifocal disease. This study represents the first report of whole genome analyses of peritoneal mesothelioma, a key step in the understanding and treatment of this disease.
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Affiliation(s)
- Brandon S Sheffield
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Anna V Tinker
- British Columbia Cancer Agency, Division of Medical Oncology, Vancouver Centre, Vancouver, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Harry Hwang
- PhenoPath Laboratories, Seattle, Washington, United States of America
| | - Hector H Li-Chang
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Amy Lum
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Julie Lorette
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Yarrow J McConnell
- University of British Columbia, Department of Surgery, Surgical Oncology, Vancouver, Canada
| | - Sophie Sun
- British Columbia Cancer Agency, Division of Medical Oncology, Vancouver Centre, Vancouver, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Allen M Gown
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada; PhenoPath Laboratories, Seattle, Washington, United States of America
| | - David G Huntsman
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - David F Schaeffer
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Andrew Churg
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Stephen Yip
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, Canada
| | - Janessa Laskin
- British Columbia Cancer Agency, Division of Medical Oncology, Vancouver Centre, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
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Røe OD, Stella GM. Malignant pleural mesothelioma: history, controversy and future of a manmade epidemic. Eur Respir Rev 2015; 24:115-31. [PMID: 25726562 PMCID: PMC9487774 DOI: 10.1183/09059180.00007014] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Asbestos is the term for a family of naturally occurring minerals that have been used on a small scale since ancient times. Industrialisation demanded increased mining and refining in the 20th century, and in 1960, Wagner, Sleggs and Marchand from South Africa linked asbestos to mesothelioma, paving the way to the current knowledge of the aetiology, epidemiology and biology of malignant pleural mesothelioma. Pleural mesothelioma is one of the most lethal cancers, with increasing incidence worldwide. This review will give some snapshots of the history of pleural mesothelioma discovery, and the body of epidemiological and biological research, including some of the controversies and unresolved questions. Translational research is currently unravelling novel circulating biomarkers for earlier diagnosis and novel treatment targets. Current breakthrough discoveries of clinically promising noninvasive biomarkers, such as the 13-protein signature, microRNAs and the BAP1 mesothelioma/cancer syndrome, are highlighted. The asbestos history is a lesson to not be repeated, but here we also review recent in vivo and in vitro studies showing that manmade carbon nanofibres could pose a similar danger to human health. This should be taken seriously by regulatory bodies to ensure thorough testing of novel materials before release in the society. Malignant pleural mesothelioma is a cancer with increasing death tolls due to the past and present use of asbestoshttp://ow.ly/DhA2y
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Blackshear PE, Pandiri AR, Nagai H, Bhusari S, Hong HH, Ton TVT, Clayton NP, Wyde M, Shockley KR, Peddada SD, Gerrish KE, Sills RC, Hoenerhoff MJ. Gene expression of mesothelioma in vinylidene chloride-exposed F344/N rats reveal immune dysfunction, tissue damage, and inflammation pathways. Toxicol Pathol 2015; 43:171-85. [PMID: 24958746 PMCID: PMC4275413 DOI: 10.1177/0192623314537885] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A majority (∼80%) of human malignant mesotheliomas are asbestos-related. However, non-asbestos risk factors (radiation, chemicals, and genetic factors) account for up to 30% of cases. A recent 2-year National Toxicology Program carcinogenicity bioassay showed that male F344/N rats exposed to the industrial toxicant vinylidene chloride (VDC) resulted in a marked increase in malignant mesothelioma. Global gene expression profiles of these tumors were compared to spontaneous mesotheliomas and the F344/N rat mesothelial cell line (Fred-PE) in order to characterize the molecular features and chemical-specific profiles of mesothelioma in VDC-exposed rats. As expected, mesotheliomas from control and VDC-exposed rats shared pathways associated with tumorigenesis, including cellular and tissue development, organismal injury, embryonic development, inflammatory response, cell cycle regulation, and cellular growth and proliferation, while mesotheliomas from VDC-exposed rats alone showed overrepresentation of pathways associated with pro-inflammatory pathways and immune dysfunction such as the nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway, interleukin (IL)-8 and IL-12 signaling, interleukin responses, Fc receptor signaling, and natural killer and dendritic cells signaling, as well as overrepresentation of DNA damage and repair. These data suggest that a chronic, pro-inflammatory environment associated with VDC exposure may exacerbate disturbances in oncogene, growth factor, and cell cycle regulation, resulting in an increased incidence of mesothelioma.
