1
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Watanabe T, Soeda S, Okoshi C, Fukuda T, Yasuda S, Fujimori K. Landscape of somatic mutated genes and inherited susceptibility genes in gynecological cancer. J Obstet Gynaecol Res 2023; 49:2629-2643. [PMID: 37632362 DOI: 10.1111/jog.15766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/26/2023] [Indexed: 08/28/2023]
Abstract
Traditionally, gynecological cancers have been classified based on histology. Since remarkable advancements in next-generation sequencing technology have enabled the exploration of somatic mutations in various cancer types, comprehensive sequencing efforts have revealed the genomic landscapes of some common forms of human cancer. The genomic features of various gynecological malignancies have been reported by several studies of large-scale genomic cohorts, including The Cancer Genome Atlas. Although recent comprehensive genomic profiling tests, which can detect hundreds of genetic mutations at a time from cancer tissues or blood samples, have been increasingly used as diagnostic clinical biomarkers and in therapeutic management decisions, germline pathogenic variants associated with hereditary cancers can also be detected using this test. Gynecological cancers are closely related to genetic factors, with approximately 5% of endometrial cancer cases and 20% of ovarian cancer cases being caused by germline pathogenic variants. Hereditary breast and ovarian cancer syndrome and Lynch syndrome are the two major cancer susceptibility syndromes among gynecological cancers. In addition, several other hereditary syndromes have been reported to be associated with gynecological cancers. In this review, we highlight the genes for somatic mutation and germline pathogenic variants commonly seen in gynecological cancers. We first describe the relationship between clinicopathological attributes and somatic mutated genes. Subsequently, we discuss the characteristics and clinical management of inherited cancer syndromes resulting from pathogenic germline variants in gynecological malignancies.
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Affiliation(s)
- Takafumi Watanabe
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Shu Soeda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Chihiro Okoshi
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Toma Fukuda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Shun Yasuda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Keiya Fujimori
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
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Skorda A, Bay ML, Hautaniemi S, Lahtinen A, Kallunki T. Kinase Inhibitors in the Treatment of Ovarian Cancer: Current State and Future Promises. Cancers (Basel) 2022; 14:6257. [PMID: 36551745 PMCID: PMC9777107 DOI: 10.3390/cancers14246257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Ovarian cancer is the deadliest gynecological cancer, the high-grade serous ovarian carcinoma (HGSC) being its most common and most aggressive form. Despite the latest therapeutical advancements following the introduction of vascular endothelial growth factor receptor (VEGFR) targeting angiogenesis inhibitors and poly-ADP-ribose-polymerase (PARP) inhibitors to supplement the standard platinum- and taxane-based chemotherapy, the expected overall survival of HGSC patients has not improved significantly from the five-year rate of 42%. This calls for the development and testing of more efficient treatment options. Many oncogenic kinase-signaling pathways are dysregulated in HGSC. Since small-molecule kinase inhibitors have revolutionized the treatment of many solid cancers due to the generality of the increased activation of protein kinases in carcinomas, it is reasonable to evaluate their potential against HGSC. Here, we present the latest concluded and on-going clinical trials on kinase inhibitors in HGSC, as well as the recent work concerning ovarian cancer patient organoids and xenograft models. We discuss the potential of kinase inhibitors as personalized treatments, which would require comprehensive assessment of the biological mechanisms underlying tumor spread and chemoresistance in individual patients, and their connection to tumor genome and transcriptome to establish identifiable subgroups of patients who are most likely to benefit from a given therapy.
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Affiliation(s)
- Aikaterini Skorda
- Cancer Invasion and Resistance Group, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Marie Lund Bay
- Cancer Invasion and Resistance Group, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Alexandra Lahtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Tuula Kallunki
- Cancer Invasion and Resistance Group, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Abstract
The RAS family of proteins is among the most frequently mutated genes in human malignancies. In ovarian cancer (OC), the most lethal gynecological malignancy, RAS, especially KRAS mutational status at codons 12, 13, and 61, ranges from 6-65% spanning different histo-types. Normally RAS regulates several signaling pathways involved in a myriad of cellular signaling cascades mediating numerous cellular processes like cell proliferation, differentiation, invasion, and death. Aberrant activation of RAS leads to uncontrolled induction of several downstream signaling pathways such as RAF-1/MAPK (mitogen-activated protein kinase), PI3K phosphoinositide-3 kinase (PI3K)/AKT, RalGEFs, Rac/Rho, BRAF (v-Raf murine sarcoma viral oncogene homolog B), MEK1 (mitogen-activated protein kinase kinase 1), ERK (extracellular signal-regulated kinase), PKB (protein kinase B) and PKC (protein kinase C) involved in cell proliferation as well as maintenance pathways thereby driving tumorigenesis and cancer cell propagation. KRAS mutation is also known to be a biomarker for poor outcome and chemoresistance in OC. As a malignancy with several histotypes showing varying histopathological characteristics, we focus on reviewing recent literature showcasing the involvement of oncogenic RAS in mediating carcinogenesis and chemoresistance in OC and its subtypes.
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Affiliation(s)
- Lubna Therachiyil
- Hamad Medical Corporation, Doha, Qatar, 3050, Qatar
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, 2713, Qatar
| | - Anjana Anand
- Hamad Medical Corporation, Doha, Qatar, 3050, Qatar
| | | | | | - Hesham M. Korashy
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, 2713, Qatar
| | - Shahab Uddin
- Hamad Medical Corporation, Doha, Qatar, 3050, Qatar
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Rinne N, Christie EL, Ardasheva A, Kwok CH, Demchenko N, Low C, Tralau-Stewart C, Fotopoulou C, Cunnea P. Targeting the PI3K/AKT/mTOR pathway in epithelial ovarian cancer, therapeutic treatment options for platinum-resistant ovarian cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 4:573-595. [PMID: 35582310 PMCID: PMC9019160 DOI: 10.20517/cdr.2021.05] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/05/2021] [Accepted: 03/16/2021] [Indexed: 12/24/2022]
Abstract
The survival rates for women with ovarian cancer have shown scant improvement in recent years, with a 5-year survival rate of less than 40% for women diagnosed with advanced ovarian cancer. High-grade serous ovarian cancer (HGSOC) is the most lethal subtype where the majority of women develop recurrent disease and chemotherapy resistance, despite over 70%-80% of patients initially responding to platinum-based chemotherapy. The phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway regulates many vital processes such as cell growth, survival and metabolism. However, this pathway is frequently dysregulated in cancers including different subtypes of ovarian cancer, through amplification or somatic mutations of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), amplification of AKT isoforms, or deletion or inactivation of PTEN. Further evidence indicates a role for the PI3K/AKT/mTOR pathway in the development of chemotherapy resistance in ovarian cancer. Thus, targeting key nodes of the PI3K/AKT/mTOR pathway is a potential therapeutic prospect. In this review, we outline dysregulation of PI3K signaling in ovarian cancer, with a particular emphasis on HGSOC and platinum-resistant disease. We review pre-clinical evidence for inhibitors of the main components of the PI3K pathway and highlight past, current and upcoming trials in ovarian cancers for different inhibitors of the pathway. Whilst no inhibitors of the PI3K/AKT/mTOR pathway have thus far advanced to the clinic for the treatment of ovarian cancer, several promising compounds which have the potential to restore platinum sensitivity and improve clinical outcomes for patients are under evaluation and in various phases of clinical trials.
