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Bell D, Afkhami M. Conundrum of 3N: nasopharyngeal nonkeratinizing non-viral carcinoma-reappraisal of fusions and report of two consecutive cases with unusual molecular findings. Virchows Arch 2024:10.1007/s00428-024-03877-7. [PMID: 39023557 DOI: 10.1007/s00428-024-03877-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/30/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Affiliation(s)
- Diana Bell
- Head and Neck/Endocrine Pathology Center of Excellence, Division of Anatomic Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, PA, 15261, USA.
| | - Michelle Afkhami
- Department of Molecular Diagnostics and Biomarkers, City of Hope Cancer Center, Duarte, CA, 91010, USA
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2
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Lanic MD, Guérin R, Wassef M, Durdilly P, Rainville V, Sater V, Jardin F, Ruminy P, Costes-Martineau V, Laé M. Detection of salivary gland and sinonasal fusions by a next-generation sequencing based, ligation-dependent, multiplex RT-PCR assay. Histopathology 2023; 83:685-699. [PMID: 37350081 DOI: 10.1111/his.14971] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
AIMS The discovery of tumour type-specific gene fusion oncogenes in benign and malignant salivary gland and sinonasal (SGSN) tumours has significantly increased our knowledge about their molecular pathology and classification. METHODS AND RESULTS We developed a new targeted multiplexed next-generation sequencing (NGS)-based method that utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR) to detect oncogenic fusion transcripts involving 116 genes, leading to 96 gene fusions known to be recurrently rearranged in these tumours. In all, 180 SGSN tumours (formalin-fixed, paraffin-embedded samples, 141 specimens and 39 core needle biopsies) from the REFCORpath (French network for rare head and neck cancers) with previously identified fusion genes by fluorescent in situ hybridisation (FISH), RT-PCR, or molecular immunohistochemistry were selected to test its specificity and sensitivity and validate its diagnostic use. Tested tumours encompassed 14 major tumours types, including secretory carcinoma, mucoepidermoid carcinoma, adenoid cystic carcinoma, salivary gland intraductal carcinoma, clear cell carcinoma, pleomorphic adenoma, adamantinoma-like Ewing Sarcoma, EWSR1::COLCA2 sinonasal sarcoma, DEK::AFF2 sinonasal carcinoma, and biphenotypic sinonasal sarcoma. In-frame fusion transcripts were detected in 97.8% of cases (176/180). Gene fusion assay results correlated with conventional techniques (immunohistochemistry [IHC], FISH, and RT-PCR) in 176/180 tumours (97.8%). CONCLUSION This targeted multiplexed NGS-based LD-RT-PCR method is a robust, highly sensitive method for the detection of recurrent gene fusions from routine clinical SGSN tumours. It can be easily customized to cover new fusions. These results are promising for implementing an integrated NGS system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses, and accelerate time to precision therapies in SGSN tumours.
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Affiliation(s)
- Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - René Guérin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Michel Wassef
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | | | - Vinciane Rainville
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Vincent Sater
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | | | - Marick Laé
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
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3
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Kumar-Sinha C, Vats P, Tran N, Robinson DR, Gunchick V, Wu YM, Cao X, Ning Y, Wang R, Rabban E, Bell J, Shankar S, Mannan R, Zhang Y, Zalupski MM, Chinnaiyan AM, Sahai V. Genomics driven precision oncology in advanced biliary tract cancer improves survival. Neoplasia 2023; 42:100910. [PMID: 37267699 PMCID: PMC10245336 DOI: 10.1016/j.neo.2023.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Biliary tract cancers (BTCs) including intrahepatic, perihilar, and distal cholangiocarcinoma as well as gallbladder cancer, are rare but aggressive malignancies with few effective standard of care therapies. METHODS We implemented integrative clinical sequencing of advanced BTC tumors from 124 consecutive patients who progressed on standard therapies (N=92 with MI-ONCOSEQ and N=32 with commercial gene panels) enrolled between 2011-2020. RESULTS Genomic profiling of paired tumor and normal DNA and tumor transcriptome (RNA) sequencing identified actionable somatic and germline genomic alterations in 54 patients (43.5%), and potentially actionable alterations in 79 (63.7%) of the cohort. Of these, patients who received matched targeted therapy (22; 40.7%) had a median overall survival of 28.1 months compared to 13.3 months in those who did not receive matched targeted therapy (32; P < 0.01), or 13.9 months in those without actionable mutations (70; P < 0.01). Additionally, we discovered recurrent activating mutations in FGFR2, and a novel association between KRAS and BRAF mutant tumors with high expression of immune modulatory protein NT5E (CD73) that may represent novel therapeutic avenues. CONCLUSIONS Overall, the identification of actionable/ potentially actionable aberrations in a large proportion of cases, and improvement in survival with precision oncology supports molecular analysis and clinical sequencing for all patients with advanced BTC.
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Affiliation(s)
- Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nguyen Tran
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Valerie Gunchick
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erica Rabban
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janice Bell
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sunita Shankar
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark M Zalupski
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Vaibhav Sahai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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4
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Peng Z, Wang Y, Fan R, Gao K, Xie S, Wang F, Zhang J, Zhang H, He Y, Xie Z, Jiang W. Treatment of Recurrent Nasopharyngeal Carcinoma: A Sequential Challenge. Cancers (Basel) 2022; 14:cancers14174111. [PMID: 36077648 PMCID: PMC9454547 DOI: 10.3390/cancers14174111] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/19/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Recurrent nasopharyngeal carcinoma is one of the major causes of death among NPC patients. However, there are no international guidelines for the treatment of patients with recurrent NPC now. In this article, we summarize past publications on clinical research and mechanistic studies related to recurrent NPC, combined with the experience and lessons learned by our institutional multidisciplinary team in the treatment of recurrent NPC. We propose an objective protocol for the treatment of recurrent NPC. Abstract Recurrent nasopharyngeal carcinoma (NPC), which occurs in 10–20% of patients with primary NPC after the initial treatment modality of intensity-modulated radiation therapy (IMRT), is one of the major causes of death among NPC patients. Patients with recurrent disease without distant metastases still have a chance to be saved, but re-treatment often carries more serious toxicities or higher risks. For this group of patients, both otolaryngologists and oncologists are committed to developing more appropriate treatment regimens that can prolong patient survival and improve survival therapy. Currently, there are no international guidelines for the treatment of patients with recurrent NPC. In this article, we summarize past publications on clinical research and mechanistic studies related to recurrent NPC, combined with the experience and lessons learned by our institutional multidisciplinary team in the treatment of recurrent NPC. We propose an objective protocol for the treatment of recurrent NPC.