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Affiliation(s)
- Pamela E Blackshear
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA Integrated Laboratory Systems, Inc., Research Triangle Park, North Carolina, USA
| | - Arun R Pandiri
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Hiroaki Nagai
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Sachin Bhusari
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Hue-Hua Hong
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Thai-Vu T Ton
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Natasha P Clayton
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Michael Wyde
- Experimental Toxicology Group, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Keith R Shockley
- Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Shyamal D Peddada
- Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kevin E Gerrish
- Laboratory of Toxicology and Pharmacology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Robert C Sills
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Mark J Hoenerhoff
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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MicroRNA and mRNA features of malignant pleural mesothelioma and benign asbestos-related pleural effusion. BIOMED RESEARCH INTERNATIONAL 2015; 2015:635748. [PMID: 25756049 PMCID: PMC4331157 DOI: 10.1155/2015/635748] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 10/27/2014] [Indexed: 12/02/2022]
Abstract
Introduction. We investigated the expression of microRNAs and mRNAs in pleural tissues from patients with either malignant pleural mesothelioma or benign asbestos-related pleural effusion. Methods. Fresh frozen tissues from a total of 18 malignant pleural mesothelioma and 6 benign asbestos-related pleural effusion patients were studied. Expression profiling of mRNA and microRNA was performed using standard protocols. Results. We discovered significant upregulation of multiple microRNAs in malignant pleural mesothelioma compared to benign asbestos-related pleural effusion. Hsa-miR-484, hsa-miR-320, hsa-let-7a, and hsa-miR-125a-5p were able to discriminate malignant from benign disease. Dynamically regulated mRNAs were also identified. MET was the most highly overexpressed gene in malignant pleural mesothelioma compared to benign asbestos-related pleural effusion. Integrated analyses examining microRNA-mRNA interactions suggested multiple altered targets within the Notch signaling pathway. Conclusions. Specific microRNAs and mRNAs may have diagnostic utility in differentiating patients with malignant pleural mesothelioma from benign asbestos-related pleural effusion. These studies may be particularly helpful in patients who reside in a region with a high incidence of mesothelioma.
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Robinson C, Solin JN, Lee YCG, Lake RA, Lesterhuis WJ. Mouse models of mesothelioma: strengths, limitations and clinical translation. Lung Cancer Manag 2014. [DOI: 10.2217/lmt.14.27] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY Mouse models of cancer are invaluable for obtaining detailed knowledge about tumor development and for screening therapeutic and preventive approaches. Mesothelioma is an unusual cancer because the same carcinogen, asbestos, causes a similar disease in both humans and animals. Unlike most other cancers, murine mesothelioma can therefore be regarded as a disease homolog, rather than a model as such. However, because asbestos-induced cancer has low penetrance and a long lag time, most translational studies have utilized more efficient models such as tumor transplantation. In consequence, many promising results have not translated into positive findings in patients. Here, we describe the widely used murine mesothelioma models and critically discuss their relative advantages and disadvantages. We emphasize the use of the appropriate model for the specific research question and the need to use multiple models in order to obtain robust and translatable data.
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Affiliation(s)
- Cleo Robinson
- National Centre for Asbestos Related Diseases, School of Medicine & Pharmacology, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Jessica N Solin
- National Centre for Asbestos Related Diseases, School of Medicine & Pharmacology, The University of Western Australia, Nedlands, WA 6009, Australia
| | - YC Gary Lee
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Richard A Lake
- National Centre for Asbestos Related Diseases, School of Medicine & Pharmacology, The University of Western Australia, Nedlands, WA 6009, Australia
| | - W Joost Lesterhuis
- National Centre for Asbestos Related Diseases, School of Medicine & Pharmacology, The University of Western Australia, Nedlands, WA 6009, Australia
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Jayaraman SS, Rayhan DJ, Hazany S, Kolodney MS. Mutational Landscape of Basal Cell Carcinomas by Whole-Exome Sequencing. J Invest Dermatol 2014; 134:213-220. [DOI: 10.1038/jid.2013.276] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 11/09/2022]
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Magge D, Zenati MS, Austin F, Mavanur A, Sathaiah M, Ramalingam L, Jones H, Zureikat AH, Holtzman M, Ahrendt S, Pingpank J, Zeh HJ, Bartlett DL, Choudry HA. Malignant peritoneal mesothelioma: prognostic factors and oncologic outcome analysis. Ann Surg Oncol 2013; 21:1159-65. [PMID: 24322529 DOI: 10.1245/s10434-013-3358-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Most patients with malignant peritoneal mesothelioma (MPM) present with late-stage, unresectable disease that responds poorly to systemic chemotherapy while, at the same time, effective targeted therapies are lacking. We assessed the efficacy of cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemoperfusion (HIPEC) in MPM. METHODS We prospectively analyzed 65 patients with MPM undergoing CRS/HIPEC between 2001 and 2010. Kaplan-Meier survival curves and multivariate Cox-regression models identified prognostic factors affecting oncologic outcomes. RESULTS Adequate CRS was achieved in 56 patients (CC-0 = 35; CC-1 = 21), and median simplified peritoneal cancer index (SPCI) was 12. Pathologic assessment revealed predominantly epithelioid histology (81 %) and biphasic histology (8 %), while lymph node involvement was uncommon (8 %). Major postoperative morbidity (grade III/IV) occurred in 23 patients (35 %), and 60-day mortality rate was 6 %. With median follow-up of 37 months, median overall survival was 46.2 months, with 1-, 2-, and 5-year overall survival probability of 77, 57, and 39 %, respectively. Median progression-free survival was 13.9 months, with 1-, 2-, and 5-year disease failure probability of 47, 68, and 83 %, respectively. In a multivariate Cox-regression model, age at surgery, SPCI >15, incomplete cytoreduction (CC-2/3), aggressive histology (epithelioid, biphasic), and postoperative sepsis were joint significant predictors of poor survival (chi square = 42.8; p = 0.00001), while age at surgery, SPCI >15, incomplete cytoreduction (CC-2/3), and aggressive histology (epithelioid, biphasic) were joint significant predictors of disease progression (Chi square = 30.6; p = 0.00001). CONCLUSIONS Tumor histology, disease burden, and the ability to achieve adequate surgical cytoreduction are essential prognostic factors in MPM patients undergoing CRS/HIPEC.