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Affiliation(s)
- Natasha Rinne
- Department of Surgery & Cancer, Imperial College London, Hammersmith campus, London W12 0NN, UK
| | | | - Anastasia Ardasheva
- Department of Surgery & Cancer, Imperial College London, Hammersmith campus, London W12 0NN, UK
| | - Chun Hei Kwok
- Department of Surgery & Cancer, Imperial College London, Hammersmith campus, London W12 0NN, UK
| | - Nikita Demchenko
- Department of Surgery & Cancer, Imperial College London, Hammersmith campus, London W12 0NN, UK
| | - Caroline Low
- Department of Metabolism Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Catherine Tralau-Stewart
- Takeda Academic Innovation, Center for External Innovation, Takeda California, San Diego, CA 92121, USA
| | - Christina Fotopoulou
- Department of Surgery & Cancer, Imperial College London, Hammersmith campus, London W12 0NN, UK
| | - Paula Cunnea
- Department of Surgery & Cancer, Imperial College London, Hammersmith campus, London W12 0NN, UK
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5
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van der Ploeg P, Uittenboogaard A, Bosch SL, van Diest PJ, Wesseling-Rozendaal YJ, van de Stolpe A, Lambrechts S, Bekkers RL, Piek JM. Signal transduction pathway activity in high-grade serous carcinoma, its precursors and Fallopian tube epithelium. Gynecol Oncol 2022; 165:114-120. [DOI: 10.1016/j.ygyno.2022.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 01/23/2023]
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Mittempergher L, Piskorz AM, Bosma AJ, Michaut M, Wisman GBA, Kluin RJC, Nieuwland M, Brugman W, van der Ven KJW, Marass F, Morris J, Rosenfeld N, Jimenez-Linan M, de Jong S, van der Zee AGJ, Brenton JD, Bernards R. Kinome capture sequencing of high-grade serous ovarian carcinoma reveals novel mutations in the JAK3 gene. PLoS One 2020; 15:e0235766. [PMID: 32639993 PMCID: PMC7343160 DOI: 10.1371/journal.pone.0235766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) remains the deadliest form of epithelial ovarian cancer and despite major efforts little improvement in overall survival has been achieved. Identification of recurring "driver" genetic lesions has the potential to enable design of novel therapies for cancer. Here, we report on a study to find such new therapeutic targets for HGSOC using exome-capture sequencing approach targeting all kinase genes in 127 patient samples. Consistent with previous reports, the most frequently mutated gene was TP53 (97% mutation frequency) followed by BRCA1 (10% mutation frequency). The average mutation frequency of the kinase genes mutated from our panel was 1.5%. Intriguingly, after BRCA1, JAK3 was the most frequently mutated gene (4% mutation frequency). We tested the transforming properties of JAK3 mutants using the Ba/F3 cell-based in vitro functional assay and identified a novel gain-of-function mutation in the kinase domain of JAK3 (p.T1022I). Importantly, p.T1022I JAK3 mutants displayed higher sensitivity to the JAK3-selective inhibitor Tofacitinib compared to controls. For independent validation, we re-sequenced the entire JAK3 coding sequence using tagged amplicon sequencing (TAm-Seq) in 463 HGSOCs resulting in an overall somatic mutation frequency of 1%. TAm-Seq screening of CDK12 in the same population revealed a 7% mutation frequency. Our data confirms that the frequency of mutations in kinase genes in HGSOC is low and provides accurate estimates for the frequency of JAK3 and CDK12 mutations in a large well characterized cohort. Although p.T1022I JAK3 mutations are rare, our functional validation shows that if detected they should be considered as potentially actionable for therapy. The observation of CDK12 mutations in 7% of HGSOC cases provides a strong rationale for routine somatic testing, although more functional and clinical characterization is required to understand which nonsynonymous mutations alterations are associated with homologous recombination deficiency.
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Affiliation(s)
- Lorenza Mittempergher
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna M. Piskorz
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Astrid J. Bosma
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Magali Michaut
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - G. Bea A. Wisman
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roelof J. C. Kluin
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wim Brugman
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Francesco Marass
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
- Department of Biosystems Science and Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - James Morris
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Mercedes Jimenez-Linan
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Steven de Jong
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ate G. J. van der Zee
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, Groningen, The Netherlands
| | - James D. Brenton
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Jagelkova M, Zelinova K, Laucekova Z, Bobrovska M, Dankova Z, Grendar M, Dokus K. Comparison of Somatic Mutation Profiles Between Formalin-Fixed Paraffin Embedded Tissues and Plasma Cell-Free DNA from Ovarian Cancer Patients Before and After Surgery. Biores Open Access 2020; 9:73-79. [PMID: 32219013 PMCID: PMC7097678 DOI: 10.1089/biores.2019.0031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ovarian carcinogenesis can be induced by a large number of somatic gene mutations. Circulating tumor DNA (ctDNA) released into peripheral blood can provide insights into the genomic landscape of cancer cells and monitor their dynamics. Our aim was to detect and compare the genetic profiles in tumor tissue and plasma before and after tumor resection in ovarian cancer patients. All three samples were collected from each patient. In this study, we used a commercial cancer panel to identify somatic mutations in 26 genes in seven selected patients through next-generation sequencing on the Illumina platform. Overall, 16 variants with pathogenic effect were identified in the TP53, PIK3CA, PTEN, APC, NRAS, KRAS, GNAS, and MET genes involved in important signaling pathways. The genetic alterations found in the presurgical plasma in six of seven ovarian cancer patients were no longer present in the plasma after tumor surgical removal. Identical variants in formalin-fixed paraffin embedded (FFPE) tissues and preoperative plasma specimens were observed in only two cases. These findings suggest that the detected presurgical pathogenic variants absent in postsurgery plasma are associated with the primary ovarian tumor. Finally, the low-identified concordance between FFPE and plasma can be due to various factors, but most likely to high tumor heterogeneity and low ctDNA level.
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Affiliation(s)
- Marianna Jagelkova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Martin, Slovakia
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
| | - Katarina Zelinova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Martin, Slovakia
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
| | - Zuzana Laucekova
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
| | - Martina Bobrovska
- Department of Pathological Anatomy, MUH and JFM CU, Martin, Slovakia
| | - Zuzana Dankova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Martin, Slovakia
| | - Marian Grendar
- Department of Bioinformatics, Biomedical Center Martin JFM CU, Martin, Slovakia
| | - Karol Dokus
- Clinic of Gynecology and Obstetrics, Martin University Hospital (MUH) and JFM CU, Martin, Slovakia
- 2nd Department of Gynecology and Obstetrics, Faculty Hospital with Policlinic of F. D. Roosevelt, Slovak Medical University, Banska Bystrica, Slovakia
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8
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Garziera M, Roncato R, Montico M, De Mattia E, Gagno S, Poletto E, Scalone S, Canzonieri V, Giorda G, Sorio R, Cecchin E, Toffoli G. New Challenges in Tumor Mutation Heterogeneity in Advanced Ovarian Cancer by a Targeted Next-Generation Sequencing (NGS) Approach. Cells 2019; 8:cells8060584. [PMID: 31197119 PMCID: PMC6627128 DOI: 10.3390/cells8060584] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) technology has advanced knowledge of the genomic landscape of ovarian cancer, leading to an innovative molecular classification of the disease. However, patient survival and response to platinum-based treatments are still not predictable based on the tumor genetic profile. This retrospective study characterized the repertoire of somatic mutations in advanced ovarian cancer to identify tumor genetic markers predictive of platinum chemo-resistance and prognosis. Using targeted NGS, 79 primary advanced (III-IV stage, tumor grade G2-3) ovarian cancer tumors, including 64 high-grade serous ovarian cancers (HGSOCs), were screened with a 26 cancer-genes panel. Patients, enrolled between 1995 and 2011, underwent primary debulking surgery (PDS) with optimal residual disease (RD < 1 cm) and platinum-based chemotherapy as first-line treatment. We found a heterogeneous mutational landscape in some uncommon ovarian histotypes and in HGSOC tumor samples with relevance in predicting platinum sensitivity. In particular, we identified a poor prognostic signature in patients with HGSOC harboring concurrent mutations in two driver actionable genes of the panel. The tumor heterogeneity described, sheds light on the translational potential of targeted NGS approach for the identification of subgroups of patients with distinct therapeutic vulnerabilities, that are modulated by the specific mutational profile expressed by the ovarian tumor.
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Affiliation(s)
- Marica Garziera
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Rossana Roncato
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Marcella Montico
- Scientific Directorate, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Sara Gagno
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Elena Poletto
- Medical Oncology, "Santa Maria della Misericordia" University Hospital, ASUIUD, 33100 Udine, Italy.
| | - Simona Scalone
- Medical Oncology Unit C, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Giorgio Giorda
- Gynecological Oncology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Roberto Sorio
- Medical Oncology Unit C, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
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Ediriweera MK, Tennekoon KH, Samarakoon SR. Role of the PI3K/AKT/mTOR signaling pathway in ovarian cancer: Biological and therapeutic significance. Semin Cancer Biol 2019; 59:147-160. [PMID: 31128298 DOI: 10.1016/j.semcancer.2019.05.012] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/28/2019] [Accepted: 05/21/2019] [Indexed: 01/09/2023]
Abstract
Ovarian cancer (OC) is a lethal gynecological cancer. The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway plays an important role in the regulation of cell survival, growth, and proliferation. Irregularities in the major components of the PI3K/AKT/mTOR signaling pathway are common in human cancers. Despite the availability of strong pre-clinical and clinical data of PI3K/AKT/mTOR pathway inhibitors in OC, there is no FDA approved inhibitor available for the treatment of OC. Here, we outline the importance of PI3K/AKT/mTOR signaling pathway in OC tumorigenesis, proliferation and progression, and pre-clinical and clinical experience with several PI3K/AKT/mTOR pathway inhibitors in OC.