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Affiliation(s)
- Zhouying Peng
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ruohao Fan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Kelei Gao
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Shumin Xie
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Fengjun Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Junyi Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hua Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuxiang He
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Radiation Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhihai Xie
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Anatomy Laboratory of Division of Nose and Cranial Base, Clinical Anatomy Center of Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence:
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MAML2-Rearranged Mucoepidermoid Carcinoma of the Parotid Gland: A Report in a 20-Month-Old Toddler. Case Rep Dent 2022; 2022:8749836. [PMID: 35392490 PMCID: PMC8983249 DOI: 10.1155/2022/8749836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/28/2022] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
Malignancies of salivary gland origin are rare in children. Mucoepidermoid carcinoma (MEC) is the most common histologic type of salivary gland neoplasm in pediatrics. We report a rare case of parotid MEC in a 20-month-old female patient. The tumor was composed of nests of epidermoid cells with nuclei appearing vesicular, pleomorphic, and hyperchromatic with an admixture of mucous cells and cystic spaces within a prominent connective tissue stroma. Immunohistochemically, the epidermoid cells showed cytokeratin 7 and P63 positivity, and mucous cells were positive for mucicarmine. Molecularly, this case was positive for MAML2 rearrangement by FISH. To our knowledge, this is one of the youngest cases of MEC of the parotid gland reported in the English literature.
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The Hippo pathway in cancer: YAP/TAZ and TEAD as therapeutic targets in cancer. Clin Sci (Lond) 2022; 136:197-222. [PMID: 35119068 PMCID: PMC8819670 DOI: 10.1042/cs20201474] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/18/2022] [Indexed: 02/07/2023]
Abstract
Tumorigenesis is a highly complex process, involving many interrelated and cross-acting signalling pathways. One such pathway that has garnered much attention in the field of cancer research over the last decade is the Hippo signalling pathway. Consisting of two antagonistic modules, the pathway plays an integral role in both tumour suppressive and oncogenic processes, generally via regulation of a diverse set of genes involved in a range of biological functions. This review discusses the history of the pathway within the context of cancer and explores some of the most recent discoveries as to how this critical transducer of cellular signalling can influence cancer progression. A special focus is on the various recent efforts to therapeutically target the key effectors of the pathway in both preclinical and clinical settings.
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7
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Papke DJ, Hornick JL. Recent advances in the diagnosis, classification and molecular pathogenesis of cutaneous mesenchymal neoplasms. Histopathology 2021; 80:216-232. [DOI: 10.1111/his.14450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022]
Affiliation(s)
- D J Papke
- Department of Pathology Brigham and Women’s Hospital and Harvard Medical School Boston MA USA
| | - J L Hornick
- Department of Pathology Brigham and Women’s Hospital and Harvard Medical School Boston MA USA
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Ong SLM, Szuhai K, Bovée JVMG. Gene fusions in vascular tumors and their underlying molecular mechanisms. Expert Rev Mol Diagn 2021; 21:897-909. [PMID: 34225547 DOI: 10.1080/14737159.2021.1950533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. AREAS COVERED This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. EXPERT OPINION The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies.
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Affiliation(s)
- Sheena L M Ong
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Zhao J, Zhao R, Xiang C, Shao J, Guo L, Han Y. YAP1-MAML2 Fusion as a Diagnostic Biomarker for Metaplastic Thymoma. Front Oncol 2021; 11:692283. [PMID: 34354947 PMCID: PMC8329546 DOI: 10.3389/fonc.2021.692283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/07/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Metaplastic thymoma is a very rare tumor with only a few case reports documented in literature. Hence, its molecular features have not been well explored. MATERIAL AND METHODS Seventeen specimens of metaplastic thymoma were sequenced and retrospectively analyzed by fluorescence in situ hybridization (FISH) and immunohistochemistry in the study. In addition, seven cases of micronodular thymoma with lymphoid stroma and nine cases of type A thymoma were also investigated. RESULTS Among these metaplastic thymomas, fifteen cases showed classical histological features, and two cases displayed characteristic micronodular-like growth patterns. DNA and RNA based next-generation sequencing identified and confirmed highly recurrent Yes Associated Protein 1 (YAP1) - Mastermind Like Transcriptional Coactivator 2 (MAML2) translocation (13/17, 76.5%) in metaplastic thymoma but not in micronodular thymoma with lymphoid stroma (0/7, 0%) and type A thymoma (0/9, 0%). In addition, six nonsense mutations were also detected in the metaplastic thymoma. FISH in microdissection specimens indicated that both epithelioid and spindle cell components harbored YAP1-MAML2 gene rearrangements. CONCLUSIONS Our study explored the genetic alterations in epithelioid and spindle cell components in metaplastic thymoma. Furthermore, YAP1-MAML2 gene rearrangements emerged as a potential diagnostic biomarker helpful for distinguishing metaplastic thymoma from type A and micronodular thymoma with lymphoid stroma.