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Affiliation(s)
- Deepa Magge
- Division of Surgical Oncology, University of Pittsburgh, Pittsburgh, PA, USA
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Park HS, Yeo HY, Chang HJ, Kim KH, Park JW, Kim BC, Baek JY, Kim SY, Kim DY. Dipeptidyl peptidase 10, a novel prognostic marker in colorectal cancer. Yonsei Med J 2013; 54:1362-9. [PMID: 24142639 PMCID: PMC3809881 DOI: 10.3349/ymj.2013.54.6.1362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
PURPOSE The dipeptidyl peptidase IV (DPPIV) gene family exhibits multiple functions and is involved in the pathogenesis of various diseases. It has attracted pharmaceutical interest in the areas of metabolic disorders as well as cancer. However, clinicopathologic significance of DPPIV family in colorectal cancer is not fully understood. MATERIALS AND METHODS The clinical relevance of DPPIV and DPP10 expression was determined by immunohistochemical staining, and by assessing its clinicopathologic correlation in 383 colorectal cancer patients with known clinical outcomes. RESULTS DPPIV was not expressed in normal colon mucosa, but it showed luminal expression in 52 of the 383 colorectal cancers (13.5%). DPPIV expression in tumors was associated with right-sided location of the colon (p=0.010) and more advanced tumor stage (p=0.045). DPP10 was expressed in normal colonic mucosa, but its expression varied in primary colorectal cancer tissues. Loss of DPP10 expression was found in 11 colorectal cancers (CRCs) (2.9%), and multivariate analysis showed that loss of DPP10 expression was an independent factor for poor patient prognosis (p=0.008). CONCLUSION DPP10 may play a role in disease progression of colorectal cancer and loss of DPP10 expression in primary CRC is significantly associated with poor survival outcomes.
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Affiliation(s)
- Heae Surng Park
- Colorectal Cancer Branch, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang 410-769, Korea.
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State-of-the-Art Technologies to Interrogate Genetic/Genomic Components of Drug Response. CURRENT GENETIC MEDICINE REPORTS 2013. [DOI: 10.1007/s40142-013-0022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Blackshear PE, Pandiri AR, Ton TVT, Clayton NP, Shockley KR, Peddada SD, Gerrish KE, Sills RC, Hoenerhoff MJ. Spontaneous mesotheliomas in F344/N rats are characterized by dysregulation of cellular growth and immune function pathways. Toxicol Pathol 2013; 42:863-76. [PMID: 23980201 DOI: 10.1177/0192623313501894] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aged male Fischer 344/N rats are prone to developing spontaneous peritoneal mesotheliomas that arise predominantly from the tunica vaginalis of the testes. A definitive cause for the predominance of this neoplasm in F344/N rats is unknown. Investigation of the molecular alterations that occur in spontaneous rat mesotheliomas may provide insight into their pathogenesis as well enable a better understanding regarding the mechanisms underlying chemically induced mesothelioma in rodents. Mesothelial cell function represents a complex interplay of pathways related to host defense mechanisms and maintenance of cellular homeostasis. Global gene expression profiles of spontaneous mesotheliomas from vehicle control male F344/N rats from 2-year National Toxicology Program carcinogenicity bioassays were analyzed to determine the molecular features of these tumors and elucidate tumor-specific gene expression profiles. The resulting gene expression pattern showed that spontaneous mesotheliomas are associated with upregulation of various growth factors, oncogenes, cytokines, pattern recognition response receptors, and pathogen-associated molecular patterns receptors, and the production of reactive oxygen and nitrogen species, as well as downregulation of apoptosis pathways. Alterations in these pathways in turn trigger molecular responses that stimulate cell proliferation and promote tumor survival and progression.