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Affiliation(s)
- Meran Keshawa Ediriweera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka
| | - Sameera Ranganath Samarakoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka
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10
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Xing D, Suryo Rahmanto Y, Zeppernick F, Hannibal CG, Kjaer SK, Vang R, Shih IM, Wang TL. Mutation of NRAS is a rare genetic event in ovarian low-grade serous carcinoma. Hum Pathol 2017; 68:87-91. [PMID: 28873354 DOI: 10.1016/j.humpath.2017.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 12/31/2022]
Abstract
Activating mutations involving the members of the RAS signaling pathway, including KRAS, NRAS, and BRAF, have been reported in ovarian low-grade serous carcinoma and its precursor lesion, serous borderline tumor (SBT). Whether additional genetic alterations in the RAS oncogene family accumulate during the progression of SBT to invasive low-grade serous carcinoma (LGSC) remains largely unknown. Although mutations of KRAS and BRAF occur at a very early stage of progression, even preceding the development of SBT, additional driving events, such as NRAS mutations, have been postulated to facilitate progression. In this study, we analyzed NRAS exon 3 mutational status in 98 cases that were diagnosed with SBT/atypical proliferative serous tumor, noninvasive LGSC, or invasive LGSC. Of the latter, NRAS Q61R (CAA to CGA) mutations were detected in only 2 of 56 (3.6%) cases. The same mutation was not detected in any of the SBTs (atypical proliferative serous tumors) or noninvasive LGSCs. Mutational analysis for hotspots in KRAS and BRAF demonstrated a wild-type pattern of KRAS and BRAF in one of the NRAS-mutated cases. Interestingly, another LGSC case with NRAS mutation harbored a concurrent BRAF V600L mutation. These findings indicate that, although recurrent NRAS mutations are present, their low prevalence indicates that NRAS plays a limited role in the development of LGSC. Further studies to identify other oncogenic events that drive LGSC progression are warranted.
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Affiliation(s)
- Deyin Xing
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Yohan Suryo Rahmanto
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Felix Zeppernick
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Charlotte G Hannibal
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Susanne K Kjaer
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark; Gynecologic Clinic, Juliane Marie Centre, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Russell Vang
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231; Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231
| | - Ie-Ming Shih
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231; Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, MD 21231.
| | - Tian-Li Wang
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231; Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231; Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, MD 21231.
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11
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Kakarmath S, Heller HT, Alexander CA, Cibas ES, Krane JF, Barletta JA, Lindeman NI, Frates MC, Benson CB, Gawande AA, Cho NL, Nehs M, Moore FD, Marqusee E, Kim MI, Larsen PR, Kwong N, Angell TE, Alexander EK. Clinical, Sonographic, and Pathological Characteristics of RAS-Positive Versus BRAF-Positive Thyroid Carcinoma. J Clin Endocrinol Metab 2016; 101:4938-4944. [PMID: 27689252 PMCID: PMC5155682 DOI: 10.1210/jc.2016-2620] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Mutations in the BRAF and RAS oncogenes are responsible for most well-differentiated thyroid cancer. Yet, our clinical understanding of how BRAF-positive and RAS-positive thyroid cancers differ is incomplete. OBJECTIVE We correlated clinical, radiographic, and pathological findings from patients with thyroid cancer harboring a BRAF or RAS mutation. DESIGN Prospective cohort study. SETTING Academic, tertiary care hospital. PATIENTS A total of 101 consecutive patients with well-differentiated thyroid cancer. MAIN OUTCOME MEASURE We compared the clinical, sonographic, and pathological characteristics of patients with BRAF-positive cancer to those with RAS-positive cancer. RESULTS Of 101 patients harboring these mutations, 71 were BRAF-positive, whereas 30 were RAS-positive. Upon sonographic evaluation, RAS-positive nodules were significantly larger (P = .04), although BRAF-positive nodules were more likely to harbor concerning sonographic characteristics (hypoechogenicity [P < .001]; irregular margins [P = .04]). Cytologically, 70% of BRAF-positive nodules were classified positive for PTC, whereas 87% of RAS-positive nodules were indeterminate (P < .001). Histologically, 96% of RAS-positive PTC malignancies were follicular variants of PTC, whereas 70% of BRAF-positive malignancies were classical variants of PTC. BRAF-positive malignancies were more likely to demonstrate extrathyroidal extension (P = .003), lymphovascular invasion (P = .02), and lymph node metastasis (P < .001). CONCLUSIONS BRAF-positive malignant nodules most often demonstrate worrisome sonographic features and are frequently associated with positive or suspicious Bethesda cytology. In contrast, RAS-positive malignancy most often demonstrates indolent sonographic features and more commonly associates with lower risk, "indeterminate" cytology. Because BRAF and RAS mutations are the most common molecular perturbations associated with well-differentiated thyroid cancer, these findings may assist with improved preoperative risk assessment by suggesting the likely molecular profile of a thyroid cancer, even when postsurgical molecular analysis is unavailable.
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Affiliation(s)
- Sujay Kakarmath
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Howard T Heller
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Caroline A Alexander
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Edmund S Cibas
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Jeffrey F Krane
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Justine A Barletta
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Neal I Lindeman
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Mary C Frates
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Carol B Benson
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Atul A Gawande
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Nancy L Cho
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Matthew Nehs
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Francis D Moore
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Ellen Marqusee
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Mathew I Kim
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - P Reed Larsen
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Norra Kwong
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Trevor E Angell
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Erik K Alexander
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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Metastasis-associated MCL1 and P16 copy number alterations dictate resistance to vemurafenib in a BRAFV600E patient-derived papillary thyroid carcinoma preclinical model. Oncotarget 2016; 6:42445-67. [PMID: 26636651 PMCID: PMC4767444 DOI: 10.18632/oncotarget.6442] [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: 09/06/2015] [Accepted: 10/22/2015] [Indexed: 01/08/2023] Open
Abstract
BRAFV600E mutation exerts an essential oncogenic function in many tumors, including papillary thyroid carcinoma (PTC). Although BRAFV600E inhibitors are available, lack of response has been frequently observed. To study the mechanism underlying intrinsic resistance to the mutant BRAFV600E selective inhibitor vemurafenib, we established short-term primary cell cultures of human metastatic/recurrent BRAFV600E-PTC, intrathyroidal BRAFV600E-PTC, and normal thyroid (NT). We also generated an early intervention model of human BRAFV600E-PTC orthotopic mouse. We find that metastatic BRAFV600E-PTC cells elicit paracrine-signaling which trigger migration of pericytes, blood endothelial cells and lymphatic endothelial cells as compared to BRAFWT-PTC cells, and show a higher rate of invasion. We further show that vemurafenib therapy significantly suppresses these aberrant functions in non-metastatic BRAFV600E-PTC cells but lesser in metastatic BRAFV600E-PTC cells as compared to vehicle treatment. These results concur with similar folds of down-regulation of tumor microenvironment–associated pro-metastatic molecules, with no effects in BRAFWT-PTC and NT cells. Our early intervention preclinical trial shows that vemurafenib delays tumor growth in the orthotopic BRAFWT/V600E-PTC mice. Importantly, we identify high copy number gain of MCL1 (chromosome 1q) and loss of CDKN2A (P16, chromosome 9p) in metastatic BRAFV600E-PTC cells which are associated with resistance to vemurafenib treatment. Critically, we demonstrate that combined vemurafenib therapy with BCL2/MCL1 inhibitor increases metastatic BRAFV600E-PTC cell death and ameliorates response to vemurafenib treatment as compared to single agent treatment. In conclusion, short-term PTC and NT cultures offer a predictive model for evaluating therapeutic response in patients with PTC. Our PTC pre-clinical model suggests that combined targeted therapy might be an important therapeutic strategy for metastatic and refractory BRAFV600E-positive PTC.
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13
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Fleitas T, Ibarrola-Villava M, Ribas G, Cervantes A. MassARRAY determination of somatic oncogenic mutations in solid tumors: Moving forward to personalized medicine. Cancer Treat Rev 2016; 49:57-64. [DOI: 10.1016/j.ctrv.2016.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022]
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14
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Pitt SC, Hernandez RA, Nehs MA, Gawande AA, Moore FD, Ruan DT, Cho NL. Identification of Novel Oncogenic Mutations in Thyroid Cancer. J Am Coll Surg 2016; 222:1036-1043.e2. [PMID: 27010584 DOI: 10.1016/j.jamcollsurg.2015.12.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/29/2015] [Accepted: 12/21/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Thyroid cancer patients frequently have favorable outcomes. However, a small subset develops aggressive disease refractory to traditional treatments. Therefore, we sought to characterize oncogenic mutations in thyroid cancers to identify novel therapeutic targets that may benefit patients with advanced, refractory disease. STUDY DESIGN Data on 239 thyroid cancer specimens collected between January 2009 and September 2014 were obtained from the Dana Farber/Brigham and Women's Cancer Center. The tumors were analyzed with the OncoMap-4 or OncoPanel high-throughput genotyping platforms that survey up to 275 cancer genes and 91 introns for DNA rearrangement. RESULTS Of the 239 thyroid cancer specimens, 128 (54%) had oncogenic mutations detected. These 128 tumors had 351 different mutations detected in 129 oncogenes or tumor suppressors. Examination of the 128 specimens demonstrated that 55% (n = 70) had 1 oncogenic mutation, and 45% (n = 48) had more than 1 mutation. The 351 oncogenic mutations were in papillary (85%), follicular (4%), medullary (7%), and anaplastic (4%) thyroid cancers. Analysis revealed that 2.3% (n = 3 genes) of the somatic gene mutations were novel. These included AR (n = 1), MPL (n = 2), and EXT2 (n = 1), which were present in 4 different papillary thyroid cancer specimens. New mutations were found in an additional 13 genes known to have altered protein expression in thyroid cancer: BLM, CBL, CIITA, EP300, GSTM5, LMO2, PRAME, SBDS, SF1, TET2, TNFAIP3, XPO1, and ZRSR2. CONCLUSIONS This analysis revealed that several previously unreported oncogenic gene mutations exist in thyroid cancers and may be targets for the development of future therapies. Further investigation into the role of these genes is warranted.