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Affiliation(s)
| | | | | | | | | | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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10
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Merritt N, Garcia K, Rajendran D, Lin ZY, Zhang X, Mitchell KA, Borcherding N, Fullenkamp C, Chimenti MS, Gingras AC, Harvey KF, Tanas MR. TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex. eLife 2021; 10:62857. [PMID: 33913810 PMCID: PMC8143797 DOI: 10.7554/elife.62857] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Epithelioid hemangioendothelioma (EHE) is a vascular sarcoma that metastasizes early in its clinical course and lacks an effective medical therapy. The TAZ-CAMTA1 and YAP-TFE3 fusion proteins are chimeric transcription factors and initiating oncogenic drivers of EHE. A combined proteomic/genetic screen in human cell lines identified YEATS2 and ZZZ3, components of the Ada2a-containing histone acetyltransferase (ATAC) complex, as key interactors of both fusion proteins despite the dissimilarity of the C terminal fusion partners CAMTA1 and TFE3. Integrative next-generation sequencing approaches in human and murine cell lines showed that the fusion proteins drive a unique transcriptome by simultaneously hyperactivating a TEAD-based transcriptional program and modulating the chromatin environment via interaction with the ATAC complex. Interaction of the ATAC complex with both fusion proteins indicates that it is a key oncogenic driver and unifying enzymatic therapeutic target for this sarcoma. This study presents an approach to mechanistically dissect how chimeric transcription factors drive the formation of human cancers. The proliferation of human cells is tightly regulated to ensure that enough cells are made to build and repair organs and tissues, while at the same time stopping cells from dividing uncontrollably and damaging the body. To get the right balance, cells rely on physical and chemical cues from their environment that trigger the biochemical signals that regulate two proteins called TAZ and YAP. These proteins control gene activity by regulating the rate at which genes are copied to produce proteins. If this process becomes dysregulated, cells can grow uncontrollably, causing cancer. In cancer cells, it is common to find TAZ and YAP fused to other proteins. In epithelioid hemangioendothelioma, a rare cancer that grows in the blood vessels, cancerous growth can be driven by a version of TAZ fused to the protein CAMTA1, or a version of YAP fused to the protein TFE3. While the role of TAZ and YAP in promoting gene activity is known, it is unclear how CAMTA1 and TFE3 contribute to cell growth becoming dysregulated. Merritt, Garcia et al. studied sarcoma cell lines to show that these two fusion proteins, TAZ-CAMTA1 and YAP-TFE3, change the pattern of gene activity seen in the cells compared to TAZ or YAP alone. An analysis of molecules that interact with the two fusion proteins identified a complex called ATAC as the cause of these changes. This complex adds chemical markers to DNA-packaging proteins, which control which genes are available for activation. The fusion proteins combine the ability of TAZ and YAP to control gene activity and the ability of CAMTA1 and TFE3 to make DNA more accessible, allowing the fusion proteins to drive uncontrolled cancerous growth. Similar TAZ and YAP fusion proteins have been found in other cancers, which can activate genes and potentially alter DNA packaging. Targeting drug development efforts at the proteins that complex with TAZ and YAP fusion proteins may lead to new therapies.
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Affiliation(s)
- Nicole Merritt
- Department of Pathology, University of Iowa, Iowa City, United States
| | - Keith Garcia
- Department of Pathology, University of Iowa, Iowa City, United States.,Cancer Biology Graduate Program, University of Iowa, Iowa City, United States
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, United States
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, United States
| | | | - Katrina A Mitchell
- Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University, St. Louis, United States
| | | | - Michael S Chimenti
- Iowa Institute of Human Genetics, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, United States
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Munir R Tanas
- Department of Pathology, University of Iowa, Iowa City, United States.,Cancer Biology Graduate Program, University of Iowa, Iowa City, United States.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, United States.,Pathology and Laboratory Medicine, Veterans Affairs Medical Center, Iowa City, United States
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Ji J, Kaneva K, Hiemenz MC, Dhall G, Davidson TB, Erdreich-Epstein A, Hawes D, Hurth K, Margol AS, Mathew AJ, Robison NJ, Schmidt RJ, Tran HN, Judkins AR, Cotter JA, Biegel JA. Clinical utility of comprehensive genomic profiling in central nervous system tumors of children and young adults. Neurooncol Adv 2021; 3:vdab037. [PMID: 33948563 PMCID: PMC8080244 DOI: 10.1093/noajnl/vdab037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Recent large-scale genomic studies have revealed a spectrum of genetic variants associated with specific subtypes of central nervous system (CNS) tumors. The aim of this study was to determine the clinical utility of comprehensive genomic profiling of pediatric, adolescent and young adult (AYA) CNS tumors in a prospective setting, including detection of DNA sequence variants, gene fusions, copy number alterations (CNAs), and loss of heterozygosity. Methods OncoKids, a comprehensive DNA- and RNA-based next-generation sequencing (NGS) panel, in conjunction with chromosomal microarray analysis (CMA) was employed to detect diagnostic, prognostic, and therapeutic markers. NGS was performed on 222 specimens from 212 patients. Clinical CMA data were analyzed in parallel for 66% (146/222) of cases. Results NGS demonstrated clinically significant alterations in 66% (147/222) of cases. Diagnostic markers were identified in 62% (138/222) of cases. Prognostic information and targetable genomic alterations were identified in 22% (49/222) and 18% (41/222) of cases, respectively. Diagnostic or prognostic CNAs were revealed by CMA in 69% (101/146) of cases. Importantly, clinically significant CNAs were detected in 57% (34/60) of cases with noncontributory NGS results. Germline cancer predisposition testing was indicated for 27% (57/212) of patients. Follow-up germline testing was performed for 20 patients which confirmed a germline pathogenic/likely pathogenic variant in 9 cases: TP53 (2), NF1 (2), SMARCB1 (1), NF2 (1), MSH6 (1), PMS2 (1), and a patient with 47,XXY Klinefelter syndrome. Conclusions Our results demonstrate the significant clinical utility of integrating genomic profiling into routine clinical testing for pediatric and AYA patients with CNS tumors.