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Affiliation(s)
- Pamela E Blackshear
- Integrated Laboratory Systems, Inc., Research Triangle Park, North Carolina, USA
| | - Arun R Pandiri
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Thai-Vu T Ton
- Cellular and Molecular Pathology Branch, Division of the National Toxicologic Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Natasha P Clayton
- Cellular and Molecular Pathology Branch, Division of the National Toxicologic Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Keith R Shockley
- Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Shyamal D Peddada
- Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kevin E Gerrish
- Microarray Core, Toxicology and Pharmacology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Robert C Sills
- Cellular and Molecular Pathology Branch, Division of the National Toxicologic Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Mark J Hoenerhoff
- Cellular and Molecular Pathology Branch, Division of the National Toxicologic Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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Integrated high-resolution array CGH and SKY analysis of homozygous deletions and other genomic alterations present in malignant mesothelioma cell lines. Cancer Genet 2013; 206:191-205. [PMID: 23830731 DOI: 10.1016/j.cancergen.2013.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/23/2013] [Accepted: 04/30/2013] [Indexed: 02/04/2023]
Abstract
High-resolution oligonucleotide array comparative genomic hybridization (aCGH) and spectral karyotyping (SKY) were applied to a panel of malignant mesothelioma (MMt) cell lines. SKY has not been applied to MMt before, and complete karyotypes are reported based on the integration of SKY and aCGH results. A whole genome search for homozygous deletions (HDs) produced the largest set of recurrent and non-recurrent HDs for MMt (52 recurrent HDs in 10 genomic regions; 36 non-recurrent HDs). For the first time, LINGO2, RBFOX1/A2BP1, RPL29, DUSP7, and CCSER1/FAM190A were found to be homozygously deleted in MMt, and some of these genes could be new tumor suppressor genes for MMt. Integration of SKY and aCGH data allowed reconstruction of chromosomal rearrangements that led to the formation of HDs. Our data imply that only with acquisition of structural and/or numerical karyotypic instability can MMt cells attain a complete loss of tumor suppressor genes located in 9p21.3, which is the most frequently homozygously deleted region. Tetraploidization is a late event in the karyotypic progression of MMt cells, after HDs in the 9p21.3 region have already been acquired.
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Vincent-Chong VK, Anwar A, Karen-Ng LP, Cheong SC, Yang YH, Pradeep PJ, Rahman ZAA, Ismail SM, Zaini ZM, Prepageran N, Kallarakkal TG, Ramanathan A, Mohayadi NABM, Rosli NSBM, Mustafa WMW, Abraham MT, Tay KK, Zain RB. Genome wide analysis of chromosomal alterations in oral squamous cell carcinomas revealed over expression of MGAM and ADAM9. PLoS One 2013; 8:e54705. [PMID: 23405089 PMCID: PMC3566089 DOI: 10.1371/journal.pone.0054705] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/14/2012] [Indexed: 12/26/2022] Open
Abstract
Despite the advances in diagnosis and treatment of oral squamous cell carcinoma (OSCC), mortality and morbidity rates have not improved over the past decade. A major drawback in diagnosis and treatment of OSCC is the lack of knowledge relating to how genetic instability in oral cancer genomes affects oral carcinogenesis. Hence, the key aim of this study was to identify copy number alterations (CNAs) that may be cancer associated in OSCC using high-resolution array comparative genomic hybridization (aCGH). To our knowledge this is the first study to use ultra-high density aCGH microarrays to profile a large number of OSCC genomes (n = 46). The most frequently amplified CNAs were located on chromosome 11q11(52%), 2p22.3(52%), 1q21.3-q22(54%), 6p21.32(59%), 20p13(61%), 7q34(52% and 72%),8p11.23-p11.22(80%), 8q11.1-q24.4(54%), 9q13-q34.3(54%), 11q23.3-q25(57%); 14q21.3-q31.1(54%); 14q31.3-q32.33(57%), 20p13-p12.3(54%) and 20q11.21-q13.33(52%). The most frequently deleted chromosome region was located on 3q26.1 (54%). In order to verify the CNAs from aCGH using quantitative polymerase chain reaction (qPCR), the three top most amplified regions and their associated genes, namely ADAM5P (8p11.23-p11.22), MGAM (7q34) and SIRPB1 (20p13.1), were selected in this study. The ADAM5P locus was found to be amplified in 39 samples and deleted in one; MGAM (24 amplifications and 3 deletions); and SIRPB1 (12 amplifications, others undetermined). On the basis of putative cancer-related annotations, two genes, namely ADAM metallopeptidase domain 9 (ADAM9) and maltase-glucoamylase alpha-glucosidase (MGAM), that mapped to CNA regions were selected for further evaluation of their mRNA expression using reverse transcriptase qPCR. The over-expression of MGAM was confirmed with a 6.6 fold increase in expression at the mRNA level whereas the fold change in ADAM9 demonstrated a 1.6 fold increase. This study has identified significant regions in the OSCC genome that were amplified and resulted in consequent over-expression of the MGAM and ADAM9 genes that may be utilized as biological markers for OSCC.