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Affiliation(s)
- Susan C Pitt
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI.
| | - Roland A Hernandez
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew A Nehs
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Atul A Gawande
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Francis D Moore
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Daniel T Ruan
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Nancy L Cho
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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15
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Bellmunt J, Werner L, Leow JJ, Mullane SA, Fay AP, Riester M, Van Hummelen P, Taplin ME, Choueiri TK, Van Allen E, Rosenberg J. Somatic Copy Number Abnormalities and Mutations in PI3K/AKT/mTOR Pathway Have Prognostic Significance for Overall Survival in Platinum Treated Locally Advanced or Metastatic Urothelial Tumors. PLoS One 2015; 10:e0124711. [PMID: 26039708 PMCID: PMC4454515 DOI: 10.1371/journal.pone.0124711] [Citation(s) in RCA: 16] [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: 10/15/2014] [Accepted: 03/05/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND An integrative analysis was conducted to identify genomic alterations at a pathway level that could predict overall survival (OS) in patients with advanced urothelial carcinoma (UC) treated with platinum-based chemotherapy. PATIENTS AND METHODS DNA and RNA were extracted from 103 formalin-fixed paraffin embedded (FFPE) invasive high-grade UC samples and were screened for mutations, copy number variation (CNV) and gene expression analysis. Clinical data were available from 85 cases. Mutations were analyzed by mass-spectrometry based on genotyping platform (Oncomap 3) and genomic imbalances were detected by comparative genomic hybridization (CGH) analysis. Regions with threshold of log2 ratio ≥0.4, or ≤0.6 were defined as either having copy number gain or loss and significantly recurrent CNV across the set of samples were determined using a GISTIC analysis. Expression analysis on selected relevant UC genes was conducted using Nanostring. To define the co-occurrence pattern of mutations and CNV, we grouped genomic events into 5 core signal transduction pathways: 1) TP53 pathway, 2) RTK/RAS/RAF pathway, 3) PI3K/AKT/mTOR pathway, 4) WNT/CTNNB1, 5) RB1 pathway. Cox regression was used to assess pathways abnormalities with survival outcomes. RESULTS 35 samples (41%) harbored mutations on at least one gene: TP53 (16%), PIK3CA (9%), FGFR3 (2%), HRAS/KRAS (5%), and CTNNB1 (1%). 66% of patients had some sort of CNV. PIK3CA/AKT/mTOR pathway alteration (mutations+CNV) had the greatest impact on OS (p=0.055). At a gene level, overexpression of CTNNB1 (p=0.0008) and PIK3CA (p=0.02) were associated with shorter OS. Mutational status on PIK3CA was not associated with survival. Among other individually found genomic alterations, TP53 mutations (p=0.07), mTOR gain (p=0.07) and PTEN overexpression (p=0.08) have a marginally significant negative impact on OS. CONCLUSIONS Our study suggests that targeted therapies focusing on the PIK3CA/AKT/mTOR pathway genomic alterations can generate the greatest impact in the overall patient population of high-grade advanced UC.
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Affiliation(s)
- Joaquim Bellmunt
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Lillian Werner
- Biostatistics and Computational Biology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Jeffrey J. Leow
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Stephanie A. Mullane
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - André P. Fay
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Markus Riester
- Biostatistics and Computational Biology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Paul Van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Mary-Ellen Taplin
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Toni K. Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Eliezer Van Allen
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Jonathan Rosenberg
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
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Loss of LKB1 and p53 synergizes to alter fallopian tube epithelial phenotype and high-grade serous tumorigenesis. Oncogene 2015; 35:59-68. [PMID: 25798842 DOI: 10.1038/onc.2015.62] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 01/09/2015] [Accepted: 01/20/2015] [Indexed: 02/06/2023]
Abstract
Liver kinase B1 (LKB1) is a tumor suppressor ubiquitously expressed serine/threonine protein kinase involved in energy metabolism and cellular polarity. In microarray experiments that compared normal tubal epithelium with high-grade serous carcinoma (HGSC), we observed a decrease in LKB1 mRNA expression in HGSC. In this study, we demonstrate that loss of cytoplasmic and nuclear LKB1 protein expression is frequently observed in tubal cancer precursor lesions as well as in both sporadic and hereditary HGSCs compared with other ovarian cancer histotypes. Bi-allelic genomic loss of LKB1 in HGSC did not account for the majority of cases with a decrease in protein expression. In vitro, shLKB1-fallopian tube epithelial (FTE) cells underwent premature cellular arrest and in ex vivo FTE culture, LKB1 loss and p53 mutant synergized to disrupt apical to basal polarity and decrease the number of ciliated cells. Overexpression of cyclin E1 allowed for bypass of LKB1-induced cellular arrest, and increased both proliferation and anchorage-independent growth of transformed FTE cells. These data suggest that LKB1 loss early in ovarian serous tumorigenesis has an integral role in tumor promotion by disrupting apical to basal polarity in the presence of mutated p53 in fallopian tube cells.
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Emmanuel C, Chiew YE, George J, Etemadmoghadam D, Anglesio MS, Sharma R, Russell P, Kennedy C, Fereday S, Hung J, Galletta L, Hogg R, Wain GV, Brand A, Balleine R, MacConaill L, Palescandolo E, Hunter SM, Campbell I, Dobrovic A, Wong SQ, Do H, Clarke CL, Harnett PR, Bowtell DDL, deFazio A. Genomic classification of serous ovarian cancer with adjacent borderline differentiates RAS pathway and TP53-mutant tumors and identifies NRAS as an oncogenic driver. Clin Cancer Res 2014; 20:6618-30. [PMID: 25316818 DOI: 10.1158/1078-0432.ccr-14-1292] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Low-grade serous ovarian carcinomas (LGSC) are Ras pathway-mutated, TP53 wild-type, and frequently associated with borderline tumors. Patients with LGSCs respond poorly to platinum-based chemotherapy and may benefit from pathway-targeted agents. High-grade serous carcinomas (HGSC) are TP53-mutated and are thought to be rarely associated with borderline tumors. We sought to determine whether borderline histology associated with grade 2 or 3 carcinoma was an indicator of Ras mutation, and we explored the molecular relationship between coexisting invasive and borderline histologies. EXPERIMENTAL DESIGN We reviewed >1,200 patients and identified 102 serous carcinomas with adjacent borderline regions for analyses, including candidate mutation screening, copy number, and gene expression profiling. RESULTS We found a similar frequency of low, moderate, and high-grade carcinomas with coexisting borderline histology. BRAF/KRAS alterations were common in LGSC; however, we also found recurrent NRAS mutations. Whereas borderline tumors harbored BRAF/KRAS mutations, NRAS mutations were restricted to carcinomas, representing the first example of a Ras oncogene with an obligatory association with invasive serous cancer. Coexisting borderline and invasive components showed nearly identical genomic profiles. Grade 2 cases with coexisting borderline included tumors with molecular features of LGSC, whereas others were typical of HGSC. However, all grade 3 carcinomas with coexisting borderline histology were molecularly indistinguishable from typical HGSC. CONCLUSION Our findings suggest that NRAS is an oncogenic driver in serous ovarian tumors. We demonstrate that borderline histology is an unreliable predictor of Ras pathway aberration and underscore an important role for molecular classification in identifying patients that may benefit from targeted agents.