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Affiliation(s)
- Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Kristiyana Kaneva
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Girish Dhall
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Division of Pediatric Hematology-Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Anat Erdreich-Epstein
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Kyle Hurth
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Ashley S Margol
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anna J Mathew
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Nathan J Robison
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Hung N Tran
- Kaiser Permanente Los Angeles Medical Center, Los Angeles, California, USA
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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12
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Zema S, Pelullo M, Nardozza F, Felli MP, Screpanti I, Bellavia D. A Dynamic Role of Mastermind-Like 1: A Journey Through the Main (Path)ways Between Development and Cancer. Front Cell Dev Biol 2020; 8:613557. [PMID: 33425921 PMCID: PMC7787167 DOI: 10.3389/fcell.2020.613557] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Major signaling pathways, such as Notch, Hedgehog (Hh), Wnt/β-catenin and Hippo, are targeted by a plethora of physiological and pathological stimuli, ultimately resulting in the modulation of genes that act coordinately to establish specific biological processes. Many biological programs are strictly controlled by the assembly of multiprotein complexes into the nucleus, where a regulated recruitment of specific transcription factors and coactivators on gene promoter region leads to different transcriptional outcomes. MAML1 results to be a versatile coactivator, able to set up synergistic interlinking with pivotal signaling cascades and able to coordinate the network of cross-talking pathways. Accordingly, despite its original identification as a component of the Notch signaling pathway, several recent reports suggest a more articulated role for MAML1 protein, showing that it is able to sustain/empower Wnt/β-catenin, Hh and Hippo pathways, in a Notch-independent manner. For this reason, MAML1 may be associated to a molecular “switch”, with the function to control the activation of major signaling pathways, triggering in this way critical biological processes during embryonic and post-natal life. In this review, we summarize the current knowledge about the pleiotropic role played by MAML proteins, in particular MAML1, and we recapitulate how it takes part actively in physiological and pathological signaling networks. On this point, we also discuss the contribution of MAML proteins to malignant transformation. Accordingly, genetic alterations or impaired expression of MAML proteins may lead to a deregulated crosstalk among the pathways, culminating in a series of pathological disorders, including cancer development. Given their central role, a better knowledge of the molecular mechanisms that regulate the interplay of MAML proteins with several signaling pathways involved in tumorigenesis may open up novel opportunities for an attractive molecular targeted anticancer therapy.
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Affiliation(s)
- Sabrina Zema
- Department of Medico-Surgical Sciences and Biotechnology, Sapienza University, Latina, Italy
| | - Maria Pelullo
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | | | - Maria Pia Felli
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Diana Bellavia
- Department of Molecular Medicine, Sapienza University, Rome, Italy
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13
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Effects of the MAML2 genetic variants in glioma susceptibility and prognosis. Biosci Rep 2020; 39:220742. [PMID: 31652449 PMCID: PMC6822528 DOI: 10.1042/bsr20192091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Abnormal expression of the mastermind-like transcriptional co-activator 2 (MAML2) gene is oncogenic in several human cancers, including glioma. However, the relevance of MAML2 variants with glioma remains unknown. We aimed to investigate the role of MAML2 polymorphisms in glioma risk and prognosis among the Chinese Han population. METHODS Seven MAML2 single-nucleotide polymorphisms (SNPs) were genotyped using Agena MassARRAY system among 575 patients with glioma and 500 age- and gender-matched healthy controls. Logistic regression was used to estimate the association between MAML2 polymorphisms and glioma risk by calculating odds ratios (ORs) and 95% confidence intervals (CI). Kaplan-Meier survival analysis and univariate, multivariate Cox proportional hazard regression analyses for hazard ratios (HRs) and 95% CIs were performed to evaluate the contribution of MAML2 polymorphisms to glioma prognosis. RESULTS MAML2 rs7938889 and rs485842 polymorphisms were associated with the reduced risk of glioma (OR = 0.69, P=0.023; and OR = 0.81, P=0.032, respectively). Rs7115578 polymorphism had a lower susceptibility to glioma in males (OR = 0.68, P=0.034), while rs4598633 variant with a higher risk in females (OR = 1.66, P=0.016). Additionally, rs7115578 AG genotype represented a poorer prognosis of glioma (HR = 1.24, P=0.033) and astrocytoma (log-rank P=0.037, HR = 1.31, P=0.036). Furthermore, rs11021499 polymorphism had lower overall survival (OS) and progression-free survival (PFS) in patients with low-grade glioma. CONCLUSION We provided some novel data suggesting MAML2 polymorphisms might contribute to glioma risk and prognosis. Future studies are warranted to validate these findings and characterize mechanisms underlying these associations.
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14
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Recurrent YAP1 and KMT2A Gene Rearrangements in a Subset of MUC4-negative Sclerosing Epithelioid Fibrosarcoma. Am J Surg Pathol 2020; 44:368-377. [PMID: 31592798 DOI: 10.1097/pas.0000000000001382] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sclerosing epithelioid fibrosarcoma (SEF) is an aggressive soft tissue sarcoma, characterized by a distinctive epithelioid phenotype in a densely sclerotic collagenous stroma, that shows frequent MUC4 immunoreactivity and recurrent gene fusions, often involving EWSR1 gene. A pathogenetic link with low-grade fibromyxoid sarcoma (LGFMS) has been suggested, due to cases with hybrid morphology as well as overlapping genetic signature. However, a small subset of SEF is negative for MUC4 and lacks the canonical EWSR1/FUS gene rearrangements. Triggered by the identification of recurrent YAP1-KMT2A gene fusions by RNA sequencing in 3 index cases of MUC4-negative, EWSR1/FUS fusion-negative SEF, we further investigated a cohort of 14 similar SEF cases (MUC4-negative, EWSR1/FUS fusion-negative) by fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction, and/or DNA-based massively parallel sequencing (MSK-IMPACT) for abnormalities in these genes. Three additional SEFs with KMT2A gene rearrangements and one additional case with YAP1 gene rearrangements were identified by FISH. In addition, one case with YAP1-KMT2A and one with KMT2A-YAP1 fusion were detected by reverse transcription-polymerase chain reaction and MSK-IMPACT, respectively. As a control group, 24 fibromyxoid spindle cell tumors, diagnosed or suspected as fusion-negative LGFMS, were also tested for YAP1 and KMT2A abnormalities by FISH, but none were positive. The YAP1/KMT2A-rearranged SEF group affected patients ranging from 10 to 86 years old (average and median: 45) of both sexes (4 females, 5 males). The tumors involved somatic soft tissues with a wide distribution, including extremities, trunk, neck, and dura. Histologically, the tumors showed variable cellularity, with monotonous ovoid to epithelioid tumor cells and hyalinized collagenous background typical of SEF. More than half of the cases showed infiltrative borders, within fat or skeletal muscle. No LGFMS component was identified. All tumors were negative for MUC4 and had an otherwise nonspecific immunophenotype. Of the 6 cases with available follow-up information, 2 had local recurrences, and 2 developed soft tissue and/or bone metastases, including 1 of them died of the disease.