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Affiliation(s)
- Vui King Vincent-Chong
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Arif Anwar
- Sengenics Sdn Bhd, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Lee Peng Karen-Ng
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok Ching Cheong
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Oral Cancer Research Team, Cancer Research Initiatives Foundation, Selangor Darul Ehsan, Malaysia
| | - Yi-Hsin Yang
- Department of Dental Hygiene, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Padmaja Jayaprasad Pradeep
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Zainal Ariff Abdul Rahman
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Siti Mazlipah Ismail
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Zuraiza Mohamad Zaini
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Narayanan Prepageran
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Otorhinolaringology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Thomas George Kallarakkal
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Anand Ramanathan
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Keng Kiong Tay
- Oral Health Division, Ministry of Health, Putrajaya, Malaysia
| | - Rosnah Binti Zain
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Eyal E, Tohami T, Amir A, Cesarkas K, Jacob-Hirsch J, Volchek Y, Nagler A, Rechavi G, Amariglio N. Detection ofBCR-ABL1mutations in chronic myeloid leukaemia by massive parallel sequencing. Br J Haematol 2012; 160:477-86. [DOI: 10.1111/bjh.12171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/29/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Eran Eyal
- Cancer Research Centre; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | - Tali Tohami
- Division of Haematology; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | - Amnon Amir
- Cancer Research Centre; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | - Karen Cesarkas
- Cancer Research Centre; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | | | - Yuliya Volchek
- Division of Haematology; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | | | | | - Ninette Amariglio
- Division of Haematology; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
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Jean D, Daubriac J, Le Pimpec-Barthes F, Galateau-Salle F, Jaurand MC. Molecular changes in mesothelioma with an impact on prognosis and treatment. Arch Pathol Lab Med 2012; 136:277-93. [PMID: 22372904 DOI: 10.5858/arpa.2011-0215-ra] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT In recent decades, research on malignant pleural mesothelioma (MPM) has been developed to improve patients' outcomes by increasing the level of confidence in MPM diagnosis and prognosis. OBJECTIVE To summarize data on genetic and epigenetic abnormalities in MPM that may be of interest for a better management of patients with MPM. DATA SOURCES Data were obtained from scientific publications on genetic and epigenetic abnormalities in MPM by studying gene mutations, DNA methylation, and gene and microRNA expression profiling. CONCLUSIONS Molecular changes in MPM consist in altered expression and in activation or inactivation of critical genes in oncogenesis, especially tumor suppressor genes at the INK4 and NF2 loci. Activation of membrane receptor tyrosine kinases and deregulation of signaling pathways related to differentiation, survival, proliferation, apoptosis, cell cycle control, metabolism, migration, and invasion have been demonstrated. Alterations that could be targeted at a global level (methylation) have been recently reported. Experimental research has succeeded especially in abolishing proliferation and triggering apoptosis in MPM cells. So far, targeted clinical approaches focusing on receptor tyrosine kinases have had limited success. Molecular analyses of series of MPM cases have shown that defined alterations are present in MPM subsets, consistent with interindividual variations of molecular alterations, and suggesting that identification of patient subgroups will be essential to develop more specific therapies.
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Affiliation(s)
- Didier Jean
- INSERM, U, Université Paris Descartes, UMR-S, Paris, France
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Kernagis DN, Hall AH, Datto MB. Genes with Bimodal Expression Are Robust Diagnostic Targets that Define Distinct Subtypes of Epithelial Ovarian Cancer with Different Overall Survival. J Mol Diagn 2012; 14:214-22. [DOI: 10.1016/j.jmoldx.2012.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 01/06/2012] [Accepted: 01/13/2012] [Indexed: 10/28/2022] Open
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A new branch on the tree: next-generation sequencing in the study of cancer evolution. Semin Cell Dev Biol 2012; 23:237-42. [PMID: 22245832 DOI: 10.1016/j.semcdb.2011.12.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/20/2011] [Accepted: 12/30/2011] [Indexed: 12/26/2022]
Abstract
Cancer is a disease caused by the accumulation of genetic alterations in association with successive waves of clonal expansion. Mapping of the human genome sequence, in conjunction with technical advances in the ability to sequence entire genomes, have provided new insight into the mutational spectra and genetic events associated with clonal evolution of cancer. Moving forward, a clearer understanding of those alterations that undergo positive and negative selection throughout carcinogenesis and leading to metastatic dissemination would provide a boon not only to our understanding of cancer evolution, but to the development of potential targets for therapeutic intervention as well.