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Affiliation(s)
- Catherine Emmanuel
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Joshy George
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Dariush Etemadmoghadam
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael S Anglesio
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Raghwa Sharma
- University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Pathology West ICPMR Westmead, Sydney, New South Wales, Australia. University of Western Sydney at Westmead Hospital, Westmead, New South Wales, Australia
| | - Peter Russell
- Department of Obstetrics, Gynaecology and Neonatology, University of Sydney, Camperdown New South Wales, Australia. Douglass Hanly Moir Pathology, Macquarie Park, New South Wales, Australia
| | - Catherine Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Sian Fereday
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Jillian Hung
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Laura Galletta
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Russell Hogg
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Gerard V Wain
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Alison Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Rosemary Balleine
- University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia. Pathology West ICPMR Westmead, Sydney, New South Wales, Australia
| | | | | | - Sally M Hunter
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Ian Campbell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alexander Dobrovic
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Stephen Q Wong
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Hongdo Do
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Christine L Clarke
- University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Paul R Harnett
- Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - David D L Bowtell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia. Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Anna deFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia.
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18
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Sadow PM, Priolo C, Nanni S, Karreth FA, Duquette M, Martinelli R, Husain A, Clohessy J, Kutzner H, Mentzel T, Carman CV, Farsetti A, Henske EP, Palescandolo E, Macconaill LE, Chung S, Fadda G, Lombardi CP, De Angelis AM, Durante O, Parker JA, Pontecorvi A, Dvorak HF, Fletcher C, Pandolfi PP, Lawler J, Nucera C. Role of BRAFV600E in the first preclinical model of multifocal infiltrating myopericytoma development and microenvironment. J Natl Cancer Inst 2014; 106:dju182. [PMID: 25063326 DOI: 10.1093/jnci/dju182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Myopericytoma (MPC) is a rare tumor with perivascular proliferation of pluripotent stem-cell-like pericytes. Although indolent, MPC may be locally aggressive with recurrent disease. The pathogenesis and diagnostic biomarkers of MPC are poorly understood. We discovered that 15% of benign MPCs (thyroid, skin; 3 of 20 samples) harbored BRAF(WT/V600E); 33.3% (1 of 3 samples) of BRAF(WT/V600E)-MPCs were multifocal/infiltrative/recurrent. Patient-MPC and primary MPC cells harbored BRAF(WT/V600E), were clonal and expressed pericytic-differentiation biomarkers crucial for its microenvironment. BRAF(WT/V600E)-positive thyroid MPC primary cells triggered in vitro (8.8-fold increase) and in vivo (3.6-fold increase) angiogenesis. Anti-BRAF(V600E) therapy with vemurafenib disrupted angiogenic and metabolic properties (~3-fold decrease) with down-regulation (~2.2-fold decrease) of some extracellular-matrix (ECM) factors and ECM-associated long non-coding RNA (LincRNA) expression, with no effects in BRAF(WT)-pericytes. Vemurafenib also inhibited (~3-fold decrease) cell viability in vitro and in BRAF(WT/V600E)-positive thyroid MPC patient-derived xenograft (PDX) mice (n = 5 mice per group). We established the first BRAF(WT/V600E)-dependent thyroid MPC cell culture. Our findings identify BRAF(WT/V600E) as a novel genetic aberration in MPC pathogenesis and MPC-associated biomarkers and imply that anti-BRAF(V600E) agents may be useful adjuvant therapy in BRAF(WT/V600E)-MPC patients. Patients with BRAF(WT/V600E)-MPC should be closely followed because of the risk for multifocality/recurrence.
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Affiliation(s)
- Peter M Sadow
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Carmen Priolo
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Simona Nanni
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Florian A Karreth
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Mark Duquette
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Roberta Martinelli
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Amjad Husain
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - John Clohessy
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Heinz Kutzner
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Thomas Mentzel
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Christopher V Carman
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Antonella Farsetti
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Elizabeth Petri Henske
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Emanuele Palescandolo
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Laura E Macconaill
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Seum Chung
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Guido Fadda
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Celestino Pio Lombardi
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Antonina M De Angelis
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Oreste Durante
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - John A Parker
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Alfredo Pontecorvi
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Harold F Dvorak
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Christopher Fletcher
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Pier Paolo Pandolfi
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Jack Lawler
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF)
| | - Carmelo Nucera
- Department of Pathology, Massachusetts General Hospital (PMS) and Department of Medicine, Brigham and Women's Hospital (CP, EPH), Harvard Medical School, Boston, MA; Unit of Endocrinology, Department of Medicine, A. Gemelli, Catholic University, Roma, Italy (SN, AP); Division of Cancer Genetics, Department of Medicine (FAK, JC, PPP) and Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Cancer Biology and Angiogenesis, Department of Pathology, Center for Vascular Biology Research (MD, CN), Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA; Department of Medicine (RM, CVC) and Department of Pathology (AH, HD, JL), Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, MA; Dermatopathologische Gemeinschaftspraxis, Siemensstrasse, Friedri chshafen, Germany (HK, TM); National Research Council (CNR-IBCN) and Department of Experimental Oncology, Regina Elena Cancer Institute, Rome, Italy (AF); Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (EP, LEM); MIT/Broad Institute, Cambridge, MA (EP, LEM); Department of Plastic and Reconstructive Surgery, National Health Insurance Service Ilsan Hospital, Ilsan, Korea (SC); Department of Pathology (GF) and Department of Surgery (CPL), A. Gemelli, Catholic University, Roma, Italy; Department of Experimental and Clinical Medicine (AMDA) and Unit of Radiotherapy (OD), University of Catanzaro, Italy; Department of Nuclear Medicine, Beth Israel Deaconess Medical Center (JAP); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (CF).
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19
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Abstract
Personalized medicine is the cornerstone of medical practice. It tailors treatments for specific conditions of an affected individual. The borders of personalized medicine are defined by limitations in technology and our understanding of biology, physiology and pathology of various conditions. Current advances in technology have provided physicians with the tools to investigate the molecular makeup of the disease. Translating these molecular make-ups to actionable targets has led to the development of small molecular inhibitors. Also, detailed understanding of genetic makeup has allowed us to develop prognostic markers, better known as companion diagnostics. Current attempts in the development of drug delivery systems offer the opportunity of delivering specific inhibitors to affected cells in an attempt to reduce the unwanted side effects of drugs.
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Affiliation(s)
- Gayane Badalian-Very
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 450 Brookline ave, Boston, MA 02115, United States. Tel.: + 1 617 513 7940; fax: + 1 617 632 5998.
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20
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Kim EH, Lee S, Park J, Lee K, Bhak J, Kim BC. New lung cancer panel for high-throughput targeted resequencing. Genomics Inform 2014; 12:50-7. [PMID: 25031567 PMCID: PMC4099348 DOI: 10.5808/gi.2014.12.2.50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/14/2014] [Accepted: 05/17/2014] [Indexed: 12/15/2022] Open
Abstract
We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at 30× sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than 1,000× coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening.