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15
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Scala M, Mojarrad M, Riazuddin S, Brigatti KW, Ammous Z, Cohen JS, Hosny H, Usmani MA, Shahzad M, Riazuddin S, Stanley V, Eslahi A, Person RE, Elbendary HM, Comi AM, Poskitt L, Salpietro V, Genomics QS, Rosenfeld JA, Williams KB, Marafi D, Xia F, Biderman Waberski M, Zaki MS, Gleeson J, Puffenberger E, Houlden H, Maroofian R. RSRC1 loss-of-function variants cause mild to moderate autosomal recessive intellectual disability. Brain 2020; 143:e31. [PMID: 32227164 PMCID: PMC7174030 DOI: 10.1093/brain/awaa070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Marcello Scala
- UCL Queen Square Institute of Neurology, University College London, London, UK.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Genetic Center of Khorasan Razavi, Mashhad, Iran
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | | | | | - Julie S Cohen
- Departments of Neurology and Pediatrics, Kennedy Krieger Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Heba Hosny
- National Institute of Neuromotor System, Cairo, Egypt
| | - Muhammad A Usmani
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Mohsin Shahzad
- Center for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Sheikh Riazuddin
- Center for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan.,National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Valentina Stanley
- Department of Neuroscience, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Atiye Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Anne M Comi
- Departments of Neurology and Pediatrics, Kennedy Krieger Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | - Vincenzo Salpietro
- UCL Queen Square Institute of Neurology, University College London, London, UK.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katie B Williams
- Department of Pediatrics, University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Marta Biderman Waberski
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Joseph Gleeson
- Department of Neuroscience, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | | | - Henry Houlden
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Reza Maroofian
- UCL Queen Square Institute of Neurology, University College London, London, UK
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16
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Agaimy A, Stoehr R, Tögel L, Hartmann A, Cramer T. YAP1-MAML2-Rearranged Poroid Squamous Cell Carcinoma (Squamoid Porocarcinoma) Presenting as a Primary Parotid Gland Tumor. Head Neck Pathol 2020; 15:361-367. [PMID: 32504288 PMCID: PMC8010054 DOI: 10.1007/s12105-020-01181-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Porocarcinoma (synonym: malignant eccrine poroma) is a rare aggressive carcinoma type with terminal sweat gland duct differentiation. The squamous variant of porocarcinoma is even less frequent and might be indistinguishable from conventional squamous cell carcinoma (SCC). We herein describe the first case of a carcinoma presenting as a primary parotid gland malignancy in a 24-year-old male without any other primary tumor. Total parotidectomy and neck dissection were performed followed by adjuvant chemoradiation. The patient remained alive and well 10 months after diagnosis. Histology showed keratinizing SCC infiltrating extensively the parotid gland with subtle poroid cell features. Oncogenic HPV infection was excluded by DNA-based testing. NGS analysis using the TruSight RNA fusion panel (Illumina) revealed a novel YAP1-MAML2 gene fusion. This gene fusion was reported recently in a subset of cutaneous porocarcinoma and poroma. This case of poroid SCC (or squamoid porocarcinoma) adds to the differential diagnosis of SCC presenting as parotid gland tumor and highlights the value of molecular testing in cases with unusual presentation.
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Affiliation(s)
- Abbas Agaimy
- grid.411668.c0000 0000 9935 6525Institute of Pathology, University Hospital, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Robert Stoehr
- grid.411668.c0000 0000 9935 6525Institute of Pathology, University Hospital, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Lars Tögel
- grid.411668.c0000 0000 9935 6525Institute of Pathology, University Hospital, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arndt Hartmann
- grid.411668.c0000 0000 9935 6525Institute of Pathology, University Hospital, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Thomas Cramer
- Department of Otorhinolaryngology, Head and Neck Surgery, Bundeswehrkrankenhaus, Berlin, Germany
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17
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YAP1-fusions in pediatric NF2-wildtype meningioma. Acta Neuropathol 2020; 139:215-218. [PMID: 31734728 DOI: 10.1007/s00401-019-02095-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/06/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
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18
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Papp E, Hallberg D, Konecny GE, Bruhm DC, Adleff V, Noë M, Kagiampakis I, Palsgrove D, Conklin D, Kinose Y, White JR, Press MF, Drapkin R, Easwaran H, Baylin SB, Slamon D, Velculescu VE, Scharpf RB. Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines. Cell Rep 2019; 25:2617-2633. [PMID: 30485824 PMCID: PMC6481945 DOI: 10.1016/j.celrep.2018.10.096] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/07/2018] [Accepted: 10/25/2018] [Indexed: 12/27/2022] Open
Abstract
To improve our understanding of ovarian cancer, we performed genome-wide analyses of 45 ovarian cancer cell lines. Given the challenges of genomic analyses of tumors without matched normal samples, we developed approaches for detection of somatic sequence and structural changes and integrated these with epigenetic and expression alterations. Alterations not previously implicated in ovarian cancer included amplification or overexpression of ASXL1 and H3F3B, deletion or underexpression of CDC73 and TGF-beta receptor pathway members, and rearrangements of YAP1-MAML2 and IKZF2-ERBB4. Dose-response analyses to targeted therapies revealed unique molecular dependencies, including increased sensitivity of tumors with PIK3CA and PPP2R1A alterations to PI3K inhibitor GNE-493, MYC amplifications to PARP inhibitor BMN673, and SMAD3/4 alterations to MEK inhibitor MEK162. Genome-wide rearrangements provided an improved measure of sensitivity to PARP inhibition. This study provides a comprehensive and broadly accessible resource of molecular information for the development of therapeutic avenues in ovarian cancer. The overall survival of patients with late-stage ovarian cancer is dismal. To identify therapeutic opportunities, Papp et al. integrate genomic, epigenomic, and expression analyses to provide a resource of molecular abnormalities in ovarian cancer cell lines and use these to identify tumors sensitive to PARP, MEK, and PI3K inhibitors.