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Greenberg E, Rechavi G, Amariglio N, Solomon O, Schachter J, Markel G, Eyal E. Mutagen-specific mutation signature determines global microRNA binding. PLoS One 2011; 6:e27400. [PMID: 22096567 PMCID: PMC3212558 DOI: 10.1371/journal.pone.0027400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/15/2011] [Indexed: 12/25/2022] Open
Abstract
Micro-RNAs (miRNAs) are small non-coding RNAs that regulate gene products at the post-transcriptional level. It is thought that loss of cell regulation by miRNAs supports cancer development. Based on whole genome sequencing of a melanoma tumor, we predict, using three different computational algorithms, that the melanoma somatic mutations globally reduce binding of miRNAs to the mutated 3'UTRs. This phenomenon reflects the nature of the characteristic UV-induced mutation, C-to-T. Furthermore, we show that seed regions are enriched with Guanine, thus rendering miRNAs prone to reduced binding to UV-mutated 3'UTRs. Accordingly, mutation patterns in non UV-induced malignancies e.g. lung cancer and leukemia do not yield similar predictions. It is suggested that UV-induced disruption of miRNA-mediated gene regulation plays a carcinogenic role. Remarkably, dark-skinned populations have significantly higher GC content in 3'UTR SNPs than light-skinned populations, which implies on evolutionary pressure to preserve regulation by trans-acting oligonucleotides under conditions with excess UV radiation.
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Affiliation(s)
- Eyal Greenberg
- Ella Institute of Melanoma, Sheba Medical Center, Ramat-Gan, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gideon Rechavi
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Oz Solomon
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jacob Schachter
- Ella Institute of Melanoma, Sheba Medical Center, Ramat-Gan, Israel
| | - Gal Markel
- Ella Institute of Melanoma, Sheba Medical Center, Ramat-Gan, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Talpiot Medical Leadership Program, Sheba Medical Center, Ramat-Gan, Israel
| | - Eran Eyal
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
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Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A 2011; 108:E1128-36. [PMID: 22065754 DOI: 10.1073/pnas.1110574108] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
DNA copy number variations (CNVs) play an important role in the pathogenesis and progression of cancer and confer susceptibility to a variety of human disorders. Array comparative genomic hybridization has been used widely to identify CNVs genome wide, but the next-generation sequencing technology provides an opportunity to characterize CNVs genome wide with unprecedented resolution. In this study, we developed an algorithm to detect CNVs from whole-genome sequencing data and applied it to a newly sequenced glioblastoma genome with a matched control. This read-depth algorithm, called BIC-seq, can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion. Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome. Eighty percent (14/16) of the small variants tested (110 bp to 14 kb) were experimentally validated by quantitative PCR, demonstrating high sensitivity and true positive rate of the algorithm. We also extended the algorithm to detect recurrent CNVs in multiple samples as well as deriving error bars for breakpoints using a Gibbs sampling approach. We propose this statistical approach as a principled yet practical and efficient method to estimate CNVs in whole-genome sequencing data.
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Sastre L. New DNA sequencing technologies open a promising era for cancer research and treatment. Clin Transl Oncol 2011; 13:301-6. [PMID: 21596657 DOI: 10.1007/s12094-011-0658-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA sequencing techniques have evolved rapidly in the last 5 years by the introduction of new sequencing machines, denominated second-generation sequencers, next-generation sequencers or massive parallel sequencers. These technologies make it possible to determine the complete sequence of the human genome, or selected regions of it, at accessible prices and in a short period of time. Therefore, it is now possible to determine the nucleotide sequence of the DNA from cancer cells and to compare it to that of normal cells to identify the genetic changes involved in cancer generation. Actually, the genome of more than 15 tumour types has been determined in the last 3 years. The results obtained have allowed the identification of new cancer driving genes, new susceptibility genes and the detailed identification of genome structural reorganisations. In this review a brief description of the new sequencing technologies will be presented. Recent findings on cancer genome and exome sequencing will be summarised. Finally, the potential applications of these new technologies to cancer prognosis, diagnosis and therapeutics will be discussed.
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Affiliation(s)
- Leandro Sastre
- Instituto de Investigaciones Biomédicas CSIC/UAM, Instituto de Investigación Sanitaria del Hospital Universitario, La Paz (IdiPaz), Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain.