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Affiliation(s)
- Eun-Hye Kim
- Theragen Bio Institute, AICT, Suwon 443-270, Korea
| | - Sunghoon Lee
- Theragen Bio Institute, AICT, Suwon 443-270, Korea
| | - Jongsun Park
- Personal Genomics Institute, Genome Research Foundation, AICT, Suwon 443-270, Korea
| | | | - Jong Bhak
- Theragen Bio Institute, AICT, Suwon 443-270, Korea. ; Personal Genomics Institute, Genome Research Foundation, AICT, Suwon 443-270, Korea
| | - Byung Chul Kim
- Personal Genomics Institute, Genome Research Foundation, AICT, Suwon 443-270, Korea. ; Clinomics Inc., Seoul 138-961, Korea
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21
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Kim YM, Lee SW, Chun SM, Kim DY, Kim JH, Kim KR, Kim YT, Nam JH, van Hummelen P, MacConaill LE, Hahn WC, Jang SJ. Analysis and comparison of somatic mutations in paired primary and recurrent epithelial ovarian cancer samples. PLoS One 2014; 9:e99451. [PMID: 24936796 PMCID: PMC4060993 DOI: 10.1371/journal.pone.0099451] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022] Open
Abstract
The TP53 mutations have been proved to be predominated in ovarian cancer in a study from The Cancer Genome Atlas (TCGA). However, the molecular characteristics of recurrent ovarian cancers following initial treatment have been poorly estimated. This study was to investigate the pattern of somatic point mutations in matched paired samples of primary and recurrent epithelial ovarian cancers, using the OncoMap mutation detection protocol. We have adapted a high-throughput genotyping platform to determine the mutation status of a large panel of known cancer genes. OncoMap v.4.4 was used to evaluate genomic DNA isolated from a set of 92 formalin-fixed, paraffin-embedded (FFPE) tumors, consisting of matched paired samples of initially diagnosed and recurrent tumors from 46 epithelial ovarian cancer (EOC) patients. Mutations were observed in 33.7% of the samples, with 29.3% of these samples having a single mutation and the remaining 4.3% having two or more mutations. Among the 41 genes analyzed, 35 mutations were found in four genes, namely, CDKN2A (2.2%), KRAS (6.5%), MLH1 (8.2%) and TP53 (20.7%). TP53 was the most frequently mutated gene, but there was no correlation between the presence of mutation in any gene and clinical prognosis. Furthermore, somatic mutations did not differ between primary and recurrent ovarian carcinomas. Every mutation present in recurrent samples was detected in the corresponding primary sample. In conclusion, these OncoMap data of Korean EOC samples provide that somatic mutations were found in CDKN2A, KRAS, MLH1, and TP53. No differences in mutational status between primary and recurrent samples were detected. To understand the biology of tumor recurrence in epithelial ovarian cancer, more studies are necessary, including epigenetic modifications or additional mutations in other genes.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adolescent
- Adult
- Aged
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/mortality
- Colorectal Neoplasms/secondary
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- DNA Mutational Analysis
- Disease-Free Survival
- Female
- Genetic Association Studies
- Genetic Predisposition to Disease
- Humans
- Kaplan-Meier Estimate
- Middle Aged
- MutL Protein Homolog 1
- Neoplasm Recurrence, Local/genetics
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/mortality
- Neoplasms, Cystic, Mucinous, and Serous/secondary
- Nuclear Proteins/genetics
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/mortality
- Ovarian Neoplasms/pathology
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins p21(ras)
- Tumor Suppressor Protein p53/genetics
- Young Adult
- ras Proteins/genetics
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Affiliation(s)
- Yong-Man Kim
- Department of Obstetrics & Gynecology, University of Ulsan, ASAN Medical Center, Seoul, Korea
- ASAN Center for Cancer Genome Discovery, ASAN Medical Center, Seoul, Korea
| | - Shin-Wha Lee
- Department of Obstetrics & Gynecology, University of Ulsan, ASAN Medical Center, Seoul, Korea
- ASAN Center for Cancer Genome Discovery, ASAN Medical Center, Seoul, Korea
| | - Sung-Min Chun
- Department of Pathology, University of Ulsan, ASAN Medical Center, Seoul, Korea
- ASAN Center for Cancer Genome Discovery, ASAN Medical Center, Seoul, Korea
| | - Dae-Yeon Kim
- Department of Obstetrics & Gynecology, University of Ulsan, ASAN Medical Center, Seoul, Korea
| | - Jong-Hyeok Kim
- Department of Obstetrics & Gynecology, University of Ulsan, ASAN Medical Center, Seoul, Korea
| | - Kyu-Rae Kim
- Department of Pathology, University of Ulsan, ASAN Medical Center, Seoul, Korea
| | - Young-Tak Kim
- Department of Obstetrics & Gynecology, University of Ulsan, ASAN Medical Center, Seoul, Korea
| | - Joo-Hyun Nam
- Department of Obstetrics & Gynecology, University of Ulsan, ASAN Medical Center, Seoul, Korea
| | - Paul van Hummelen
- Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Laura E. MacConaill
- Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - William C. Hahn
- Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Se Jin Jang
- Department of Pathology, University of Ulsan, ASAN Medical Center, Seoul, Korea
- ASAN Center for Cancer Genome Discovery, ASAN Medical Center, Seoul, Korea
- * E-mail:
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22
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Sonnenberg A, Marciniak JY, Skowronski EA, Manouchehri S, Rassenti L, Ghia EM, Widhopf GF, Kipps TJ, Heller MJ. Dielectrophoretic isolation and detection of cancer-related circulating cell-free DNA biomarkers from blood and plasma. Electrophoresis 2014; 35:1828-36. [PMID: 24723219 DOI: 10.1002/elps.201400016] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/16/2014] [Accepted: 03/18/2014] [Indexed: 12/18/2022]
Abstract
Conventional methods for the isolation of cancer-related circulating cell-free (ccf) DNA from patient blood (plasma) are time consuming and laborious. A DEP approach utilizing a microarray device now allows rapid isolation of ccf-DNA directly from a small volume of unprocessed blood. In this study, the DEP device is used to compare the ccf-DNA isolated directly from whole blood and plasma from 11 chronic lymphocytic leukemia (CLL) patients and one normal individual. Ccf-DNA from both blood and plasma samples was separated into DEP high-field regions, after which cells (blood), proteins, and other biomolecules were removed by a fluidic wash. The concentrated ccf-DNA was detected on-chip by fluorescence, and then eluted for PCR and DNA sequencing. The complete process from blood to PCR required less than 10 min; an additional 15 min was required to obtain plasma from whole blood. Ccf-DNA from the equivalent of 5 μL of CLL blood and 5 μL of plasma was amplified by PCR using Ig heavy-chain variable (IGHV) specific primers to identify the unique IGHV gene expressed by the leukemic B-cell clone. The PCR and DNA sequencing results obtained by DEP from all 11 CLL blood samples and from 8 of the 11 CLL plasma samples were exactly comparable to the DNA sequencing results obtained from genomic DNA isolated from CLL patient leukemic B cells (gold standard).
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Affiliation(s)
- Avery Sonnenberg
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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Simon R, Roychowdhury S. Implementing personalized cancer genomics in clinical trials. Nat Rev Drug Discov 2013; 12:358-69. [PMID: 23629504 DOI: 10.1038/nrd3979] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The recent surge in high-throughput sequencing of cancer genomes has supported an expanding molecular classification of cancer. These studies have identified putative predictive biomarkers signifying aberrant oncogene pathway activation and may provide a rationale for matching patients with molecularly targeted therapies in clinical trials. Here, we discuss some of the challenges of adapting these data for rare cancers or molecular subsets of certain cancers, which will require aligning the availability of investigational agents, rapid turnaround of clinical grade sequencing, molecular eligibility and reconsidering clinical trial design and end points.
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Affiliation(s)
- Richard Simon
- Biometric Research Branch, US National Cancer Institute, Bethesda, Maryland 20892-7434, USA
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Abstract
Borderline ovarian tumors represent an understudied subset of ovarian tumors. Most studies investigating aberrations in borderline tumors have focused on KRAS/BRAF mutations. In this study, we conducted an extensive analysis of mutations and single-nucleotide polymorphisms (SNPs) in borderline ovarian tumors. Using the Sequenom MassArray platform, we investigated 160 mutations/polymorphisms in 33 genes involved in cell signaling, apoptosis, angiogenesis, cell cycle regulation and cellular senescence. Of 52 tumors analyzed, 33 were serous, 18 mucinous and 1 endometrioid. KRAS c.35G>A p.Gly12Asp mutations were detected in eight tumors (six serous and two mucinous), BRAF V600E mutations in two serous tumors, and PIK3CA H1047Y and PIK3CA E542K mutations in a serous and an endometrioid BOT, respectively. CTNNB1 mutation was detected in a serous tumor. Potentially functional polymorphisms were found in vascular endothelial growth factor (VEGF), ABCB1, FGFR2 and PHLPP2. VEGF polymorphisms were the most common and detected at four loci. PHLPP2 polymorphisms were more frequent in mucinous as compared with serous tumors (P=0.04), with allelic imbalance in one case. This study represents the largest and most comprehensive analysis of mutations and functional SNPs in borderline ovarian tumors to date. At least 25% of borderline ovarian tumors harbor somatic mutations associated with potential response to targeted therapeutics.
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Abstract
Epithelial ovarian cancer frequently presents at an advanced stage where the cornerstone of management remains surgery and platinum-based chemotherapy. Unfortunately, despite sometimes dramatic initial responses, advanced ovarian cancer almost invariably relapses. Little progress has been made in the identification of effective targeted-therapies for ovarian cancer. The majority of clinical trials investigating novel agents have been negative and the only approved targeted-therapy is bevacizumab, for which reliable predictive biomarkers still elude us. Ovarian cancer is treated as a uniform disease. Yet, biological studies have highlighted the heterogeneity of this malignancy with marked differences in histology, oncogenesis, prognosis, chemo-responsiveness, and molecular profile. Recent high throughput molecular analyses have identified a huge number of genomic/phenotypic alterations. Broadly speaking, high grade serous carcinomas (type II) display significant genomic instability and numerous amplifications and losses; low grade (type I) tumors are genomically stable but display frequent mutations. Importantly, many of these genomic alterations relate to known oncogenes for which targeted-therapies are available or in development. There is today a real potential for personalized medicine in ovarian cancer. We will review the current literature regarding the molecular characterization of epithelial ovarian cancer and discuss the biological rationale for a number of targeted strategies. In order to translate these biological advances into meaningful clinical improvements for our patients, it is imperative to incorporate translational research in ovarian cancer trials, a number of strategies will be proposed such as the acquisition of quality tumor samples, including sequential pre- and post-treatment biopsies, the potential of liquid biopsies, and novel trial designs more adapted to the molecular era of ovarian cancer research.
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Kohn EC, Hurteau J. Ovarian cancer : making its own rules-again. Cancer 2012; 119:474-6. [PMID: 23233093 DOI: 10.1002/cncr.27833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 08/21/2012] [Indexed: 01/05/2023]
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Abstract
Although improvements in genomic technologies during the past decade have greatly advanced our understanding of the genomic alterations that contribute to lung cancer, and the disease has (to a degree) become a paradigm for individualized cancer treatment in solid tumors, additional challenges must be addressed before the goal of personalized cancer therapy can become a reality for lung cancer patients.