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Affiliation(s)
- Eniko Papp
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dorothy Hallberg
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gottfried E Konecny
- Division of Hematology and Oncology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Daniel C Bruhm
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vilmos Adleff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michaël Noë
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ioannis Kagiampakis
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doreen Palsgrove
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dylan Conklin
- Division of Hematology and Oncology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Yasuto Kinose
- Department of Obstetrics and Gynecology Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James R White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael F Press
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hariharan Easwaran
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dennis Slamon
- Division of Hematology and Oncology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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19
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Yoshida A, Arai Y, Tanzawa Y, Wakai S, Hama N, Kawai A, Shibata T. KMT2A
(
MLL
) fusions in aggressive sarcomas in young adults. Histopathology 2019; 75:508-516. [DOI: 10.1111/his.13926] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 05/24/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Akihiko Yoshida
- Department of Pathology and Clinical Laboratories National Cancer Centre Hospital TokyoJapan
- Rare Cancer Centre National Cancer Centre Hospital TokyoJapan
| | - Yasuhito Arai
- Division of Cancer Genomics National Cancer Centre Research Institute TokyoJapan
| | - Yoshikazu Tanzawa
- Department of Musculoskeletal Oncology National Cancer Centre Hospital Tokyo Japan
| | - Susumu Wakai
- Department of Pathology and Clinical Laboratories National Cancer Centre Hospital TokyoJapan
| | - Natsuko Hama
- Division of Cancer Genomics National Cancer Centre Research Institute TokyoJapan
| | - Akira Kawai
- Rare Cancer Centre National Cancer Centre Hospital TokyoJapan
- Department of Musculoskeletal Oncology National Cancer Centre Hospital Tokyo Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics National Cancer Centre Research Institute TokyoJapan
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20
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Sekine S, Kiyono T, Ryo E, Ogawa R, Wakai S, Ichikawa H, Suzuki K, Arai S, Tsuta K, Ishida M, Sasajima Y, Goshima N, Yamazaki N, Mori T. Recurrent YAP1-MAML2 and YAP1-NUTM1 fusions in poroma and porocarcinoma. J Clin Invest 2019; 129:3827-3832. [PMID: 31145701 DOI: 10.1172/jci126185] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Poroma is a benign skin tumor exhibiting terminal sweat gland duct differentiation. The present study aimed to explore the potential role of gene fusions in the tumorigenesis of poromas. RNA sequencing and reverse transcription PCR identified highly recurrent YAP1-MAML2 and YAP1-NUTM1 fusions in poromas (92/104 lesions, 88.5%) and their rare malignant counterpart, porocarcinomas (7/11 lesions, 63.6%). A WWTR1-NUTM1 fusion was identified in a single lesion of poroma. Fluorescent in-situ hybridization confirmed genomic rearrangements involving these genetic loci. Immunohistochemical staining could readily identify the YAP1 fusion products as nuclear expression of the N-terminal portion of YAP1 with a lack of the C-terminal portion. YAP1 and WWTR1, also known as YAP and TAZ, respectively, encode paralogous transcriptional activators of TEAD, which are negatively regulated by the Hippo signaling pathway. The YAP1 and WWTR1 fusions strongly transactivated a TEAD reporter and promoted anchorage-independent growth, confirming their tumorigenic roles. Our results demonstrate the frequent presence of transforming YAP1 fusions in poromas and porocarcinomas and suggest YAP1/TEAD-dependent transcription as a candidate therapeutic target against porocarcinoma.
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Affiliation(s)
- Shigeki Sekine
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology
| | - Tohru Kiyono
- Division of Carcinogenesis and Cancer Prevention.,Department of Cell Culture Technology, and
| | | | | | - Susumu Wakai
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Hitoshi Ichikawa
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | | | - Satoru Arai
- Department of Dermatology, St. Luke's International Hospital, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology and Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Mitsuaki Ishida
- Department of Pathology and Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Yuko Sasajima
- Department of Pathology, Teikyo University School of Medicine, Tokyo, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Naoya Yamazaki
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Taisuke Mori
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology
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21
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Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E, Butler A, Benes CH, McDermott U, Dow D, Iorio F, Stronach E, Yang F, Yusa K, Saez-Rodriguez J, Garnett MJ. Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening. Nat Commun 2019; 10:2198. [PMID: 31097696 PMCID: PMC6522557 DOI: 10.1038/s41467-019-09940-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Many gene fusions are reported in tumours and for most their role remains unknown. As fusions are used for diagnostic and prognostic purposes, and are targets for treatment, it is crucial to assess their function in cancer. To systematically investigate the role of fusions in tumour cell fitness, we utilized RNA-sequencing data from 1011 human cancer cell lines to functionally link 8354 fusion events with genomic data, sensitivity to >350 anti-cancer drugs and CRISPR-Cas9 loss-of-fitness effects. Established clinically-relevant fusions were identified. Overall, detection of functional fusions was rare, including those involving cancer driver genes, suggesting that many fusions are dispensable for tumour fitness. Therapeutically actionable fusions involving RAF1, BRD4 and ROS1 were verified in new histologies. In addition, recurrent YAP1-MAML2 fusions were identified as activators of Hippo-pathway signaling in multiple cancer types. Our approach discriminates functional fusions, identifying new drivers of carcinogenesis and fusions that could have clinical implications. Gene fusions are observed in many cancers but their link to tumour fitness is largely unknown. Here, transcriptomic analysis combined with pharmacological and CRISPR-Cas9 screening of cancer cell lines was used to evaluate the functional linkage between fusions and tumour fitness.