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Abstract
Pleural malignancies, including primary malignant pleural mesothelioma and secondary pleural metastasis of various tumours resulting in malignant pleural effusion, are frequent and lethal diseases that deserve devoted translational research efforts for improvements to be introduced to the clinic. This paper highlights select clinical advances that have been accomplished recently and that are based on preclinical research on pleural malignancies. Examples are the establishment of folate antimetabolites in mesothelioma treatment, the use of PET in mesothelioma management and the discovery of mesothelin as a marker of mesothelioma. In addition to established translational advances, this text focuses on recent research findings that are anticipated to impact clinical pleural oncology in the near future. Such progress has been substantial, including the development of a genetic mouse model of mesothelioma and of transplantable models of pleural malignancies in immunocompetent hosts, the deployment of stereological and imaging methods for integral assessment of pleural tumour burden, as well as the discovery of the therapeutic potential of aminobiphosphonates, histone deacetylase inhibitors and ribonucleases against malignant pleural disease. Finally, key obstacles to overcome towards a more rapid advancement of translational research in pleural malignancies are outlined. These include the dissection of cell-autonomous and paracrine pathways of pleural tumour progression, the study of mesothelioma and malignant pleural effusion separately from other tumours at both the clinical and preclinical levels, and the expansion of tissue banks and consortia of clinical research of pleural malignancies.
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Hoban CJ, Franklin W, Kopecky KJ, Baker LH. SWOG Cooperative Group Biorepository Resource: Access for Scientific Research Studies. Clin Cancer Res 2011; 17:5239-46. [DOI: 10.1158/1078-0432.ccr-10-3138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
SWOG (formerly the Southwest Oncology Group), a National Cancer Institute–supported cooperative group, conducts multiinstitutional, multidisciplinary clinical trials for adult patients with cancer, covering a wide range of solid tumors and hematologic cancers. The group has amassed a large set of biospecimens, collected from patients in numerous studies over many years and linked to clinical data. SWOG is now actively promoting the use of this unique scientific resource by making it available to a much wider group of researchers. This biospecimen resource offers material for research on disease mechanisms, genomic changes associated with cancer progression, markers of response and resistance to therapies, diagnosis or detection of recurrence, and more. By collecting, storing, and distributing the specimens, SWOG provides the framework for translational scientists to complete the feedback loop from “bedside to bench.” This article provides an overview of the group's biospecimen resources and guidelines for gaining access to them. Clin Cancer Res; 17(16); 5239–46. ©2011 AACR.
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Affiliation(s)
- Carolyn J. Hoban
- Authors' Affiliations: 1Southwest Oncology Group and University of Michigan, Ann Arbor, Michigan; 2University of Colorado, Department of Pathology, Denver, Colorado; and 3Southwest Oncology Group Statistical Center and Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wilbur Franklin
- Authors' Affiliations: 1Southwest Oncology Group and University of Michigan, Ann Arbor, Michigan; 2University of Colorado, Department of Pathology, Denver, Colorado; and 3Southwest Oncology Group Statistical Center and Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kenneth J. Kopecky
- Authors' Affiliations: 1Southwest Oncology Group and University of Michigan, Ann Arbor, Michigan; 2University of Colorado, Department of Pathology, Denver, Colorado; and 3Southwest Oncology Group Statistical Center and Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Laurence H. Baker
- Authors' Affiliations: 1Southwest Oncology Group and University of Michigan, Ann Arbor, Michigan; 2University of Colorado, Department of Pathology, Denver, Colorado; and 3Southwest Oncology Group Statistical Center and Fred Hutchinson Cancer Research Center, Seattle, Washington
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Halmos B, Powell CA. Update in lung cancer and oncological disorders 2010. Am J Respir Crit Care Med 2011; 184:297-302. [PMID: 21804121 PMCID: PMC3175537 DOI: 10.1164/rccm.201103-0370up] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/04/2011] [Indexed: 01/15/2023] Open
Affiliation(s)
| | - Charles A. Powell
- Division of Pulmonary and Critical Care Medicine, Columbia University Medical Center, New York, New York
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Woollard PM, Mehta NA, Vamathevan JJ, Van Horn S, Bonde BK, Dow DJ. The application of next-generation sequencing technologies to drug discovery and development. Drug Discov Today 2011; 16:512-9. [DOI: 10.1016/j.drudis.2011.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 02/24/2011] [Accepted: 03/17/2011] [Indexed: 12/17/2022]
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Sriram KB, Relan V, Clarke BE, Duhig EE, Yang IA, Bowman RV, Lee YCG, Fong KM. Diagnostic molecular biomarkers for malignant pleural effusions. Future Oncol 2011; 7:737-52. [DOI: 10.2217/fon.11.45] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Malignant pleural effusions (MPEs) are a common and important cause of cancer-related mortality and morbidity. Prompt diagnosis using minimally invasive tests is important because the median survival after diagnosis is only 4–9 months. Pleural fluid cytology is pivotal to current MPE diagnostic algorithms but has limited sensitivity (30–60%). Consequently, many patients need to undergo invasive diagnostic tests such as thoracoscopic pleural biopsy. Recent genomic, transcriptomic, methylation and proteomic studies on cells within pleural effusions have identified novel molecular diagnostic biomarkers that demonstrate potential in complementing cytology in the diagnosis of MPEs. Several challenges will need to be addressed prior to the incorporation of these molecular tests into routine clinical diagnosis, including validation of molecular diagnostic markers in well-designed prospective, comparative and cost–effectiveness studies. Ultimately, minimally invasive diagnostic tests that can be performed quickly will enable clinicians to provide the most effective therapies for patients with MPEs in a timely fashion.