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Affiliation(s)
- Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, 450 Brookline Ave., Dana 1539, Boston, MA 02215, USA.
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Rodig SJ, Cheng J, Wardzala J, DoRosario A, Scanlon JJ, Laga AC, Martinez-Fernandez A, Barletta JA, Bellizzi AM, Sadasivam S, Holloway DT, Cooper DJ, Kupper TS, Wang LC, DeCaprio JA. Improved detection suggests all Merkel cell carcinomas harbor Merkel polyomavirus. J Clin Invest 2012; 122:4645-53. [PMID: 23114601 DOI: 10.1172/jci64116] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 09/06/2012] [Indexed: 12/31/2022] Open
Abstract
A human polyomavirus was recently discovered in Merkel cell carcinoma (MCC) specimens. The Merkel cell polyomavirus (MCPyV) genome undergoes clonal integration into the host cell chromosomes of MCC tumors and expresses small T antigen and truncated large T antigen. Previous studies have consistently reported that MCPyV can be detected in approximately 80% of all MCC tumors. We sought to increase the sensitivity of detection of MCPyV in MCC by developing antibodies capable of detecting large T antigen by immunohistochemistry. In addition, we expanded the repertoire of quantitative PCR primers specific for MCPyV to improve the detection of viral DNA in MCC. Here we report that a novel monoclonal antibody detected MCPyV large T antigen expression in 56 of 58 (97%) unique MCC tumors. PCR analysis specifically detected viral DNA in all 60 unique MCC tumors tested. We also detected inactivating point substitution mutations of TP53 in the two MCC specimens that lacked large T antigen expression and in only 1 of 56 tumors positive for large T antigen. These results indicate that MCPyV is present in MCC tumors more frequently than previously reported and that mutations in TP53 tend to occur in MCC tumors that fail to express MCPyV large T antigen.
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Affiliation(s)
- Scott J Rodig
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Daniels AB, Lee JE, MacConaill LE, Palescandolo E, Van Hummelen P, Adams SM, DeAngelis MM, Hahn WC, Gragoudas ES, Harbour JW, Garraway LA, Kim IK. High throughput mass spectrometry-based mutation profiling of primary uveal melanoma. Invest Ophthalmol Vis Sci 2012; 53:6991-6. [PMID: 22977135 DOI: 10.1167/iovs.12-10427] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
PURPOSE We assessed for mutations in a large number of oncogenes and tumor suppressor genes in primary uveal melanomas using a high-throughput profiling system. METHODS DNA was extracted and purified from 134 tissue samples from fresh-frozen tissues (n = 87) or formalin-fixed, paraffin-embedded tissues (n = 47) from 124 large uveal melanomas that underwent primary treatment by enucleation. DNA was subjected to whole genome amplification and MALDI-TOF mass spectrometry-based mutation profiling (>1000 mutations tested across 120 oncogenes and tumor suppressor genes) using the OncoMap3 platform. All candidate mutations, as well as commonly occurring mutations in GNAQ and GNA11, were validated using homogeneous mass extension (hME) technology. RESULTS Of 123 samples, 97 (79%, representing 89 unique tumors) were amplified successfully, passed all quality control steps, and were assayed with the OncoMap platform. A total of 58 mutation calls was made for 49 different mutations across 26 different genes in 34/98 (35%) samples. Of 91 tumors that underwent hME validation, 83 (91%) harbored mutations in the GNAQ (47%) or GNA11 (44%) genes, while hME validation revealed two tumors with mutations in EGFR. These additional mutations occurred in tumors that also had mutations in GNAQ or GNA11. CONCLUSIONS The vast majority of primary large uveal melanomas harbor mutually-exclusive mutations in GNAQ or GNA11, but very rarely have the oncogenic mutations that are reported commonly in other cancers. When present, these other mutations were found in conjunction with GNAQ/GNA11 mutations, suggesting that these other mutations likely are not the primary drivers of oncogenesis in uveal melanoma.
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Affiliation(s)
- Anthony B Daniels
- Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114-3096, USA
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Targeting Notch, a key pathway for ovarian cancer stem cells, sensitizes tumors to platinum therapy. Proc Natl Acad Sci U S A 2012; 109:E2939-48. [PMID: 23019585 DOI: 10.1073/pnas.1206400109] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chemoresistance to platinum therapy is a major obstacle that needs to be overcome in the treatment of ovarian cancer patients. The high rates and patterns of therapeutic failure seen in patients are consistent with a steady accumulation of drug-resistant cancer stem cells (CSCs). This study demonstrates that the Notch signaling pathway and Notch3 in particular are critical for the regulation of CSCs and tumor resistance to platinum. We show that Notch3 overexpression in tumor cells results in expansion of CSCs and increased platinum chemoresistance. In contrast, γ-secretase inhibitor (GSI), a Notch pathway inhibitor, depletes CSCs and increases tumor sensitivity to platinum. Similarly, a Notch3 siRNA knockdown increases the response to platinum therapy, further demonstrating that modulation of tumor chemosensitivity by GSI is Notch specific. Most importantly, the cisplatin/GSI combination is the only treatment that effectively eliminates both CSCs and the bulk of tumor cells, indicating that a dual combination targeting both populations is needed for tumor eradication. In addition, we found that the cisplatin/GSI combination therapy has a synergistic cytotoxic effect in Notch-dependent tumor cells by enhancing the DNA-damage response, G(2)/M cell-cycle arrest, and apoptosis. Based on these results, we conclude that targeting the Notch pathway could significantly increase tumor sensitivity to platinum therapy. Our study suggests important clinical applications for targeting Notch as part of novel treatment strategies upon diagnosis of ovarian cancer and at recurrence. Both platinum-resistant and platinum-sensitive relapses may benefit from such an approach as clinical data suggest that all relapses after platinum therapy are increasingly platinum resistant.
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Involvement of autophagy in ovarian cancer: a working hypothesis. J Ovarian Res 2012; 5:22. [PMID: 22974323 PMCID: PMC3506510 DOI: 10.1186/1757-2215-5-22] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/11/2012] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a lysosomal-driven catabolic process that contributes to preserve cell and tissue homeostases through the regular elimination of damaged, aged and redundant self-constituents. In normal cells, autophagy protects from DNA mutation and carcinogenesis by preventive elimination of pro-oxidative mitochondria and protein aggregates. Mutations in oncogenes and oncosuppressor genes dysregulate autophagy. Up-regulated autophagy may confer chemo- and radio-resistance to cancer cells, and also a pro-survival advantage in cancer cells experiencing oxygen and nutrient shortage. This fact is the rationale for using autophagy inhibitors along with anti-neoplastic therapies. Yet, aberrant hyper-induction of autophagy can lead to cell death, and this phenomenon could also be exploited for cancer therapy. The actual level of autophagy in the cancer cell is greatly affected by vascularization, inflammation, and stromal cell infiltration. In addition, small non-coding microRNAs have recently emerged as important epigenetic modulators of autophagy. The present review focuses on the potential involvement of macroautophagy, and on its genetic and epigenetic regulation, in ovarian cancer pathogenesis and progression.
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Maeng CH, Lee J, van Hummelen P, Park SH, Palescandolo E, Jang J, Park HY, Kang SY, MacConaill L, Kim KM, Shim YM. High-throughput genotyping in metastatic esophageal squamous cell carcinoma identifies phosphoinositide-3-kinase and BRAF mutations. PLoS One 2012; 7:e41655. [PMID: 22870241 PMCID: PMC3411721 DOI: 10.1371/journal.pone.0041655] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 06/27/2012] [Indexed: 12/20/2022] Open
Abstract
Background Given the high incidence of metastatic esophageal squamous cell carcinoma, especially in Asia, we screened for the presence of somatic mutations using OncoMap platform with the aim of defining subsets of patients who may be potential candidate for targeted therapy. Methods and Materials We analyzed 87 tissue specimens obtained from 80 patients who were pathologically confirmed with esophageal squamous cell carcinoma and received 5-fluoropyrimidine/platinum-based chemotherapy. OncoMap 4.0, a mass-spectrometry based assay, was used to interrogate 471 oncogenic mutations in 41 commonly mutated genes. Tumor specimens were prepared from primary cancer sites in 70 patients and from metastatic sites in 17 patients. In order to test the concordance between primary and metastatic sites from the patient for mutations, we analyzed 7 paired (primary-metastatic) specimens. All specimens were formalin-fixed paraffin embedded tissues and tumor content was >70%. Results In total, we have detected 20 hotspot mutations out of 80 patients screened. The most frequent mutation was PIK3CA mutation (four E545K, five H1047R and one H1047L) (N = 10, 11.5%) followed by MLH1 V384D (N = 7, 8.0%), TP53 (R306, R175H and R273C) (N = 3, 3.5%), BRAF V600E (N = 1, 1.2%), CTNNB1 D32N (N = 1, 1.2%), and EGFR P733L (N = 1, 1.2%). Distributions of somatic mutations were not different according to anatomic sites of esophageal cancer (cervical/upper, mid, lower). In addition, there was no difference in frequency of mutations between primary-metastasis paired samples. Conclusions Our study led to the detection of potentially druggable mutations in esophageal SCC which may guide novel therapies in small subsets of esophageal cancer patients.