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Affiliation(s)
- Gabriele Picco
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth D Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Luz Garcia Alonso
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Fiona M Behan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emanuel Gonçalves
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Graham Bignell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Matchan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ruby Banerjee
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elizabeth Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Adam Butler
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cyril H Benes
- Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Ultan McDermott
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,AstraZeneca, CRUK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - David Dow
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Research and Development, GlaxoSmithKline, Stevenage, SG1 2NY, UK.,Research and Development, GlaxoSmithKline, Collegeville, PA, 19426-0989, USA
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Euan Stronach
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Research and Development, GlaxoSmithKline, Stevenage, SG1 2NY, UK.,Research and Development, GlaxoSmithKline, Collegeville, PA, 19426-0989, USA
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Institute for Computational Biomedicine, Faculty of Medicine, Bioquant, Heidelberg University, 69120, Heidelberg, Germany
| | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK. .,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
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22
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Ooft ML, van Ipenburg J, van de Loo RJM, de Jong R, Moelans CB, de Bree R, de Herdt MJ, Koljenović S, Baatenburg de Jong R, Hardillo J, Willems SM. Differences in cancer gene copy number alterations between Epstein-Barr virus-positive and Epstein-Barr virus-negative nasopharyngeal carcinoma. Head Neck 2018; 40:1986-1998. [PMID: 29927011 DOI: 10.1002/hed.25195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 01/21/2018] [Accepted: 03/02/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) treatment is mainly based on clinical staging. We hypothesize that better understanding of the molecular heterogeneity of NPC can aid in better treatment decisions. Therefore, the purpose of this study was to present our exploration of cancer gene copy-number alterations (CNAs) of Epstein-Barr virus (EBV)-positive and EBV-negative NPC. METHODS Multiplex ligation-dependent probe amplification was applied to detect CNAs of 36 cancer genes (n = 103). Correlation between CNAs, clinicopathological features, and survival were examined. RESULTS The CNAs occurred significantly more in EBV-negative NPC, with PIK3CA and MCCC1 (P < .001) gain/amplification occurring more frequently. Gain/amplification of cyclin-L1 (CCNL1) and PTK2 (P < .001) predict worse disease-free survival (DFS) in EBV-positive NPC. CONCLUSION The EBV-positive and EBV-negative NPC show some similarities in cancer gene CNAs suggesting a common pathogenic route but also important differences possibly indicating divergence in oncogenesis. Copy number gain/amplification of CCNL1 and PTK2 are possibly good predictors of survival in EBV-positive NPC.
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Affiliation(s)
- Marc Lucas Ooft
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jolique van Ipenburg
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rob J M van de Loo
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rick de Jong
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martine J de Herdt
- Department of Otorhinolaryngology - Head and Neck Surgery, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Senada Koljenović
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - R Baatenburg de Jong
- Department of Otorhinolaryngology - Head and Neck Surgery, Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Hardillo
- Department of Otorhinolaryngology - Head and Neck Surgery, Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Stefan Martin Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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23
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Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. Oncotarget 2016; 6:5477-89. [PMID: 25849937 PMCID: PMC4467381 DOI: 10.18632/oncotarget.3491] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/04/2015] [Indexed: 01/03/2023] Open
Abstract
Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome.
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24
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Bruce JP, Yip K, Bratman SV, Ito E, Liu FF. Nasopharyngeal Cancer: Molecular Landscape. J Clin Oncol 2015; 33:3346-55. [DOI: 10.1200/jco.2015.60.7846] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a unique epithelial malignancy arising from the superior aspect of the pharyngeal mucosal space, associated with latent Epstein-Barr virus infection in most cases. The capacity to characterize cancer genomes in unprecedented detail is now providing insights into the genesis and molecular underpinnings of this disease. Herein, we provide an overview of the molecular aberrations that likely drive nasopharyngeal tumor development and progression. The contributions of major Epstein-Barr virus–encoded factors, including proteins, small RNAs, and microRNAs, along with their interactions with pathways regulating cell proliferation and survival are highlighted. We review recent analyses that clearly define the role of genetic and epigenetic variations affecting the human genome in NPC. These findings point to the impact of DNA methylation and histone modifications on gene expression programs that promote this malignancy. The molecular interactions that allow NPC cells to evade immune recognition and elimination, which is crucial for the survival of cells expressing potentially immunogenic viral proteins, are also described. Finally, the potential utility of detecting host and viral factors for the diagnosis and prognosis of NPC is discussed. Altogether, the studies summarized herein have greatly expanded our knowledge of the molecular biology of NPC, yet much remains to be uncovered. Emerging techniques for using and analyzing well-annotated biospecimens from patients with NPC will ultimately lead to a greater level of understanding, and enable improvements in precision therapies and clinical outcomes.