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Affiliation(s)
| | - Vandana Relan
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
| | - Belinda E Clarke
- Department of Anatomical Pathology, The Prince Charles Hospital, Queensland, Australia
| | - Edwina E Duhig
- Department of Anatomical Pathology, The Prince Charles Hospital, Queensland, Australia
| | - Ian A Yang
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
| | - Rayleen V Bowman
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
| | - YC Gary Lee
- School of Medicine & Pharmacology & CAARR, University of Western Australia, Perth, Australia
- Respiratory Department, Sir Charles Gairdner Hospital, Perth, Australia
- Pleural Disease Unit, Lung Institute of Western Australia, Perth, Australia
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
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Kim RY, Xu H, Myllykangas S, Ji H. Genetic-based biomarkers and next-generation sequencing: the future of personalized care in colorectal cancer. Per Med 2011; 8:331-345. [PMID: 23662107 PMCID: PMC3646399 DOI: 10.2217/pme.11.16] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The past 5 years have witnessed extraordinary advances in the field of DNA sequencing technology. What once took years to accomplish with Sanger sequencing can now be accomplished in a matter of days with next-generation sequencing (NGS) technology. This has allowed researchers to sequence individual genomes and match combinations of mutations with specific diseases. As cancer is inherently a disease of the genome, it is not surprising to see NGS technology already being applied to cancer research with promises of greater understanding of carcinogenesis. While the task of deciphering the cancer genomic code remains ongoing, we are already beginning to see the application of genetic-based testing in the area of colorectal cancer. In this article we will provide an overview of current colorectal cancer genetic-based biomarkers, namely mutations and other genetic alterations in cancer genome DNA, discuss recent advances in NGS technology and speculate on future directions for the application of NGS technology to colorectal cancer diagnosis and treatment.
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Affiliation(s)
- Redecca Y Kim
- Author for correspondence: Department of General Surgery, Stanford University, CCSR 1115, 269 Campus Drive, Stanford, CA 94305, USA Tel.:+1 650 723 4000
| | - Hua Xu
- Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - Samuel Myllykangas
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, USA
| | - Hanlee Ji
- Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, USA
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Murakami H, Mizuno T, Taniguchi T, Fujii M, Ishiguro F, Fukui T, Akatsuka S, Horio Y, Hida T, Kondo Y, Toyokuni S, Osada H, Sekido Y. LATS2 is a tumor suppressor gene of malignant mesothelioma. Cancer Res 2011; 71:873-83. [PMID: 21245096 DOI: 10.1158/0008-5472.can-10-2164] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Malignant mesothelioma (MM) is an aggressive neoplasm associated with asbestos exposure. We carried out genome-wide array-based comparative genomic hybridization analysis with 14 MM cell lines. Three cell lines showed overlapping homozygous deletion at chromosome 13q12, which harbored the LATS2 (large tumor suppressor homolog 2) gene. With 6 other MM cell lines and 25 MM tumors, we found 10 inactivating homozygous deletions or mutations of LATS2 among 45 MMs. LATS2 encodes a serine/threonine kinase, a component of the Hippo tumor-suppressive signaling pathway, and we transduced LATS2 in MM cells with its mutation. Transduction of LATS2 inactivated oncoprotein YAP, a transcriptional coactivator, via phosphorylation, and inhibited MM cell growth. We also analyzed LATS2 immunohistochemically and found that 13 of 45 MM tumors had low expression of LATS2. Because NF2 is genetically mutated in 40% to 50% of MM, our data indicate that Hippo pathway dysregulation is frequent in MM cells with inactivation of LATS2 or an upstream regulator of this pathway, Merlin, which is encoded by NF2. Thus, our results suggest that the inactivation of LATS2 is one of the key mechanisms for constitutive activation of YAP, which induces deregulation of MM cell proliferation.
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Affiliation(s)
- Hideki Murakami
- Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Japan
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