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Affiliation(s)
- Chi Hoon Maeng
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
| | - Paul van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Se Hoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jiryeon Jang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ha Young Park
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - So Young Kang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Mog Shim
- Department of Thoracic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Lee J, van Hummelen P, Go C, Palescandolo E, Jang J, Park HY, Kang SY, Park JO, Kang WK, MacConaill L, Kim KM. High-throughput mutation profiling identifies frequent somatic mutations in advanced gastric adenocarcinoma. PLoS One 2012; 7:e38892. [PMID: 22723903 PMCID: PMC3377730 DOI: 10.1371/journal.pone.0038892] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 05/14/2012] [Indexed: 12/12/2022] Open
Abstract
Background Gastric cancer is one of the leading cancer types in incidence and mortality, especially in Asia. In order to improve survival, identification of a catalogue of molecular alterations underlying gastric cancer is a critical step for developing and designing genome-directed therapies. Methodology/Principal Findings The Center for Cancer Genome Discovery (CCGD) at the Dana-Farber Cancer Institute (DFCI) has adapted a high-throughput genotyping platform to determine the mutation status of a large panel of known cancer genes. The mutation detection platform, termed OncoMap v4, interrogates 474 “hotspot” mutations in 41 genes that are relevant for cancer. We performed OncoMap v4 in formalin-fixed paraffin-embedded (FFPE) tissue specimens from 237 gastric adenocarcinomas. Using OncoMap v4, we found that 34 (14.4%) of 237 gastric cancer patients harbored mutations. Among mutations we screened, PIK3CA mutations were the most frequent (5.1%) followed by p53 (4.6%), APC (2.5%), STK11 (2.1%), CTNNB1 (1.7%), and CDKN2A (0.8%). Six samples harbored concomitant somatic mutations. Mutations of CTNNB1 were significantly more frequent in EBV-associated gastric carcinoma (P = 0.046). Our study led to the detection of potentially druggable mutations in gastric cancer which may guide novel therapies in subsets of gastric cancer patients. Conclusions/Significance Using high throughput mutation screening platform, we identified that PIK3CA mutations were the most frequently observed target for gastric adenocarcinoma.
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Affiliation(s)
- Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Paul van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christina Go
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jiryeon Jang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ha Young Park
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - So Young Kang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
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Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, Dawson SJ, Piskorz AM, Jimenez-Linan M, Bentley D, Hadfield J, May AP, Caldas C, Brenton JD, Rosenfeld N. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 2012; 4:136ra68. [PMID: 22649089 DOI: 10.1126/scitranslmed.3003726] [Citation(s) in RCA: 964] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plasma of cancer patients contains cell-free tumor DNA that carries information on tumor mutations and tumor burden. Individual mutations have been probed using allele-specific assays, but sequencing of entire genes to detect cancer mutations in circulating DNA has not been demonstrated. We developed a method for tagged-amplicon deep sequencing (TAm-Seq) and screened 5995 genomic bases for low-frequency mutations. Using this method, we identified cancer mutations present in circulating DNA at allele frequencies as low as 2%, with sensitivity and specificity of >97%. We identified mutations throughout the tumor suppressor gene TP53 in circulating DNA from 46 plasma samples of advanced ovarian cancer patients. We demonstrated use of TAm-Seq to noninvasively identify the origin of metastatic relapse in a patient with multiple primary tumors. In another case, we identified in plasma an EGFR mutation not found in an initial ovarian biopsy. We further used TAm-Seq to monitor tumor dynamics, and tracked 10 concomitant mutations in plasma of a metastatic breast cancer patient over 16 months. This low-cost, high-throughput method could facilitate analysis of circulating DNA as a noninvasive "liquid biopsy" for personalized cancer genomics.
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Affiliation(s)
- Tim Forshew
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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Caiola E, Rulli E, Fruscio R, Buda A, Broggini M, Marabese M. KRas-LCS6 polymorphism does not impact on outcomes in ovarian cancer. Am J Cancer Res 2012; 2:298-308. [PMID: 22679560 PMCID: PMC3365808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/17/2012] [Indexed: 06/01/2023] Open
Abstract
Epithelial ovarian cancer is a malignancy with high rate of death due to an advanced disease at diagnosis and frequent relapse after chemotherapy. Nowadays, there is a lack of knowledge for clear risk factors and predictive and/or prognostic genetic markers although genomic alterations such as mutations in p53, PTEN, BRCA1/BRCA2, HER2, KRAS and PI3K genes have been associated to this pathology. A genomic variant in the 3' untraslated region of cancer related gene KRAS, is able to disrupt the let-7 miRNA binding site. The SNP, commonly named KRAS-LCS6, determines the substitution of the more abundant T-allele to a G-allele which was observed to increase the KRAS expression and in turn to activate the downstream pathway at higher levels if compared to the T-allele. In this study we assessed the role of the KRAS-LCS6 polymorphism (rs61764370) in 97 early (stages I and II) and 232 advanced (stages III and IV) ovarian cancer patients in order to associate this SNP to any physiopathological characteristic of the patients cohort, including progression free survival and overall survival, with a follow up data longer than ten years. Our data indicate that KRAS-LCS6 polymorphism is not relevant in ovarian cancer, in fact, in our cohort of patients, is not associated to any outcome or physiopathological characteristic.
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Affiliation(s)
- Elisa Caiola
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche “Mario Negri”Milan, Italy
| | - Eliana Rulli
- Laboratory of Clinical Trials, Department of Oncology, Istituto di Ricerche Farmacologiche “Mario Negri”Milan, Italy
| | - Robert Fruscio
- Clinic of Obstetrics and Gynecology, University of Milan-Bicocca, San Gerardo HospitalMonza, Italy
| | - Alessandro Buda
- Clinic of Obstetrics and Gynecology, University of Milan-Bicocca, San Gerardo HospitalMonza, Italy
| | - Massimo Broggini
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche “Mario Negri”Milan, Italy
| | - Mirko Marabese
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche “Mario Negri”Milan, Italy
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37
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Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, Wu YM, Cao X, Kalyana-Sundaram S, Sam L, Balbin OA, Quist MJ, Barrette T, Everett J, Siddiqui J, Kunju LP, Navone N, Araujo JC, Troncoso P, Logothetis CJ, Innis JW, Smith DC, Lao CD, Kim SY, Roberts JS, Gruber SB, Pienta KJ, Talpaz M, Chinnaiyan AM. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med 2011; 3:111ra121. [PMID: 22133722 PMCID: PMC3476478 DOI: 10.1126/scitranslmed.3003161] [Citation(s) in RCA: 448] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Individual cancers harbor a set of genetic aberrations that can be informative for identifying rational therapies currently available or in clinical trials. We implemented a pilot study to explore the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the tumor, targeted whole-exome sequencing of tumor and normal DNA, and transcriptome sequencing (RNA-Seq) of the tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic colorectal cancer in which we identified somatic point mutations in NRAS, TP53, AURKA, FAS, and MYH11, plus amplification and overexpression of cyclin-dependent kinase 8 (CDK8). The second patient had malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced cancer generates a comprehensive, individual mutational landscape to facilitate biomarker-driven clinical trials in oncology.
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Affiliation(s)
- Sameek Roychowdhury
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew K. Iyer
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan R. Robinson
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J. Lonigro
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shanker Kalyana-Sundaram
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620024, India
| | - Lee Sam
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - O. Alejandro Balbin
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael J. Quist
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Terrence Barrette
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica Everett
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lakshmi P. Kunju
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nora Navone
- Division of Cancer Medicine, Department of Genitourinary Medical Oncology, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - John C. Araujo
- Division of Cancer Medicine, Department of Genitourinary Medical Oncology, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Patricia Troncoso
- Division of Cancer Medicine, Department of Genitourinary Medical Oncology, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher J. Logothetis
- Division of Cancer Medicine, Department of Genitourinary Medical Oncology, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey W. Innis
- Department of Human Genetics and Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - David C. Smith
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher D. Lao
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Y. Kim
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | - J. Scott Roberts
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Health Behavior and Health Education, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen B. Gruber
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kenneth J. Pienta
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Moshe Talpaz
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
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