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Affiliation(s)
- Jeff P. Bruce
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth Yip
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Emma Ito
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
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25
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Russo A, Pacchierotti F, Cimini D, Ganem NJ, Genescà A, Natarajan AT, Pavanello S, Valle G, Degrassi F. Genomic instability: Crossing pathways at the origin of structural and numerical chromosome changes. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:563-580. [PMID: 25784636 DOI: 10.1002/em.21945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/02/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
Genomic instability leads to a wide spectrum of genetic changes, including single nucleotide mutations, structural chromosome alterations, and numerical chromosome changes. The accepted view on how these events are generated predicts that separate cellular mechanisms and genetic events explain the occurrence of these types of genetic variation. Recently, new findings have shed light on the complexity of the mechanisms leading to structural and numerical chromosome aberrations, their intertwining pathways, and their dynamic evolution, in somatic as well as in germ cells. In this review, we present a critical analysis of these recent discoveries in this area, with the aim to contribute to a deeper knowledge of the molecular networks leading to adverse outcomes in humans following exposure to environmental factors. The review illustrates how several technological advances, including DNA sequencing methods, bioinformatics, and live-cell imaging approaches, have contributed to produce a renewed concept of the mechanisms causing genomic instability. Special attention is also given to the specific pathways causing genomic instability in mammalian germ cells. Remarkably, the same scenario emerged from some pioneering studies published in the 1980s to 1990s, when the evolution of polyploidy, the chromosomal effects of spindle poisons, the fate of micronuclei, were intuitively proposed to share mechanisms and pathways. Thus, an old working hypothesis has eventually found proper validation.
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Affiliation(s)
| | - Francesca Pacchierotti
- Laboratory of Toxicology, Unit of Radiation Biology and Human Health, ENEA CR Casaccia, Rome, Italy
| | - Daniela Cimini
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia
| | - Neil J Ganem
- Department of Pharmacology, Division of Hematology and Oncology, Boston University School of Medicine, Boston, Massachusetts
| | - Anna Genescà
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | - Sofia Pavanello
- Department of Cardiac, Thoracic and Vascular Sciences, Unit of Occupational Medicine, University of Padova, Italy
| | - Giorgio Valle
- Department of Biology, University of Padova, Padova, Italy
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26
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Pajtler KW, Witt H, Sill M, Jones DTW, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM. Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. Cancer Cell 2015; 27:728-43. [PMID: 25965575 PMCID: PMC4712639 DOI: 10.1016/j.ccell.2015.04.002] [Citation(s) in RCA: 774] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/26/2015] [Accepted: 04/08/2015] [Indexed: 12/17/2022]
Abstract
Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.
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Affiliation(s)
- Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, 45147 Essen, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Fabian Kratochwil
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruth Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Pascal Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jüri Reimand
- The Donnelly Center, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, 125047 Moscow, Russia
| | - Steve Mack
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Vijay Ramaswamy
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - David Capper
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Leonille Schweizer
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Laura Sieber
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Andrea Wittmann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Zhiqin Huang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Daniel Fults
- University of Utah, Salt Lake City, UT 84132, USA
| | - Helen Toledano
- Pediatric Hematology Oncology, Schneider Children's Medical Center of Israel, 49202 Petah Tikva, Israel
| | - Smadar Avigad
- Department of Molecular Oncology, Schneider Children's Medical Center of Israel, Tel Aviv University, 49202 Tel Aviv, Israel
| | - Lindsey M Hoffman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nicholas Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Ekkehard Hewer
- Department of Pathology, University of Bern, 3010 Bern, Switzerland
| | - Karel Zitterbart
- Department of Pediatric Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, 61300 Brno, Czech Republic; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 65653 Brno, Czech Republic
| | - Mark Gilbert
- Division of Cancer Medicine, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Terri S Armstrong
- Division of Cancer Medicine, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Family Health, University of Texas Health Science Center-SON, Houston, TX 77030, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey C Allen
- Departments of Pediatrics and Neurology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Matthias A Karajannis
- Division of Pediatric Hematology and Oncology, Departments of Pediatrics and Otolaryngology, NYU Langone Medical Center, New York, NY 10016, USA
| | - David Zagzag
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Martin Hasselblatt
- Institute for Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany
| | - Olaf Witt
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - V Peter Collins
- Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Katja von Hoff
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn, 53127 Bonn, Germany
| | - Gary Bader
- The Donnelly Center, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael D Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Richard Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kenneth Aldape
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Andrey Korshunov
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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29
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Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC. Copy number variation is a fundamental aspect of the placental genome. PLoS Genet 2014; 10:e1004290. [PMID: 24785991 PMCID: PMC4006706 DOI: 10.1371/journal.pgen.1004290] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
Discovery of lineage-specific somatic copy number variation (CNV) in mammals has led to debate over whether CNVs are mutations that propagate disease or whether they are a normal, and even essential, aspect of cell biology. We show that 1,000N polyploid trophoblast giant cells (TGCs) of the mouse placenta contain 47 regions, totaling 138 Megabases, where genomic copies are underrepresented (UR). UR domains originate from a subset of late-replicating heterochromatic regions containing gene deserts and genes involved in cell adhesion and neurogenesis. While lineage-specific CNVs have been identified in mammalian cells, classically in the immune system where V(D)J recombination occurs, we demonstrate that CNVs form during gestation in the placenta by an underreplication mechanism, not by recombination nor deletion. Our results reveal that large scale CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during embryogenesis and are propagated by a mechanism of underreplication. Generally, every mammalian cell has the same complement of each part of its genome. However, copy number variation (CNV) can occur, where, compared to the rest of its genome, a cell has either more or less of a specific genomic region. It is unknown whether CNVs cause disease, or whether they are a normal aspect of cell biology. We investigated CNVs in polyploid trophoblast giant cells (TGCs) of the mouse placenta, which have up to 1,000 copies of the genome in each cell. We found that there are 47 regions with decreased copy number in TGCs, which we call underrepresented (UR) domains. These domains are marked in the TGC progenitor cells and we suggest that they gradually form during gestation due to slow replication versus fast replication of the rest of the genome. While UR domains contain cell adhesion and neuronal genes, they also contain significantly fewer genes than other genomic regions. Our results demonstrate that CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during pregnancy.
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Affiliation(s)
- Roberta L. Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Edward B. Chuong
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, Tallahassee Florida, United States of America
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Tallahassee Florida, United States of America
| | - Anton Valouev
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Julie C. Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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